title: C57_H3K27ac_rep1

city: Cincinnati

first: Jennifer

middle: M

last: Felton

state: Ohio

address: 3333 Burnet Ave, ML7028

department: Department of Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
RNAseq; raw sequence read quality was assesed using FASTQC/0.11.7. Adapter sequences were trimmed using CutAdapt/1.81 and TrimGalore/0.4.2. Reads were aligned to the mm9 geneome and RefSeq-based transcriptome using STAR/2.5. Duplicate were removed with PICARD/1.89. FeatureCount and calculateFPKMs were used to quantify FPKM values. Expression thresholds were determined using expression levels of known expressed eosinophil genes, with >5 FPKM in both replicates indicating genes that are expressed by eosinophils and <5 FPKM indicating genes that are silent/repressed/lowly expressed.
GO analysis was performed using Enricher
Gene expression heatmaps were generated in Rstudio using ggplot2
ChIPseq + ATACseq; raw sequence read quality was assessed with FASTQC/0.11.7, adapter sequences were trimmed with CutAdapt/1.8.1 and TrimGalore/0.4.2, prior to alignment of reads to the mm9 genome and RefSeq-based transcriptome using BOWTIE/2.3.4.1. Duplicates were removed using PICARD/1.89 and peaks were called using MACS/2.1.0 with a q-value of 0.01. Presence of peaks in expressed genes and co-marked regions were determined using BEDtools/2.27.0.
ATAC and CHIP tracks are visualised using IGV browser. TSS density heatmaps were generated using deepTools2. MAnorm, HOMER and ROSE were performed as described in methods.
Genome_build: mm9
Supplementary_files_format_and_content: Tab deliminated raw feature counts of each RNAseq file.  Aligned and trimmed called peaks for ChIP & ATAC samples.

molecule: genomic DNA

source_name: Bone marrow derived eosinophils (bmEos)

growth_protocol: bmEos were generated from unselcted bone marrow progenitor cells over 14 days in culture. Confluency was maintained at 1x10^6/mL in RPMI1640+20% FCS, P/S, L-glutamine, HEPES, NEAA and  Sodium Pyruvate supplemented with SCF + FLT3L for the first 4 days prior to switching to IL-5 for the reminader of the culture. Media was changed and cytokines were replenshied every 2 days.

extract_protocol:
Cultures were harvested and cells were washed in PBS prior to downstream analysis. RNA was harvested using Trizol followed by purification with the Zymo MicroRNA kit (R2061). ChIP lysates were generated from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ATAC-seq: A total of 6.5x104 viable eosinophils were pelleted at 500 g for 5 minutes at 4 C prior to resuspension in 50 uL ATAC-Resuspension Buffer (ATAC-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 made up to 50 mL in ddH2O) with added 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin. Samples were incubated on ice for 3 minutes prior to washing in 1 mL cold ATAC-RSB containing 0.1% Tween-20 only. Nuclei were pelleted at 500 g for 10 minutes at 4 C prior to addition of 50 uL transposition mixture (2X TD buffer, 100 nM transposase enzyme, 5 uL ddH2O, 1% Digitonin, 10% Tween-20 made up to 50 mL in 1X PBS) and incubated at 37 C for 30 minutes. After tagmentation, the transposased DNA was purified using the MiniElute Reaction Cleanup Kit (28204, Qiagen).
RNA libraries were prepared for sequencing according to the TruSeq Stranded mRNA kit protcol. ChIP libraries were constructed by ChIPmentation. ATAC libraries were constructed with the OMNI-ATAC protocol.

treatment_protocol: (Days 0-3): 1x10^6/mL + Stem Cell Factor (SCF; 100ng/mL) + FMS-like tyrosine kinase 3 ligand  (FLT3-L; 100ng/mL). (Days 4-14): 1x10^6/mL + murine interleukin 5 (IL-5, 10ng/mL)

tag: strain

value: Bone marrow derived eosinophils (bmEos)

tag: culture length

value: 14 days

tag: chip antibody

value: H3K27ac (C15410196, Diagenode)


title: EC_239_RRKO_Shear

status: Public on Jun 08 2021

type: SRA

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

country: USA

institute: UC San Diego

library_source: transcriptomic

data_processing:
Data was processed through STAR, with gene alignement trough samTools and featureCounts
Count matrix was analyzed using R software 4.0.3
DeSeq2 was used for normalization, Relative Log Expression, and adjusted p-values
topGO Bioconductor ontology database was used for gene ontology analysis
Data also processed and presented via python
Genome_build: hg38
Supplementary_files_format_and_content: Raw and normalized data counts in txt format

molecule: total RNA

organism: Homo sapiens

growth_protocol: iPSC-Derived ECs were grown in EGM2 media after differentiation

extract_protocol:
RNA was extracted via Trizol-chloroform extraction as noted in the paper. Under limited RNA quantities, Qiagen miRNeasy Mini Kit was used (Qiagen, 217004). RNA quality assessed using TapeStation (Agilent)
Library prepped using Illumina TruSeq Stranded RNA, High Throughput Library Prep Kit, sequenced using Illumina NovaSeq S4 for single-end reads

treatment_protocol: TNFalpha treated ECs were treated 12 hours before isolation at 1uM concentration

tag: cell type

value: iPSC-derived endothelial cells

tag: genotype

value: RRKO

tag: condition

value: Shear


title: C57_ATAC_rep2

organism: Mus musculus

tag: tissue


title: single cell of Hematopoietic Stem Cell 68

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

country: China

institute: GIBH

description:
barcodes.tsv
genes.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hematopoietic Stem Cells

tag: treatment

value: untreatment


title: EC_233_RRKO_Shear


title: EC_236_RRKO_Shear


title: C57_ATAC_rep1


title: EC_230_RRKO_Shear


title: H3K4me1_rep2

value: BALB/c

value: H3K4me1 (C15410194, Diagenode)


title: single cell of Hematopoietic Stem Cell 66

description:
barcodes.tsv
genes.tsv


title: EC_237_RRWT_Shear

value: RRWT


title: H3K4me1_rep1


title: single cell of Hematopoietic Stem Cell 67

description:
barcodes.tsv
genes.tsv


title: EC_235_RRWT_Shear


title: H3K4me3_rep2

value: H3K4me3 (17-614, Millpore)


title: EC_231_RRWT_Shear


title: single cell of Hematopoietic Stem Cell 64

description:
barcodes.tsv
genes.tsv


title: EC_234_RRWT_Shear


title: ATAC_rep2


title: single cell of Hematopoietic Stem Cell 63

description:
barcodes.tsv
genes.tsv


title: C57_H3K27ac_rep2


title: H3K27ac_rep2


title: single cell of Hematopoietic Stem Cell 65

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 62

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 61

description:
barcodes.tsv
genes.tsv


title: EC_219_RRKO_Static

value: Static


title: 8_5_S35 (PD-1_8Gy_2)

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR, embedded algorism of Partek Flow software (Partek Inc)
Gene counts were normalized to counts per million and added 0.0001 with Partek Flow software (Partek Inc)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
HKP1-bearing lungs were harvested,mechanically grinded, and RNA was extracted using RNeasy plus kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HKP1-bearing lungs

tag: time

value: 24-48 hr psot-RT


title: 8_6_S36 (PD-1_8Gy_3)


title: single cell of Hematopoietic Stem Cell 60

description:
barcodes.tsv
genes.tsv


title: EC_214_RRKO_Static


title: 4_6_S30 (PD-1 4Gy_3)


title: 8_4_S34 (PD-1_8Gy_1)


title: EC_221_RRKO_Static


title: single cell of Hematopoietic Stem Cell 58

description:
barcodes.tsv
genes.tsv


title: EC_222_RRWT_Static


title: single cell of Hematopoietic Stem Cell 59

description:
barcodes.tsv
genes.tsv


title: 4_5_S29 (PD-1 4Gy_2)


title: single cell of Hematopoietic Stem Cell 57

description:
barcodes.tsv
genes.tsv


title: 4_4_S28 (PD-1 4Gy_1)


title: EC_220_RRWT_Static


title: EC_213_RRWT_Static


title: single cell of Hematopoietic Stem Cell 56

description:
barcodes.tsv
genes.tsv


title: 0-5_S17 (PD-1_0Gy_2)


title: EC_206_RRWT_Static


title: single cell of Hematopoietic Stem Cell 55

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 54

description:
barcodes.tsv
genes.tsv


title: 0-4_S16 (PD-1_0Gy_1)


title: 8_3_S33 (IgG_8Gy_3)


title: single cell of Hematopoietic Stem Cell 53

description:
barcodes.tsv
genes.tsv


title: 8_2_S32 (IgG_8Gy_2)


title: Bronchial Organoids - SARS-Cov-2 Infection_48h

city: Shenzhen

first: Liang

last: Yang

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: SUStech

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 (v2.1.0) .
Htseq-count software is used to obtain the number of reads on each gene in each sample.  The FPKM(Fragments Per Kilobase per Million) value of gene is calculated by clifflinks software.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Bronchial Organoids

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: SARS-Cov-2 Infection 48h


title: single cell of Hematopoietic Stem Cell 52

description:
barcodes.tsv
genes.tsv


title: Bronchial Organoids - SARS-Cov-2 Infection_Mock

value: untreated


title: EC_207_RRKO_Static


title: 8_1_S31 (IgG_8Gy_1)


title: Bronchial Organoids - SARS-Cov-2 Infection_72h

value: SARS-Cov-2 Infection 72h


title: 4_3_S27 (IgG_4Gy_2)


title: single cell of Hematopoietic Stem Cell 51

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 50

description:
barcodes.tsv
genes.tsv


title: 4_2_S26 (IgG_4Gy_1)


title: single cell of Hematopoietic Stem Cell 49

description:
barcodes.tsv
genes.tsv


title: 0-3_S15 (IgG_0Gy_3)


title: single cell of Hematopoietic Stem Cell 48

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 47

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 46

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 45

description:
barcodes.tsv
genes.tsv


title: H3K4me3_ChIPseq_rep1

extract_protocol:
Cultures were harvested and cells were washed in PBS prior to downstream analysis. RNA was harvested using Trizol followed by purification with the Zymo MicroRNA kit (R2061). ChIP lysates were generated from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ATAC-seq: A total of 6.5x104 viable eosinophils were pelleted at 500 g for 5 minutes at 4 C prior to resuspension in 50 uL ATAC-Resuspension Buffer (ATAC-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 made up to 50 mL in ddH2O) with added 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin. Samples were incubated on ice for 3 minutes prior to washing in 1 mL cold ATAC-RSB containing 0.1% Tween-20 only. Nuclei were pelleted at 500 g for 10 minutes at 4 C prior to addition of 50 uL transposition mixture (2X TD buffer, 100 nM transposase enzyme, 5 uL ddH2O, 1% Digitonin, 10% Tween-20 made up to 50 mL in 1X PBS) and incubated at 37 C for 30 minutes. After tagmentation, the transposased DNA was purified using the MiniElute Reaction Cleanup Kit (28204, Qiagen).
RNA libraries were prepared for sequencing according to the TruSeq Stranded mRNA kit protcol. ChIP libraries were constructed by ChIPmentation. ATAC libraries were constructed with the OMNI-ATAC protocol.
RNAseq, ChIPseq and ATACseq

value: Bone marrow derived eosinophils (bmEos)

value: 14 days


title: single cell of Hematopoietic Stem Cell 44

description:
barcodes.tsv
genes.tsv


title: PU1_ChIPseq

value: PU.1 (sc-352, SantaCruz)


title: ATAC_seq_rep1


title: single cell of Hematopoietic Stem Cell 43

description:
barcodes.tsv
genes.tsv


title: PE4

type: RNA

city: Harbin

first: Chenguang

last: Dai

address: Youzheng Street 23#,Nangang District

institute: Harbin Medical University

description: lncRNA and mRMA expression data from Serum of pregnant woman who later developed preeclampsia   (before the 20th week of gestation )

