title: Input_T24_donor1


title: plus Th17 Adcy10-/- rep 1

status: Public on Oct 01 2021

type: SRA

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

country: USA

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were aligned to the mouse genome (mm9) using STAR_2.4.0f1 with default parameters, and SAMTOOLS v0.1.19 was used for sorting and indexing reads. CuffLinks was then used to calculate normalized expression levels (FPKM; Fragments Per Kilobase of transcripts per Million reads) Counts were calculated using htseq-count
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: T cells

extract_protocol:
RNA was isolated according to specifications of the RNA Easy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spleens or lymph nodes from male Adcy10-/- and wild type C57Bl/6 mice age 8-10 weeks were excised and mechanically disrupted to obtain single cell suspensions.  Cells were treated with a red blood cell lysis buffer (155 mM Ammonium chloride, 10 mM sodium bicarbonate, 0.1 mM EDTA in PBS pH 7.4) for two minutes and enriched for CD4+ T cells using a magnetic bead negative selection (Miltenyi).  T cells were cultured in 96-well plates coated the night before with 200 uL of 10 µg/mL anti-CD3 antibody (BD biosciences) in IMDM modified with 1% sodium pyruvate, 1% L-glutamine, 1% pen/strep, and 10% FBS (Thermo Fischer), in the presence of 2 µg/mL anti-CD28 antibody (BD biosciences), 20 ng/mL recombinant mouse