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: serum( before the 20th week of gestation) of patients with preeclampsia (PE) (n=5) and matched normotensive pregnant (NP) women (n=5)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Serum from maternal whole peripheral blood was collected before the 20th week of gestation and stored at -80°C until use.

tag: sample type

value: preeclampsia


title: PE3

source_name: Serum of pregnant woman who later developed preeclampsia  (before the 20th week of gestation )


title: PE1


title: single cell of Hematopoietic Stem Cell 41

description:
barcodes.tsv
genes.tsv


title: H3K27ac_ChIPseq_rep1

value: H3K27ac (C15410196, Diagenode)


title: single cell of Hematopoietic Stem Cell 42

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells


title: PE5


title: single cell of Hematopoietic Stem Cell 40

description:
barcodes.tsv
genes.tsv

value: untreatment


title: 1222C

type: genomic

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

description: Folic acid in trimester 1, placebo in trimesters 2 and 3.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

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

data_processing:
BeadStudio software and RnBeads through R.
Beta values

source_name: Cord blood

label_protocol: Standard Illumina Protocol.

growth_protocol: Cord blood was collected at birth in EDTA tubes and frozen at -80degC.

extract_protocol: Genomic DNA was isolated from cord blood using QiAMP DNA Blood Mini kit (Qiagen), according to manufacturer’s instructions. Genomic DNA isolated was assessed for purity and integrity prior to quantification using the Picogreen fluorescent assay.

value: Cord blood

tag: sample group

value: PLACEBO


title: single cell of Hematopoietic Stem Cell 39

description:
barcodes.tsv
genes.tsv


title: PE2


title: 0-2_S14 (IgG_0Gy_2)


title: 0-1_S13 (IgG_0Gy_1)


title: 1224C

description: Folic acid in trimesters 1-3.

value: TREATMENT


title: single cell of Hematopoietic Stem Cell 37

description:
barcodes.tsv
genes.tsv


title: normotensive pregnant-control4

description: lncRNA and mRMA expression data from Serum of normotensive pregnant women  (before the 20th week of gestation )

value: normotensive pregnant


title: 1212C


title: 1220C

description: Folic acid in trimesters 1-3.


title: normotensive pregnant-control2

source_name: Serum of normotensive pregnant women (before the 20th week of gestation )


title: normotensive pregnant-control5


title: normotensive pregnant-control3


title: single cell of Hematopoietic Stem Cell 36

description:
barcodes.tsv
genes.tsv


title: normotensive pregnant-control1


title: 1205C


title: 1209C


title: Skin-psoriasis lesion-02

city: Wonju

first: Seung-Phil

last: Hong

address: 20 Ilsan-ro

department: Department of Dermatology

country: South Korea

institute: Yonsei University Wonju College of Medicine

description: lesional skin: RNA sequencing

data_processing:
To separate human RNA seq reads, we used bbpsplit including bbmap package(https://sourceforge.net/projects/bbmap/)
Low quality reads were filtered according to the following criteria; N-ratio > 0.1 and ratio of less than Phred quality score 20 > 0.4
Filtered reads were mapped to the human reference genome (Ensembl release 72) using the aligner STAR v.2.3.0e.
Gene expression level was measured with Cufflinks v2.1.1 (Trapnell C. et al, 2010) using the gene annotation database of Ensembl release 72.
For differential expression analysis, gene level count data were generated using HTSeq-count v0.5.4p3 (Anders S. et al, 20140) tool with the option "-m intersection-nonempty” and -r option considering paired-end sequence.
Genome_build: mm9
Supplementary_files_format_and_content: To characterize the identified genes from DEG analysis, GO based trend test was performed using the Fisher’s exact test

molecule: polyA RNA

source_name: human skin

extract_protocol:
RNA extract from epidermis and skin, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: psoriasis

value: skin (epidermis+dermis)

tag: age (yr-old)


title: 1201C

description: Folic acid in trimesters 1-3.


title: single cell of Hematopoietic Stem Cell 34

description:
barcodes.tsv
genes.tsv


title: Skin-psoriasis lesion-01

description: lesional skin: RNA sequencing


title: single cell of Hematopoietic Stem Cell 33

description:
barcodes.tsv
genes.tsv


title: Skin-atopic dermatitis lesion-01

description: lesional skin: RNA sequencing

value: atopic dermatitis


title: 1198C

description: Folic acid in trimesters 1-3.


title: single cell of Hematopoietic Stem Cell 38

description:
barcodes.tsv
genes.tsv


title: 1197C

description: Folic acid in trimesters 1-3.


title: single cell of Hematopoietic Stem Cell 35

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 30

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 32

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 31

description:
barcodes.tsv
genes.tsv


title: TB2: Intestinal Tuberculosis

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

country: India

institute: Institute of Post Graduate Medical Education & Research

description: Inflamed Tissue from Intestinal Tuberculosis patients

data_processing:
The adaptors were trimmed using cutadapt tool. . A Phred score Q15 cut-off was applied for quality trimming, and reads less than 16 bases were also removed before downstream analysis.
Bowtie2 was used for mapping with the human genome hg19 as well as miRNAs in mirbase21. Reads were aligned locally with one base seed mismatch within a k-mer size of 19 bases. Samtools was used to assess the depth of coverage.
Differentially expressed miRNAs were obtained using DESeq2 packages in R software.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts

source_name: Colonoscopic biopsy Tissue

extract_protocol:
Colonoscopic/Sigmoidoscopic biopsy tissues were powdered keeping frozen in liquid nitrogen and the total RNA was isolated using TRIzol (Invitrogen, CA) following the manufacturer's protocol. Quality of each RNA was verified using Bioanalyzer (Agilent, CA) and RNA integrity number (RIN) ≥6.5 was considered for Next Generation Sequencing (NGS).
Total RNA isolated from colonoscopic/sigmoidoscopic biopsy tissues were subjected to high throughput small RNA sequence analysis using Illumina HiSeq2500 in Medgenome Labs Private Limited, Bangalore, India. In brief, total RNA was ligated to 3’and 5’ adaptors, followed by reverse transcription and amplification using Truseq Small RNA Sample Prep Kit (Illumina, USA). The RNA fragment of length 145-160nt was gel purified to enrich small RNA library and sequenced.

tag: disase

value: Intestinal Tuberculosis

value: Liver

tag: etiology

value: Uninfected

tag: gender

value: Female


title: TB3: Intestinal Tuberculosis


title: 1193C


title: 1192C

description: Folic acid in trimesters 1-3.


title: CD3: Crohn's Disease

description: Inflamed Tissue from Crohn's disease patients

value: Crohn's Disease

value: Male


title: 1190C


title: CD2: Crohn's Disease


title: 1189C


title: single cell of Hematopoietic Stem Cell 27

description:
barcodes.tsv
genes.tsv


title: 1200C


title: Skin-atopic dermatitis lesion-02

description: lesional skin: RNA sequencing


title: CD1: Crohn's Disease


title: single cell of Hematopoietic Stem Cell 26

description:
barcodes.tsv
genes.tsv


title: 1188C

description: Folic acid in trimesters 1-3.


title: TB1: Intestinal Tuberculosis


title: N-4: Normal non-inflammed

description: Normal Liver Tissue from Haemorrhoids patients

value: Normal


title: single cell of Hematopoietic Stem Cell 25

description:
barcodes.tsv
genes.tsv


title: 1185C

description: Folic acid in trimesters 1-3.


title: N-3: Normal non-inflammed


title: 1195C

description: Folic acid in trimesters 1-3.


title: 1187C


title: single cell of Hematopoietic Stem Cell 24

description:
barcodes.tsv
genes.tsv


title: N-2: Normal non-inflammed


title: single cell of Hematopoietic Stem Cell 23

description:
barcodes.tsv
genes.tsv


title: 1183C


title: single cell of Hematopoietic Stem Cell 22

description:
barcodes.tsv
genes.tsv


title: 1173C


title: single cell of Hematopoietic Stem Cell 21

description:
barcodes.tsv
genes.tsv


title: 1177C


title: single cell of Hematopoietic Stem Cell 28

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 29

description:
barcodes.tsv
genes.tsv


title: large artery atherosclerosis stroke 4

city: Shandong

first: Shuai

address: Qingdao, Shandong,China

institute: he Affiliated Hospital of Qingdao University

data_processing:
The libraries were sequenced on an Illumina Hiseq 2500 platform
Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default
StringTie (v2.1.1) was used to calculate FPKMs of  lncRNAs  in each Sample (Mihaela Pertea et al. 2016).
The circRNA was identified using find_circ (Sebastian Memczak et al., 2013).
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: plasma exosome

extract_protocol:
Plasma  were collected, extracted exosomes, and RNA was obtained using miRNeasy Serum/Plasma Advanced kit.rRNA-depleted RNA by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina ® (NEB, USA) was used with 20ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LAA stroke

value: untreated


title: large artery atherosclerosis stroke 5


title: 1161C


title: single cell of Hematopoietic Stem Cell 20

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

value: untreatment


title: 1157C

value: Cord blood

value: PLACEBO


title: 1156C

description: Folic acid in trimesters 1-3.

value: TREATMENT


title: single cell of Hematopoietic Stem Cell 19

description:
barcodes.tsv
genes.tsv


title: large artery atherosclerosis stroke 1


title: large artery atherosclerosis stroke 2


title: healthy control 5

data_processing:
The libraries were sequenced on an Illumina Hiseq 2500 platform
Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default
StringTie (v2.1.1) was used to calculate FPKMs of  lncRNAs  in each Sample (Mihaela Pertea et al. 2016).
The circRNA was identified using find_circ (Sebastian Memczak et al., 2013).
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample/SAMN18977481

value: healthy control


title: single cell of Hematopoietic Stem Cell 18

description:
barcodes.tsv
genes.tsv


title: 1152C


title: single cell of Hematopoietic Stem Cell 16

description:
barcodes.tsv
genes.tsv


title: 1151C


title: single cell of Hematopoietic Stem Cell 15

description:
barcodes.tsv
genes.tsv


title: 1141C


title: healthy control 3


title: healthy control 2


title: healthy control 4


title: 1145C


title: single cell of Hematopoietic Stem Cell 14

description:
barcodes.tsv
genes.tsv


title: healthy control 1


title: 1139C


title: 1138C


title: single cell of Hematopoietic Stem Cell 13

description:
barcodes.tsv
genes.tsv


title: 1136C


title: 1134C

description: Folic acid in trimesters 1-3.


title: AALE YAP/TAZ siRNA 2

city: Boston

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

description: Gene expression from AALE cells treated with YAP/TAZ siRNA.

data_processing:
FASTQ files were generated and demultiplexed using the Illumina BaseSpace platform.
FASTQ files were aligned to the human genome (hg19) using STAR v2.5.3a in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Transcript and gene level counts were generated using RSEM v1.3.0 and Ensembl annotation (build 92).
Genome_build: hg19
Supplementary_files_format_and_content: N/A

source_name: Bronchial basal epithelial cells transformed with SV40/hTERT

growth_protocol: Cells were grown in SAGM Small Airway Epithelial Cell Growth Medium (BulletKit, Lonza, CC-3118).

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kit.
Illumina® TruSeq® RNA Sample Preparation Kit v2

treatment_protocol: Cells were transfected with control siRNAs and siRNA targeting YAP and TAZ using RNAiMAX (ThermoFisher).  Cells were subsequently grown for 48 hours before lysing and RNA collection.

tag: cell line

value: AALE

value: YAP/TAZ siRNA


title: single cell of Hematopoietic Stem Cell 10

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 11

description:
barcodes.tsv
genes.tsv


title: large artery atherosclerosis stroke 3


title: SPORE 43672 YAP/TAZ siRNA 3

description: Gene expression from SPORE 43672 cells treated with YAP/TAZ siRNA.

source_name: Bronchial epithelial cells derived from low grade dysplastic lesion

value: SPORE 43672


title: AALE YAP/TAZ siRNA 3


title: AALE YAP/TAZ siRNA 1


title: SPORE 43672 YAP/TAZ siRNA 2


title: single cell of Hematopoietic Stem Cell 8

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 17

description:
barcodes.tsv
genes.tsv


title: SPORE 43672 YAP/TAZ siRNA 1


title: 1132C


title: 1131C

description: Folic acid in trimesters 1-3.


title: 1127C

description: Folic acid in trimesters 1-3.


title: single cell of Hematopoietic Stem Cell 6

description:
barcodes.tsv
genes.tsv


title: 1126C


title: HBEC YAP/TAZ siRNA 2

description: Gene expression from HBECs treated with YAP/TAZ siRNA.

source_name: Bronchial basal epithelial cells

value: HBEC


title: HBEC YAP/TAZ siRNA 3


title: T3D top component replicate 1

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

description:
X3616.KO.33
3616-KO-33-TACGGTCT-TCTTTCCC

organism: Mammalian orthoreovirus 3 Dearing

source_name: T3D top component

growth_protocol: L929 murine fibroblasts (L cells) were maintained in suspension in glass bottles containing a magnetic stir bar or as monolayers in flasks in Joklik’s minimum essential medium (JMEM; US Biological). Baby hamster kidney cells expressing bacteriophage T7 RNA polymerase under the control of a cytomegalovirus promoter (BHK-T7; Komoto et al. 2014) were maintained in Dulbecco’s minimum essential medium (DMEM; Corning) and were treated with 1 mg/mL Geneticin (Gibco) every other passage. All media were supplemented with 5% fetal bovine serum (FBS; Gibco) 2 mM L-glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin (Corning), and 25 ng/mL amphotericin B.

extract_protocol:
Infected cell pellets were thawed, incubated with 0.14% deoxycholate for 30 min on ice, then sonicated in the presence of Vertrel XF to release virus particles from cells. Virions and TC particles were separated by ultracentrifugation at 25,000 × g in a 1.2-1.4 g/cm3 cesium chloride density gradient. Mock virions and TC particles were collected by aligning gradients containing virions and TC particles next to mock gradients, marking the expected position of virions and TC particles onto the mock gradient, aspirating liquid above the expected position, and transferring 250 µL of the gradient from the expected position of virions and TC particles into clean Eppendorf tubes. Mock preparations and complete virus particles and TC particles were collected and dialyzed in virion storage buffer (150 mM NaCl, 15 mM MgCl2, 10 mM Tris-HCl, pH 7.4). Purified reovirus particles were treated with 1 U/µL benzonase (Sigma) for 1 h at 37°C to degrade extra-particle nucleic acids. RNA content was analyzed by Bioanalyzer (Agilent) before libraries were prepared.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), then Illumina-ready libraries were sequenced by 150 base pair paired-end sequencing on the NovaSeq 6000 Sequencing System (Illumina)

treatment_protocol: L cells (2 × 108) in suspension were adsorbed with media (mock), rsT1L or rsT3DIT1L1 reovirus at a multiplicity of ~10 PFU/cell at 37°C for 48 h. Infected cells were pelleted by centrifugation at 3,000 rpm for 10 min prior to resuspension in homogenization buffer (25 mM NaCl, 10 mM Tris-HCl, pH 7.4, 10 mM β-mercaptoethanol) and stored at -80°C.

value: top component


title: 1122C


title: single cell of Hematopoietic Stem Cell 12

description:
barcodes.tsv
genes.tsv


title: HBEC YAP/TAZ siRNA 1


title: single cell of Hematopoietic Stem Cell 5

description:
barcodes.tsv
genes.tsv


title: T3D reovirus replicate 3

description:
X2924.TT.8
2924-TT-8-ACTTGAAT-TCTTTCCC

source_name: T3D reovirus

value: virion


title: T3D reovirus replicate 2

description:
X2924.TT.4
2924-TT-4-TGACCAAT-TCTTTCCC


title: single cell of Hematopoietic Stem Cell 4

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 9

description:
barcodes.tsv
genes.tsv


title: 1118C

description: Folic acid in trimesters 1-3.


title: single cell of Hematopoietic Stem Cell 3

description:
barcodes.tsv
genes.tsv


title: 1116C


title: AALE control siRNA 3

description: Gene expression from AALE cells treated with control siRNA.

value: control siRNA


title: AALE control siRNA 2


title: single cell of Hematopoietic Stem Cell 2

description:
barcodes.tsv
genes.tsv


title: T3D reovirus replicate 1

description:
X2924.TT.3
2924-TT-3-TTAGGCAT-TCTTTCCC


title: AALE control siRNA 1


title: T1L top component replicate 3

description:
X2924.TT.7
2924-TT-7-CAGATCAT-TCTTTCCC

organism: Mammalian orthoreovirus 1 Lang

source_name: T1L top component


title: 1115C

description: Folic acid in trimesters 1-3.


title: T1L top component replicate 2

description:
X2924.TT.6
2924-TT-6-GCCAATAT-TCTTTCCC


title: T3D top component replicate 2

description:
X3616.KO.34
3616-KO-34-CCAGTATC-TCTTTCCC


title: T1L top component replicate 1

description:
X2924.TT.5
2924-TT-5-ACAGTGAT-TCTTTCCC


title: SPORE 43672 control siRNA 2

description: Gene expression from SPORE 43672 cells treated with control siRNA.


title: SPORE 43672 control siRNA 3

source_name: Bronchial epithelial cells derived  from low grade dysplastic lesion


title: T1L reovirus replicate 2

description:
X2924.TT.2
2924-TT-2-CGATGTAT-TCTTTCCC

source_name: T1L reovirus


title: 1113C


title: SPORE 43672 control siRNA 1


title: 1120C


title: 2812_STC1_C

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline https://github.com/crazyhottommy/pyflow-ChIPseq. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2 (Langmead et al., 2009). Duplicate reads were removed using SAMBLASTER (Faust and Hall, 2014) before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5 (Li et al., 2009). To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0 (Ramirez et al., 2014) to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Cell Line

growth_protocol: Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center. Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing. Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

tag: chip-antibody

value: melanoma short-term patient culture cell line

tag: cell genotype

value: BRAF mutation


title: 2792_STC1_C


title: 1112C

description: Folic acid in trimesters 1-3.


title: T1L reovirus replicate 1

description:
X2924.TT.1
2924-TT-1-ATCACGAT-TCTTTCCC


title: HBEC control siRNA 3

description: Gene expression from HBECs treated with control siRNA.


title: 1110C


title: HBEC control siRNA 2


title: single cell of Hematopoietic Stem Cell 1

description:
barcodes.tsv
genes.tsv

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization


title: 1107C


title: HBEC control siRNA 1


title: 1099C

description: Folic acid in trimesters 1-3.


title: 2761_STC1_C


title: 1114C

description: Folic acid in trimesters 1-3.


title: AALE NRG1 overexpression vector 3

description: Gene expression from AALE cells transfected with NRG1 overexpression vector.

data_processing:
FASTQ files were generated and demultiplexed using the Illumina BaseSpace platform.
FASTQ files were aligned to the human genome (hg19) using STAR v2.5.3a in a two-pass manner.
Quality control was performed using FastQC v0.11.3 and RSeQC v2.6.4 and summarized using MultiQC v0.9.
Transcript and gene level counts were generated using RSEM v1.3.0 and Ensembl annotation (build 92).
Genome_build: hg19

treatment_protocol: Cells were transduced with a lentiviral control vector or a lentiviral vector overexpressing NRG1. Stable pools of cells were selected and RNA was extracted from cell lysates.

value: NRG1 overexpression vector


title: 2559_STC1_C


title: 2698_STC1_C


title: 2549_STC1_C


title: 1092C

description: Folic acid in trimesters 1-3.


title: 1088C


title: AALE NRG1 overexpression vector 2


title: AALE NRG1 overexpression vector 1


title: 2765_STC1_C


title: 2379_STC1_C


title: 1087C


title: D3-5 colon

city: Barcelona

first: Neus

last: Agell

address: C/Casanova 143

department: Biomedicina

country: Spain

institute: Universitat de Barcelona

hyb_protocol: Following fragmentation, 10 ug of fragmented and labeled cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Primeview array.

scan_protocol: Arrays were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneCHip Scanner 3000 System.

data_processing: Data was analyzed with Transcriptome Analysis Console (TAC) using RMA analysis

label: biotin

label_protocol: 150ng of each RNA sample were processed according to 3’IVT PLUS chemistry. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured in DMEM-HAM’s F12 10% FBS

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (74104, Qiagen) following manufacturer’s instructions. RNA integrity was confirmed in a Bioanalyzer 2100 (Agilent).

tag: expression

value: Colorectal Cancer


title: AALE control vector 3

description: Gene expression from AALE cells transfected with control vector.

value: control vector


title: A4-23 colon


title: 1085C

description: Folic acid in trimesters 1-3.


title: 2357_STC1_C

tag: cell type


title: 1084C


title: AALE control vector 2


title: D1-17 colon


title: AALE control vector 1


title: 2173_STC1_C


title: M-WM793B_C

value: melanoma cell line from Cancer Cell Line Encyclopedia


title: 1082C

description: Folic acid in trimesters 1-3.

value: Cord blood


title: M-WM266_C


title: BMDM_auranofin-treated_LPS/ATP-treated_rep2

city: Seoul

first: Jungwook

last: Hwang

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

institute: Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea

description: processed data file: BMDM_FPKM.txt

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC v0.11.7 and Trimmomatic v0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0
And then, transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016)
Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was isolated using Trizol® reagent (Thermo Fisher Scientific, Waltham, MA, USA)
Library construction was performed by Macrogen Inc. (Macrogen, Seoul, Korea). 1 µg of total RNA was used to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

tag: strain

value: bone marrow

value: treated with LPS (100 ng/mL), ATP (1mM), and Auranofin (0.1 µM)

value: Bone marrow derived macrophage


title: 1078C

value: PLACEBO


title: D1-8 colon


title: S2-22 colon


title: A4-6 colon


title: Backfat WT rep4_RNAseq

city: Jeonju

first: Devender

last: Arora

address: 1500, Kongjwipatjwi-Ro, Iseo-Myeon, Wanju-gun

institute: NIAS

data_processing:
For WGBS data the sequence reads were first checked for quality and trimmed using trim galore and and alignment were subjected to the filtration of duplicate reads with sam_blaster and sorted using SAMtools subsequently mapped against sus scrofa11.1 using Bismark
For RNAseq data Sequence reads were first checked for quality and trimmed using trimmoatic tool and all quality-filtered PE reads were aligned to the Sscrofa genome (Sscrofa11.1) retrieved from the University of California Santa Cruz (UCSC) browser using Hisat2
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: Bismark report
Supplementary_files_format_and_content: Raw counts

organism: Sus scrofa

source_name: Backfat

extract_protocol:
gDNA from Nanchukmacdon pig backfat and liver was subjected to bisulfite conversion using the fragment size (250bp±25bp), WGBS was performed with MethylMiner Methylated DNA Enrichment kit, and then a sequencing library was constructed using the Illumina Paired-end sequencing on an Illumina, NovaSeq, 150bpX2.
Total RNAs from Liver and Backfat were prepared using TRIzol (Invitrogen) and a RNeasy RNA Purification Kit with DNase treatment (Qiagen), according to the instruction manual.  One microliter of cleaned total RNA was consumed to check RNA quality using BioAnalyzer 2011 with an RNA chip (RIN > 7 and 28S:18S ratio > 1.0). Messenger RNA sequencing libraries were generated using an mRNA Seq Sample Prep Kit following the manufacturer’s manual (Illumina). 5 ug of poly(A) mRNA was isolated from the total RNA using oligo-dT beads. The mRNA was then fragmented and randomly primed for reverse transcription, followed by the second-strand synthesis to create double-stranded cDNA fragments. The double-stranded short cDNA fragments were purified with a QiaQuick PCR extraction kit (Qiagen) and resuspended in an EB buffer. Each end of cDNA was repaired with a combination of fill-in reactions and blunted by exonuclease. The addition of A-base was applied to the blunt end DNA followed by sequencing adaptor ligation. The required fragments were purified by agarose gel electrophoresis and a QIAquick Gel Extraction Kit (Qiagen), and enriched by PCR amplification.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

value: Backfat

tag: age

value: 22 months

value: Normal


title: 1074C

tag: tissue


title: BMDM_auranofin-treated_LPS/ATP-treated_rep1

description: processed data file: BMDM_FPKM.txt

tag: treatment


title: A4-19 colon


title: M-WM165_C


title: S2-6 colon


title: 1069C

description: Folic acid in trimesters 1-3.

value: TREATMENT


title: M-WM115_C


title: M-HS934_C


title: Backfat WT rep2_RNAseq


title: BMDM_control_LPS/ATP-treated_rep1

description: processed data file: BMDM_FPKM.txt

value: treated with LPS (100 ng/mL) and ATP (1 mM)


title: S1-18 colon


title: Backfat WT rep5_RNAseq


title: 1067C

description: Folic acid in trimesters 1-3.


title: Backfat WT rep1_RNAseq


title: AHSC_auranofin-treated_rep2

description: processed data file: AHSC_FPKM.txt

value: liver

value: treated with Auranofin (0.03 µM)

value: Activated hepatic stellate cell


title: M-G361_C

value: BRAF mutation


title: 1064C

description: Folic acid in trimesters 1-3.


title: AHSC_auranofin-treated_rep1

description: processed data file: AHSC_FPKM.txt


title: M-940_C


title: M-96_C


title: 1063C

description: Folic acid in trimesters 1-3.


title: Backfat WT rep3_RNAseq


title: 1062C


title: AHSC_control_rep2

description: processed data file: AHSC_FPKM.txt

value: untreated


title: AHSC_control_rep1

description: processed data file: AHSC_FPKM.txt


title: BMDM_control_LPS/ATP-treated_rep2

description: processed data file: BMDM_FPKM.txt


title: Liver WT rep4_RNAseq

source_name: Liver

value: Liver


title: M-61_C

value: melanoma cell line from Cancer Cell Line Encyclopedia


title: 1061C

source_name: Cord blood

value: Cord blood


title: Liver WT rep2_RNAseq


title: day7 C1qbp-KO rep2

city: Xiamen

first: liu

last: kai

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

data_processing:
Illumina Casava1.8 software used for basecalling.
The original data (Raw Data) were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed, then mapped to mm10 whole genome using Hisat2 v2.0.5 with parameters --dta –t –p 4
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample, the formula is shown as: FPKM=(10^6*F)/(NL/10^3). F is the number of fragments in a certain sample that is assigned to a certain gene, N is the total number of mapped reads in the certain sample and L is the length of the certain gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Cells were lysed and RNA was harvested using QIAGEN RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naive cells were beads purified from mice spleen. On day 3, 5, 7 post-infection with LCMV Armstrong, transferred P14 cells were sorted from the spleen of donor mice.

value: spleen

tag: genotype

value: C1qpb KO

tag: Sex

value: female

value: day 7 post-infection

value: 11 weeks

value: CD8+ T cells

tag: cell subtype


title: Liver WT rep1_RNAseq

value: 22 months

tag: disease state

value: Normal


title: 1066C

description: Folic acid in trimesters 1-3.

tag: sample group

value: TREATMENT


title: day7 C1qbp-KO rep1


title: M-A2058_C


title: 1053C

description: Folic acid in trimesters 1-3.


title: M-57_C


title: Backfat WT rep5_gDNA

value: Backfat


title: Backfat WT rep4_gDNA


title: Liver WT rep3_RNAseq


title: M-52_C


title: 1050C

description: Folic acid in trimesters 1-3.


title: Liver WT rep5_RNAseq


title: 1043C

value: PLACEBO


title: day7 WT rep1

value: wild type


title: M-48_C

value: BRAF mutation


title: 1042C


title: M-22_C


title: day5 C1qbp-KO rep1

value: male

value: day 5 post-infection


title: day5 C1qbp-KO rep2


title: M-12_C

value: melanoma cell line from Cancer Cell Line Encyclopedia


title: 1041C

description: Folic acid in trimesters 1-3.

value: Cord blood


title: M-84_C


title: Backfat WT rep3_gDNA


title: Backfat WT rep1_gDNA


title: day7 WT rep2

value: spleen


title: 1037C

description: Folic acid in trimesters 1-3.


title: day5 WT rep2


title: Liver WT rep5_gDNA

value: Liver


title: day5 WT rep1


title: 1036C


title: cumulus cells pool from spontaneous/estrous follicles_4

city: Knoxville

first: Sarah

middle: E

last: Moorey

state: Tennessee

address: 2506 River Drive

department: Animal Science

institute: University of Tennessee

description:
spont_cc_4
cc_cpm_geo.txt

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 (Illumina, Inc, San Diego, CA) to produce 100 nucleotide long, single end reads.
Libraries were re-sequenced (Illumina HiSeq 2000; 100 nucleotide long, single end reads) to increase depth of coverage; therefore each sample has two FASTQ files.
Sequence adaptors were removed and remaining sequences were filtered for quality using fqtrim.
Filtered sequences were aligned to the Bos taurus reference genome UMD3.1 using Hisat2mapper.
FeatureCounts was used to quantify transcript abundance in each oocyte or cumulus cell pool using Bos taurus gene annotation from Ensembl.
Count data from the two sequencing events were merged and we calculated counts per million (CPM) and filtered count data generated for oocyte and CC pools to retain only transcripts with at least 5 CPM in at least 4 oocyte pools or 5 CC pools. We then utilized the Bioconductor packages “edgeR” and “DESeq2” to perform differential gene expression analyses between oocyte or CC pools from small compared to large follicles, small compared to spontaneous follicles, and large compared to spontaneous follicles
Genome_build: Bos taurus reference genome UMD3.1
Supplementary_files_format_and_content: Table with counts per million for every gene and every sample

organism: Bos taurus

source_name: cumulus cells pools

extract_protocol:
Oocytes or associated cumulus cells were individually snap frozen in lysis buffer. Pools for four oocytes or associated CC were combined, and total RNA extracted using the AllPrep® DNA/RNA Micro Kit (Qiagen, Germantown, MD) with on-column DNAse digestion following manufacturer’s instructions.
Full RNA eluate per pool of 4 oocytes or corresponding CC samples was used as input material for the reverse transcription and amplification with the Ovation® RNA-Seq System V2 (NuGen Technologies, Inc., San Carlos, CA) following manufacturer’s in-structions. Amplified cDNA was purified with the MinElute® Reaction Cleanup Kit (Qiagen, Germantown, MD) and libraries were prepared using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina, Inc., San Diego, CA).

treatment_protocol: Preovualtory follicle development was synchronized by injection of gonadotropin releasing hormone (GnRH)  on day -9, injection of prostaglandin F2 alpha on d -2, and second injection of GnRH on d0 to induce a preovualtory gonadotropin surge in cows that did not display estrus  [small follicle classification (largest follicle on d0 ≤11.7 mm);  large follicle classification (follicle ≥12.7mm)]. The cows that displayed estrus did not recieve the second GnRH injection, but endogenously triggered their gonadotropin surge near the onset of estrus [spontaneous/estrous classification (follicle size variable)]. Oocytes and cumulus cells were collected ~23 hours post second GnRH injection or estrus.

tag: developmental stage

value: ~20 hours post GnRH injection or estrus

value: cumulus cells

value: spontaneous/estrous


title: cumulus cells pool from spontaneous/estrous follicles_5

description:
spont_cc_5
cc_cpm_geo.txt


title: Liver WT rep4_gDNA


title: 1035C

description: Folic acid in trimesters 1-3.


title: cumulus cells pool from spontaneous/estrous follicles_3

description:
spont_cc_3
cc_cpm_geo.txt


title: day3 C1qbp-KO rep2

value: C1qpb KO

value: day 3 post-infection

value: 11 weeks

value: CD8+ T cells


title: 1033C


title: cumulus cells pool from spontaneous/estrous follicles_2

description:
spont_cc_2
cc_cpm_geo.txt


title: day3 C1qbp-KO rep1


title: Liver WT rep3_gDNA

value: 22 months

value: Normal


title: day3 WT rep2

value: wild type


title: 1032C

description: Folic acid in trimesters 1-3.

value: TREATMENT


title: Liver WT rep2_gDNA


title: cumulus cells pool from spontaneous/estrous follicles_1

description:
spont_cc_1
cc_cpm_geo.txt


title: day3 WT rep1

value: male


title: cumulus cells pool from large follicles_6

description:
large_cc_6
cc_cpm_geo.txt

value: large


title: 1031C

description: Folic acid in trimesters 1-3.


title: Liver WT rep1_gDNA


title: naïve C1qbp-KO rep2

value: female

value: naive cells

value: 9 weeks


title: 1030C

value: Cord blood

value: PLACEBO


title: cumulus cells pool from large follicles_4

description:
large_cc_4
cc_cpm_geo.txt

value: ~20 hours post GnRH injection or estrus

value: cumulus cells


title: 1022C

description: Folic acid in trimesters 1-3.


title: 1028C

description: Folic acid in trimesters 1-3.


title: naïve C1qbp-KO rep1

value: spleen

value: C1qpb KO


title: cumulus cells pool from large follicles_3

description:
large_cc_3
cc_cpm_geo.txt


title: cumulus cells pool from large follicles_5

description:
large_cc_5
cc_cpm_geo.txt


title: naïve WT rep2


title: cumulus cells pool from large follicles_2

description:
large_cc_2
cc_cpm_geo.txt


title: 1024C


title: 1019C

description: Folic acid in trimesters 1-3.


title: cumulus cells pool from large follicles_1

description:
large_cc_1
cc_cpm_geo.txt


title: Mock infected L929 murine fibroblasts  replicate 1

description:
X2924.TT.15
2924-TT-15-CCAACAAT-TCTTTCCC

source_name: L929 murine fibroblasts

value: L929 murine fibroblasts


title: cumulus cells pool from small follicles_6

description:
small_cc_6
cc_cpm_geo.txt

value: small


title: powv2_rep1 [hBVPs]

city: Stony Brook

first: Jonas

last: Nascimento Conde

address: Life Sciences Building

institute: Stony Brook University

description: Gene expression data from human brain microvascular endothelial cells POWV-infected 2 dpi

hyb_protocol: Samples were hybridized to GeneChip Human Clariom S Arrays (Affymetrix) using the Hydridization, Wash and Stain kit (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). Arrays were scanned at the Stony Brook Genomics Core Facility.

data_processing: Raw data was processed with the Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with Transcriptome Analysis Console (TAC) Software (Affymetrix).

source_name: POWV-infected primary brain vascular pericytes day 2

label_protocol: Fragmented and labeled single-stranded cDNA was generated from total RNA using the GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: hBVPs (passage 5), derived from elutriation of dispase-dissociated normal human brain cortex tissue were purchased from Cell Biologics (H-6023), and were grown in endothelial cell basal medium-2 MV (EBM-2 MV; Lonza) supplemented with EGM-2 MV SingleQuots (Lonza) and incubation at 37°C and 5% CO2.

extract_protocol: Total RNA was purified using RNeasy (Qiagen) following the manufacturer protocol.

treatment_protocol: POWV-LI-9 was allowed to adsorb to ~80% confluent hBVP monolayers for 1 h. Following adsorption, monolayers were washed with PBS and grown in supplemented Pericyte Media with 10% FBS. RNA was extracted 1-3 dpi. Mock-infected cells were used as control.

value: primary brain vascular pericytes

tag: viral infection

value: POWV


title: 1018C

description: Folic acid in trimesters 1-3.


title: 1016C

description: Folic acid in trimesters 1-3.


title: powv1_rep1 [hBVPs]

description: Gene expression data from human brain microvascular endothelial cells POWV-infected 1 dpi

source_name: POWV-infected primary brain vascular pericytes day 1


title: powv3_rep1 [hBVPs]

description: Gene expression data from human brain microvascular endothelial cells POWV-infected 3 dpi

source_name: POWV-infected primary brain vascular pericytes day 3


title: mock3_rep1 [hBVPs]

description: Gene expression data from human brain microvascular endothelial cells mock-infected 1 dpi

source_name: mock-infected primary brain vascular pericytes day 3

value: mock


title: cumulus cells pool from small follicles_5

description:
small_cc_5
cc_cpm_geo.txt


title: mock1_rep1 [hBVPs]

description: Gene expression data from human brain microvascular endothelial cells mock-infected 2 dpi

source_name: mock-infected primary brain vascular pericytes day 1


title: naïve WT rep1

value: wild type

value: CD8+ T cells


title: Treated2-1

city: Nanjing

first: Panpan

last: Guo

state: Jiang Shu

address: High-tech District

department: medical college

institute: Nanjing University

data_processing:
The illumina high-throughput sequencing results initially existed as original image data files and were converted into original sequencing sequence (raw read) by BCL2FastQ2
The raw read were filtrated through removing adaptor, low-quality and N ratio greater than 5% sequence.
The filtrated read was mapped to Mus_musculus.GRCm38.91 whole genome using softwave HISAT2.
Gene expression value was quantitatively estimated through Fragments per Kilobase per Million Mapped Fragments (FPKM)
Gene differential expression between the three groups was analyzed by DESeq2.
Genome_build: Mus_musculus.GRCm38.91
Supplementary_files_format_and_content: Excel file of gene differential expression between groups

source_name: macrophages

growth_protocol: Macrophages differentiated from bone marrow mononuclear cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin and mM-CSF (20 ng/ml).

extract_protocol:
The subtype of cells were sorted by flow cytometry and RNA were isolated utilizing the trizol reagents.
RNA libraries were prepared for sequencing using Illumina protocols

treatment_protocol: Cells were treated with or without IFNβ (100uU/ml) for 64h.

value: macrophages

value: IFNβ


title: powv3_rep1 [hBMECs]

source_name: POWV-infected primary brain microvascular endothelial cells day 3

growth_protocol: hBMECs (passage 3), derived from elutriation of dispase-dissociated normal human brain cortex tissue were purchased from Cell Biologics (H-6023), and were grown in endothelial cell basal medium-2 MV (EBM-2 MV; Lonza) supplemented with EGM-2 MV SingleQuots (Lonza) and incubation at 37°C and 5% CO2.

treatment_protocol: POWV-LI-9 was allowed to adsorb to ~80% confluent hBMEC monolayers for 1 h. Following adsorption, monolayers were washed with PBS and grown in supplemented EBM-2 MV with 5% FBS. RNA was extracted 1-3 dpi. Mock-infected cells were used as control.

value: human brain microvascular endothelial cells


title: cumulus cells pool from small follicles_4

description:
small_cc_4
cc_cpm_geo.txt


title: Treated1-3


title: powv2_rep1 [hBMECs]

source_name: POWV-infected primary brain microvascular endothelial cells day 2


title: mock2_rep1 [hBVPs]

description: Gene expression data from human brain microvascular endothelial cells mock-infected 3 dpi

source_name: mock-infected primary brain  vascular pericytes day 2


title: 1009C

description: Folic acid in trimesters 1-3.

value: TREATMENT


title: Mock infected L929 murine fibroblasts  replicate 2

description:
X2924.TT.16
2924-TT-16-TAATCGAT-TCTTTCCC


title: 1012C

description: Folic acid in trimesters 1-3.

value: Cord blood


title: cumulus cells pool from small follicles_2

description:
small_cc_2
cc_cpm_geo.txt


title: cumulus cells pool from small follicles_3

description:
small_cc_3
cc_cpm_geo.txt


title: 1011C

description: Folic acid in trimester 1, placebo in trimesters 2 and 3.

value: PLACEBO


title: Treated1-2


title: Treated2-2


title: 1007C


title: oocyte pool from spontaneous/estrous follicles_4

description:
spont_oocyte_4
oocyte_cpm_geo.txt

source_name: oocyte pool

value: ~20 hours post GnRH injection or estrus

value: oocyte

value: spontaneous/estrous


title: 1004C


title: cumulus cells pool from small follicles_1

description:
small_cc_1
cc_cpm_geo.txt

value: cumulus cells


title: CON3

value: Control


title: Treated1-1


title: T1L infected L929 murine fibroblasts replicate 2

description:
X3616.KO.32
3616-KO-32-GGAATGTC-TCTTTCCC

organism:
Mus musculus
Mammalian orthoreovirus 1 Lang

value: L929 murine fibroblasts


title: powv1_rep1 [hBMECs]

source_name: POWV-infected primary brain microvascular endothelial cells day 1


title: CON2


title: oocyte pool from spontaneous/estrous follicles_3

description:
spont_oocyte_3
oocyte_cpm_geo.txt


title: 1003C

description: Folic acid in trimesters 1-3.


title: CON1


title: oocyte pool from spontaneous/estrous follicles_2

description:
spont_oocyte_2
oocyte_cpm_geo.txt


title: oocyte pool from spontaneous/estrous follicles_1

description:
spont_oocyte_1
oocyte_cpm_geo.txt


title: PBS_CD45_plus_S6_2W

city: New York

address: 1300 York Ave

institute: Weill Cornell Medical College

description: Single cell 10x Genomics Chromium

data_processing:
The scRNA-seq data were analyzed with the custom Partek Flow software (Partek Inc), based on the Seurat R package. The raw sequencing data were aliagned to the mouse transcriptome reference (mm10) by STAR after Triming the tag sequences. The deduplication of UMIs, filtering of noise signals, and quantification of cell barcodes were performed to generate the single cell counts data of each sample. Single-cell QA/QC was then controlled by the total number of genes (≤ ~6,000), UMIs (≤ ~40,000), and the percentage of mitochondria genes (≤ 10%) according to each sample. The filtered counts were normalized to counts permillion (CPM), added 1.0 and Log2.0 scaled.
Genome_build: mm10

source_name: Lung

growth_protocol: HKP1 tumor cells (1.5E5 cells) were injected into mice (Scgb1a1cre /iDTR mice) through tail vein in in 100 µL of sterile PBS.

extract_protocol:
Single cell suspensions were prepared from lungs of and stained for CD45 and DAPI. DAPI-negative/CD45+ cells were sorted via fluorescence-activated cell sorting (FACS).
10x Genomics Chromium was employed to add barcoded primer gel beads to each single cell.  The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following standard protocol of10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays , followed by sequencing in Illumina NovaSeq6000 at the Genomics and Epigenetics Core Facility at Weill Cornell Medicine.

treatment_protocol: At day 3-7 post-administration of HKP1 cells, mice were treated with Tamoxifen (2 mg/20g in corn oil)  via i.p. for 5 days. At day 6, mice were treated with anti–PD-1 (clone RMP1-14, BioXCell) (250 μg/mouse, i.p.) antibodies. At day 8-9, mice were treated wtih 2 doses of diphtheria toxin (600ng/20g, i.p.). For radiation therapy (RT), mice were irradiated with , 4Gy for 3 consecutive days from day 10 to 12 using Small Animal Radiation Research Platform (Xstrahl, USA). Lungs were harvested at day 1 after RT for single cell sequencing analysis.

value: Scgb1a1cre /iDTR

value: HKP1-bearing lungs

tag: time

value: 24-48 hr psot-RT


title: DT_CD45_plus_S8_2W

description: Single cell  10x Genomics Chromium


title: F1-ES-ATAC-rep3

city: Shenzhen

first: Lei

last: Li

state: --- Select a state ---

address: China

department: Institute of Systems and Physical Biology

institute: Shenzhen Bay Laboratory

data_processing:
Quality of sequence reads from ATAC-seq of F1 ESCs and F1 fibroblast cells are checked by fastqc, and adapters are removed by trim_galore (version 0.6.5). Processed reads are all aligned to  reference genome mm10 and reference genome of SPRET/EiJ (http://www.sanger.ac.uk/) separately by bowtie2 (version 2.4.1) with parameters -p 8 -X 2000
After reads alignment, multi-mapping reads and duplicated reads are removed by samtools (version 1.9) and Picard toolkit (version 2.0.1), respectively.
Uniquely mapped reads were assigned to the genome with less mapping edit distance. The reads with equal mapping distance to both genomes were designated as common reads. Genomic alignment coordinates of the reads that were assigned to SPRET/EiJ were then converted to the corresponding locations in the C57BL/6J reference genome using the g2gtools software (version 0.1.29).
All bam files, after filtering and liftover, were converted to bigwig file by bamCoverage (version 3.3.1) in deeptools.
Peaks are called by macs2 with reads from two alleles merged and  parameters: -f BAMPE -g mm --keep-dup all --nomodel --nolambda -B.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for mapped reads in each allele of each sample.
Supplementary_files_format_and_content: narrowPeaks file for each sample in bed format.

organism: Mus musculus x Mus spretus

source_name: ES cells

extract_protocol:
Lysates from F1-fibroblasts and F1-ESCs were used for ATAC-seq library construction
The ATAC-seq libraries of F1-ESCs and F1-fibroblasts were prepared as previously described with minor modifications (Corces, Trevino et al. 2017, Liang, Li et al. 2021). Briefly, 50000 fresh cells were lysed in lysis buffer for 10 minutes on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 g for 10 minutes to remove the supernatant. Nuclei were then incubated with the Tn5 transposase (Vazyme) in tagmentation buffer at 37 °C for 30 minutes. After tagmentation, PCR was performed to amplify the library for 12 cycles under the following PCR conditions: 72 °C for 3 minutes; 98 °C for 30 seconds; and thermocycling at 98 °C for 15 seconds, 60 °C for 30 seconds and 72 °C for 40 seconds; followed by 5 minutes at 72 °C. After the PCR reaction, libraries were purified with DNA purification beads (Vazyme). The libraries were sent to Annoroad for sequencing and 2 × 150 bp reads were obtained.

value: C57BL/6J x SPRET/EiJ

value: ES cells


title: oocyte pool from large follicles_6

description:
large_oocyte_6
oocyte_cpm_geo.txt

value: large


title: F1-ES-ATAC-rep2


title: mock3_rep1 [hBMECs]

source_name: mock-infected primary brain microvascular endothelial cells day 3

tag: cell line

value: mock


title: mock1_rep1 [hBMECs]

source_name: mock-infected primary brain microvascular endothelial cells day 1

value: human brain microvascular endothelial cells


title: F1-ES-ATAC-rep1


title: 4Gy-CD45-plus_S16

first: Dingcheng

last: Gao

description: Single cell RNA sequencing

growth_protocol: HKP1 tumor cells (1.5E5 cells) were injected into mice (8-week old female C57BL/6) through tail vein in in 100 µL of sterile PBS.

extract_protocol:
Single cell suspensions were prepared from lungs of and stained for CD45 and DAPI. DAPI-negative CD45- and CD45+ cells were sorted via fluorescence-activated cell sorting (FACS).
10x Genomics Chromium was employed to add barcoded primer gel beads to each single cell.  The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following standard protocol of10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays , followed by sequencing in Illumina NovaSeq6000 at the Genomics and Epigenetics Core Facility at Weill Cornell Medicine.

treatment_protocol: At day 6 post-administration of HKP1 cells, BLI data were collected and mice were grouped such that each treatment cohort possessed similar mean tumor burdens. For radiation therapy (RT), mice were irradiated with different doses (0 or 4Gy) for 3 consecutive days from day 10 to 12 using Small Animal Radiation Research Platform (Xstrahl, USA). Lungs were harvested at 24-48 hours after last day of RT.


title: 4Gy-CD45-minus_S17

description: Single cell RNA sequencing


title: Backfat WT rep2_gDNA

source_name: Backfat

value: Backfat

value: 22 months

value: Normal


title: oocyte pool from large follicles_5

description:
large_oocyte_5
oocyte_cpm_geo.txt

value: ~20 hours post GnRH injection or estrus


title: oocyte pool from large follicles_4

description:
large_oocyte_4
oocyte_cpm_geo.txt

value: oocyte


title: F1-fibroblast-ATAC-rep2

source_name: fibroblasts

value: fibroblasts


title: F1-fibroblast-ATAC-rep3


title: mock2_rep1 [hBMECs]

source_name: mock-infected primary brain microvascular endothelial cells day 2


title: T1L infected L929 murine fibroblasts replicate 1

description:
X3616.KO.31
3616-KO-31-GAACGGTT-TCTTTCCC

source_name: L929 murine fibroblasts


title: F1-fibroblast-ATAC-rep1


title: 0Gy-CD45-minus_S15

description: Single cell RNA sequencing


title: oocyte pool from large follicles_3

description:
large_oocyte_3
oocyte_cpm_geo.txt


title: oocyte pool from large follicles_2

description:
large_oocyte_2
oocyte_cpm_geo.txt


title: RNAseq_rep2

city: Cincinnati

first: Jennifer

last: Felton

address: 3333 Burnet Ave, ML7028

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNAseq; raw sequence read quality was assesed using FASTQC/0.11.7. Adapter sequences were trimmed using CutAdapt/1.81 and TrimGalore/0.4.2. Reads were aligned to the mm9 geneome and RefSeq-based transcriptome using STAR/2.5. Duplicate were removed with PICARD/1.89. FeatureCount and calculateFPKMs were used to quantify FPKM values. Expression thresholds were determined using expression levels of known expressed eosinophil genes, with >5 FPKM in both replicates indicating genes that are expressed by eosinophils and <5 FPKM indicating genes that are silent/repressed/lowly expressed.
GO analysis was performed using Enricher
Gene expression heatmaps were generated in Rstudio using ggplot2
ChIPseq + ATACseq; raw sequence read quality was assessed with FASTQC/0.11.7, adapter sequences were trimmed with CutAdapt/1.8.1 and TrimGalore/0.4.2, prior to alignment of reads to the mm9 genome and RefSeq-based transcriptome using BOWTIE/2.3.4.1. Duplicates were removed using PICARD/1.89 and peaks were called using MACS/2.1.0 with a q-value of 0.01. Presence of peaks in expressed genes and co-marked regions were determined using BEDtools/2.27.0.
ATAC and CHIP tracks are visualised using IGV browser. TSS density heatmaps were generated using deepTools2. MAnorm, HOMER and ROSE were performed as described in methods.
Genome_build: mm9
Supplementary_files_format_and_content: Tab deliminated raw feature counts of each RNAseq file.  Aligned and trimmed called peaks for ChIP & ATAC samples.

source_name: Bone marrow derived eosinophils (bmEos)

extract_protocol:
Cultures were harvested and cells were washed in PBS prior to downstream analysis. RNA was harvested using Trizol followed by purification with the Zymo MicroRNA kit (R2061). ChIP lysates were generated from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ATAC-seq: A total of 6.5x104 viable eosinophils were pelleted at 500 g for 5 minutes at 4 C prior to resuspension in 50 uL ATAC-Resuspension Buffer (ATAC-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 made up to 50 mL in ddH2O) with added 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin. Samples were incubated on ice for 3 minutes prior to washing in 1 mL cold ATAC-RSB containing 0.1% Tween-20 only. Nuclei were pelleted at 500 g for 10 minutes at 4 C prior to addition of 50 uL transposition mixture (2X TD buffer, 100 nM transposase enzyme, 5 uL ddH2O, 1% Digitonin, 10% Tween-20 made up to 50 mL in 1X PBS) and incubated at 37 C for 30 minutes. After tagmentation, the transposased DNA was purified using the MiniElute Reaction Cleanup Kit (28204, Qiagen).
RNA libraries were prepared for sequencing according to the TruSeq Stranded mRNA kit protcol. ChIP libraries were constructed by ChIPmentation. ATAC libraries were constructed with the OMNI-ATAC protocol.
RNAseq, ChIPseq and ATACseq

value: BALB/c

value: Bone marrow derived eosinophils (bmEos)

tag: culture length

value: 14 days

tag: chip antibody


title: oocyte pool from small follicles_6

description:
small_oocyte_6
oocyte_cpm_geo.txt

value: small


title: oocyte pool from large follicles_1

description:
large_oocyte_1
oocyte_cpm_geo.txt


title: RNAseq_rep1


title: 0Gy-CD45-plus_S14

description: Single cell RNA sequencing

value: HKP1-bearing lungs


title: oocyte pool from small follicles_4

description:
small_oocyte_4
oocyte_cpm_geo.txt


title: oocyte pool from small follicles_5

description:
small_oocyte_5
oocyte_cpm_geo.txt


title: QAKA sample 2

city: Cologne

last: Maßen

address: Joseph-Stelzmann-Straße 9B

country: Germany

institute: MPI Biology of Ageing

data_processing:
sequencing reads were mapped to yeast genome (R64)
Gene counts were obtained from featureCounts of the Rsubread package (R/Bioconductor).
Gene set enrichment analysis was performed using R package fgsea
Genome_build: sacCer3
Supplementary_files_format_and_content: sample (columns) and genes (rows) -wise read count table

organism: Saccharomyces cerevisiae

source_name: liquid culture

growth_protocol: Yeast was grown in YPD to mid-log phase

extract_protocol:
RNA was isolated using the hot phenol protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: mid-log phase


title: QAKA sample 3


title: single cell of Hematopoietic Stem Cell 7

city: Guangzhou

first: Tian

last: Zhang

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

description:
barcodes.tsv
genes.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Hematopoietic Stem Cells

value: untreatment


title: QAKA sample 1


title: oocyte pool from small follicles_3

description:
small_oocyte_3
oocyte_cpm_geo.txt


title: QA sample 4


title: QA sample 2


title: intestine 1month 30%CR

city: bunkyo-ku

first: Kenji

last: Saito

department: Department of Applied Biological Chemistry

country: Japan

institute: The Univeristy of Tokyo

description:
i-1m-30
Rats fed reduced amount of diet.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: rat intestine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: 5-week-old rats were purchased from Japan SLC (Tokyo, Japan).

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: strain

value: Wistar

value: Small intestine

tag: gender

value: Male

tag: dietary restriction

value: 30% reduction

value: 1 month


title: QA sample 1


title: intestine 1month 20%CR

description:
i-1m-20
Rats fed reduced amount of diet.

tag: tissue

value: 20% reduction


title: QAKA sample 4

tag: genotype


title: KA sample 4


title: QA sample 3


title: intestine 1month control

description:
i-1m-C
Rats fed control diet.


title: intestine 1month 10%CR

description:
i-1m-10
Rats fed reduced amount of diet.

value: 10% reduction


title: intestine 1month 5%CR

description:
i-1m-5
Rats fed reduced amount of diet.

value: 5% reduction


title: QA sample 2 ChIP

data_processing:
fastq reads were mapped to sacCer3 genome using bowtie2. Mapped reads were indexed and merged using samtools.
Reads were converted to bigwig using deepTools bamcoverage with a binsize of 10 and normalization to genomic content.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files, merged and normalized to genomic content

extract_protocol:
Yeast was grown into mid-log phase, (OD600nm 0.6) in YPD, and 50 ml were harvested and placed into 50ml falcon tubes. 1% formaldehyde (final concentration) was added and cultures were left to rotate at room temperature for 30 minutes to allow for crosslinking. Cultures were centrifuged (3K, 2 min, 4ºC) and supernatant was discarded. Cell pellets were resuspended in 20 ml cold PBS, centrifuged as above and the supernatant discarded again. This washing was repeated 2 times in total and cells were then transferred to 2 ml eppendorf tubes and kept on ice. Pellets were then resuspended in 500 µl SDS buffer (1% SDS, 10mM EDTA, 50mM Tris-Cl (pH 8.0), plus protease inhibitors) on ice. About 200 µl of acid-washed glass beads were added and tubes were vortexed at top speed at room temperature for 6x 1 min, with 3 min on ice in between. The bottoms of the tubes were pierced with a hot needle and place in 15ml falcon tubes, which were centrifuged (2k, 30 seconds) to release the cell lysate. Lysates were sonicated to produce fragments of 200-600bp. Sonicated samples were transferred to 1.5 ml Eppendorf tubes, centrifuged (20 min, 14K, 4ºC) and diluted in 5 ml of cold IP buffer (0.01% SDS, 1.1%Triton-X-100, 1.2mM EDTA, 16.7MM Tris-Cl (pH 8.0), 167mM NaCl, plus protease inhibitors). 50 µl were taken as input control and stored at -20ºC. For the IP, 1 ml of chromatin was placed in siliconized Eppendorf tubes and 2 µg of antibody was added. Chromatin/antibody mix was place on rotating wheel at 4ºC overnight. 30 µl of Protein G Dynabeads TM were washed 3x in IP buffer and added to the chromatin/antibody mix. This was incubated at room temperature on a rotating wheel for 90 minutes. Beads were washed for 3 min with each wash buffer (1 ml TSE (1% Triton-X-100, 0.1%SDS, 2mM EDTA, 20mM Tris-Cl (pH 8.0)) plus 150 mM NaCl, 1ml TSE plus 500 mM NaCl, 1 ml LiCl wash (0.25M LiCl, 1% NP-40, 1% dioxycholate, 1mM EDTA, 10mM Tris-Cl (pH 8.0)), 1 ml TE (pH8.0)). IP was eluted using 200 µl of Elution buffer (1% SDS, 0.1M NaHCO3), made fresh on the day, on a rotating wheel for 30min at room temperature. 20 µl of 5M NaCl was added to all samples, which were then incubated at 95ºC for 15 min, or overnight at 65ºC, to reverse the formaldehyde crosslink. 5 µg of DNase-free RNase was then added for 30 min at 37ºC and then the DNA was purified using a Qiagen PCR purification kit
ChIP-seq libraries were generated from two independent biological replicates of IgG, Nhp2-myc and input following a previously published protocol (Ford et al, 2014)

value: Nhp2 (Proteintech 15128-1-AP)


title: KA sample 2


title: RET32

city: Vejle

first: Luisa

last: Matos do Canto

address: Beriderbakken 4

department: Biochemistry and Immunology

country: Denmark

institute: Vejle Hospital

description: naive biopsies

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

scan_protocol: Arrays were imaged using the Illumina HiScan system with the standard recommended Illumina scanner setting

data_processing: data were processed using R language. Briefly, β values were normalized and batch effects were removed. Probes with low quality (detection p-value >0.05), mapped in X/Y chromosomes and cross-reactive were filtered out, as previously described by Pidsley R et al. (2016 - DOI: 10.1186/s13059-016-1066-1)

label: Cy5 and Cy3

source_name: rectal adenocarcinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from pre-treatment biopsies of rectal tissue using a phenol-chloroform-isoamyl alcohol (25:24:1) solution-based protocol.

tag: response

value: pIR


title: adipose 1month 30%CR, rep2

description:
a-1m-30(2)
Rats fed reduced amount of diet.

source_name: rat adipose tissue

value: Adipose tissue


title: KA sample 1


title: RET31

description: naive biopsies


title: QA sample 2 input control


title: N4

description: normal tissue

source_name: Normal rectal tissue

value: NT


title: RET30

description: naive biopsies


title: N5

description: normal tissue


title: N1

description: normal tissue


title: N2

description: normal tissue


title: WT sample 2 ChIP

value: WT


title: WT sample 4

value: wt


title: WT sample 2 input control

value: mid-log phase


title: WT sample 3


title: N3

description: normal tissue


title: adipose 1month 10%CR, rep2

description:
a-1m-10(2)
Rats fed reduced amount of diet.


title: oocyte pool from small follicles_2

description:
small_oocyte_2
oocyte_cpm_geo.txt

source_name: oocyte pool

value: ~20 hours post GnRH injection or estrus

value: oocyte

tag: treatment

value: small


title: adipose 1month 20%CR, rep2

description:
a-1m-20(2)
Rats fed reduced amount of diet.

value: Wistar


title: oocyte pool from small follicles_1

description:
small_oocyte_1
oocyte_cpm_geo.txt


title: adipose 1month 5%CR, rep2

description:
a-1m-5(2)
Rats fed reduced amount of diet.

value: Male


title: QA sample 1 ChIP


title: WT sample 2


title: RET27

description: naive biopsies


title: WT sample 1 ChIP


title: adipose 1month control, rep2

description:
a-1m-C(2)
Rats fed control diet.


title: WT sample 1


title: RET17

description: naive biopsies


title: RET24

description: naive biopsies


title: QA sample 1 input control


title: scRNA-seq_Sample 2

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
We conducted all the preprocessing steps: generating, demultiplexing FASTQ files from the raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 mouse transcriptome (cellranger, v3.0.2, 10X Genomics), demultiplexing cell-hashing data, and generating of raw gene count matrices using Cumulus (v0.8.0, Li, Bo, Joshua Gould, Yiming Yang, Siranush Sarkizova, Marcin Tabaka, Orr Ashenberg, Yanay Rosen et al. "Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq." bioRxiv (2019): 823682), a cloud based data analysis framework. The pipelines were run in Terra Cloud Platform (http://app.terra.bio).
We filtered out low-quality cells with less than 500 genes detected and low-expressed genes expressed in fewer than 50 cells. The filtered raw gene expression matric was cell-normalised over total number of counts, multiplied by 10,000 and log transformed.
Genome_build: mm10

source_name: Channel 2; Tum 877 WT, dLN 877 WT, ndLN 877 WT, Tum 685 KO, dLN 685 KO, ndLN 685 KO

growth_protocol: MC38-OVAdim (0.5 x106) cells were injected subcutaneously in 100 μl PBS on the flank.

extract_protocol:
After flow sorting, cells from each sample was resuspended in PBS containing 2% FCS and stained with oligo tagged TotalSeq antibodies directed against CD45 for 30 minutes on ice. Cells were washed and pooled accordingly, centrifuged at 1200rcf for % minutes at 4 degrees and resuspending in 31.7 ul of PBS + 2% FCS. For each 10X channel 6 samples were combined: WT1-Tumour, dLN, ndLN; KO1 Tumour, dLN, ndLN; WT2-Tumour, dLN, ndLN; KO2 Tumour, dLN, ndLN.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 5’ Reagent Kits  according to manufacturer’s instructions.

treatment_protocol: Single cell suspension was obtained after tumour digestion with 50ug/ml Liberase TM (Roche) + 20ug/ml DNAse I (Roche) at 37°C for 30 minutes. Haematopoietic cells were enriched by density gradient centrifugation with 30% Percoll (GE Healthcare Life Sciences) for 20 min at 1800 rpm (no brake) followed by passing through a 40-μm cell strainer. DCs were obtained from LNs after 50ug/ml Liberase TM (Roche) + 20ug/ml DNAse I (Roche) at 37°C for 30 minutes.

value: mixed sample (Tumour, dLN, ndLN)

value: CD45+ cells-with enrichment for DC

value: mixed sample (non-demultiplexed)


title: adipose 1month 30%CR, rep1

description:
a-1m-30(1)
Rats fed reduced amount of diet.

value: 30% reduction

value: 1 month


title: RET15

description: naive biopsies


title: adipose 1month 20%CR, rep1

description:
a-1m-20(1)
Rats fed reduced amount of diet.

value: 20% reduction


title: RET19

description: naive biopsies

value: pIR


title: F18D_WGBS

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

institute: Chinese Academy of Sciences

description:
rapid air drying after continue grown for 18-week of non-acclimated plants
Methylation profile of gene promoters.xlsx
sample name:
12

data_processing:
BSMAP was used to map clean reads to reference with 2 forward strands.
Methylation level  was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Putative  DMRs were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5 CpG (CHG or CHH) sites with a 2-fold change in methylation level and Fisher test p value <= 0.05.
Genome_build: GCA_001598015.1 Boea_hygrometrica.v1
Supplementary_files_format_and_content: excel file include the methylation level of CG, CHG and CHH in the promoter region of each gene

organism: Dorcoceras hygrometricum

growth_protocol: The seeds of B. hygrometrica plants collected from natural habitats were planted in ordinary potting soil in a well-watered greenhouse at 25°C with a photoperiod of 15 h light/9 h dark and a relative humidity of 60% for three months.

extract_protocol:
Genomic DNA used for WGBS was extracted from leaves of B. hygrometrica using a Plant Genomic DNA Kit (Tiangen Biotech, Beijing, China). Approximately 45 leaves detached from at least 15 individual plants were pooled for DNA extraction in each biological replicate.
The DNA library of each treatment was constructed from a pool comprising equal quantities of DNA samples from six biological replicates. Genomic DNA was subjected to sonication, 3’A addition, adaptor ligation, followed by bisulfite modified with a ZYMO EZ DNA methylation-Gold kit (Zymo Research, Orange, CA, USA), gel purification and PCR amplification. Sequencing was performed on an Illumina HiSeq X Ten platform (Illumina Inc., San Diego, CA, USA) with PE150 mode.

treatment_protocol: Three-month-old seedlings were subjected to slow soil-drying, re-watering, rapid air-drying, and rehydration. Both acclimated and non-acclimated plants were subjected to rapid air-drying and rehydration after continuous cultured for 4 and 18 weeks, respectively.

value: seedling leaves

value: dehydrated


title: scRNA-seq_Sample 1

source_name: Channel 1;Tum 963 WT, dLN 963 WT, ndLN 963 WT, Tum 650 KO, dLN 650 KO, ndLN 650 KO

extract_protocol:
After flow sorting, cells from each sample was resuspended in PBS containing 2% FCS and stained with oligo tagged TotalSeq antibodies directed against CD45 for 30 minutes on ice. Cells were washed and pooled accordingly, centrifuged at 1200rcf for % minutes at 4 degrees and resuspending in 31.7 ul of PBS + 2% FCS. For each 10X channel 6 samples were combined: WT1-Tumour, dLN, ndLN; KO1 Tumour, dLN, ndLN; WT2-Tumour, dLN, ndLN; KO2 Tumour, dLN, ndLN.
Single-cell RNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 5’ Reagent Kits according to manufacturer’s instructions.


title: WT sample 1 input control

value: WT


title: RET26

description: naive biopsies


title: adipose 1month 10%CR, rep1

description:
a-1m-10(1)
Rats fed reduced amount of diet.

value: Adipose tissue

value: 10% reduction


title: Aim2 KO control 3

city: Calgary

first: Daniel

last: Muruve

state: Alberta

address: 3280 Hospital Dr. NW

department: Medicine

country: Canada

institute: University of Calgary

hyb_protocol: NanoString nCounter PanCancer mouse IO360 gene expression assay protocol. Hybridization buffer was mixed with the nCounter Pancancer mouse IO360 Panel Reporter CodeSet to prepare a master mix. Then, RNA was combined with the master mix, followed by addition of nCounter Panel Capture CodeSet. Samples were incubated for 18 hours at 65 °C.

scan_protocol: Raw counts of mRNA hybridized to oligos were counted at maximum scan resolution using the NanoString nCounter Digital analyzer.

data_processing: Analysis was performed using the nSolver analysis software (2.0). All samples that passed QC were normalized to the geometric mean of the positive technical controls, then normalized all to the geometric mean of the housekeeping genes.

source_name: Kidney

extract_protocol: Total RNA using RNeasy RNA extraction kit (Qiagen).

value: Kidney

value: Aim2 KO

tag: Sex

value: Female

tag: age

value: 8-10 weeks

value: Control


title: RET18

description: naive biopsies


title: RET22

description: naive biopsies


title: A18D_WGBS

description:
rapid air drying after continue grown for 18-week of acclimated plants
Methylation profile of gene promoters.xlsx
sample name:
11


title: Aim2 KO control 2


title: RET20

description: naive biopsies


title: adipose 1month control, rep1

description:
a-1m-C(1)
Rats fed control diet.

value: Wistar

value: Male


title: adipose 1month 5%CR, rep1

description:
a-1m-5(1)
Rats fed reduced amount of diet.

value: 5% reduction


title: F18_WGBS

description:
continue grown for 18-week without acclimation
Methylation profile of gene promoters.xlsx
sample name:
10

value: fresh


title: RET25

description: naive biopsies


title: Aim2 KO control 1


title: RET8

description: naive biopsies


title: F4D_WGBS

description:
rapid air drying after continue grown for 4-week of non-acclimated plants
Methylation profile of gene promoters.xlsx
sample name:
8


title: adipose 1week 30%CR, rep2

description:
a-1w-30(2)
Rats fed reduced amount of diet.

value: 30% reduction

value: 1 week


title: Aim2 WT control 2

value: Aim2 WT


title: Aim2 WT control 1


title: adipose 1week 20%CR, rep2

description:
a-1w-20(2)
Rats fed reduced amount of diet.

value: 20% reduction


title: A4D_WGBS

description:
rapid air drying after continue grown for 4-week of acclimated plants
Methylation profile of gene promoters.xlsx
sample name:
7

value: seedling leaves

value: dehydrated


title: F4_WGBS

description:
continue grown for 4-week without acclimation
Methylation profile of gene promoters.xlsx
sample name:
6


title: adipose 1week 10%CR, rep2

description:
a-1w-10(2)
Rats fed reduced amount of diet.

value: Adipose tissue


title: Aim2 KO NTS 3

value: Nephrotoxic serum


title: A4_WGBS

description:
continue grown for 4-week after acclimation
Methylation profile of gene promoters.xlsx
sample name:
5


title: Aim2 KO NTS 2

value: Kidney


title: adipose 1week 5%CR, rep2

description:
a-1w-5(2)
Rats fed reduced amount of diet.


title: adipose 1week control, rep2

description:
a-1w-C(2)
Rats fed control diet.


title: RET5

description: naive biopsies

value: pIR


title: RET6

description: naive biopsies


title: Aim2 KO NTS 1

value: Aim2 KO

value: Female


title: A_WGBS

description:
rehydrated after slow soil drying
Methylation profile of gene promoters.xlsx
sample name:
3

source_name: rehydrated after slow soil drying

value: rehydrated


title: A18_WGBS

description:
continue grown for 18-week after acclimation
Methylation profile of gene promoters.xlsx
sample name:
9


title: AD_WGBS

description:
rapid air drying of fresh plants after acclimation
Methylation profile of gene promoters.xlsx
sample name:
4


title: RET3

description: naive biopsies


title: RET4

description: naive biopsies


title: SD_WGBS

description:
slow soil drying of fresh plants
Methylation profile of gene promoters.xlsx
sample name:
2

source_name: slow soil drying of fresh plants


title: Aim2 WT control 3

value: 8-10 weeks

value: Control


title: T3D infected L929 murine fibroblasts replicate 2

city: Nashville

first: Jeff

last: Rathmell

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

description:
X2924.TT.14
2924-TT-14-ATGAGCAT-TCTTTCCC

organism:
Mus musculus
Mammalian orthoreovirus 3 Dearing

extract_protocol:
Infected cell pellets were thawed, incubated with 0.14% deoxycholate for 30 min on ice, then sonicated in the presence of Vertrel XF to release virus particles from cells. Virions and TC particles were separated by ultracentrifugation at 25,000 × g in a 1.2-1.4 g/cm3 cesium chloride density gradient. Mock virions and TC particles were collected by aligning gradients containing virions and TC particles next to mock gradients, marking the expected position of virions and TC particles onto the mock gradient, aspirating liquid above the expected position, and transferring 250 µL of the gradient from the expected position of virions and TC particles into clean Eppendorf tubes. Mock preparations and complete virus particles and TC particles were collected and dialyzed in virion storage buffer (150 mM NaCl, 15 mM MgCl2, 10 mM Tris-HCl, pH 7.4). Purified reovirus particles were treated with 1 U/µL benzonase (Sigma) for 1 h at 37°C to degrade extra-particle nucleic acids. RNA content was analyzed by Bioanalyzer (Agilent) before libraries were prepared.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), then Illumina-ready libraries were sequenced by 150 base pair paired-end sequencing on the NovaSeq 6000 Sequencing System (Illumina)

value: L929 murine fibroblasts


title: F_WGBS

description:
fresh plants
Methylation profile of gene promoters.xlsx
sample name:
1

source_name: fresh plants

value: fresh


title: Aim2 WT NTS 3


title: Aim2 WT NTS 2


title: Aim2 WT NTS 1


title: T3D infected L929 murine fibroblasts replicate 1

description:
X2924.TT.13
2924-TT-13-GTAGAGAT-TCTTTCCC


title: RET12

description: naive biopsies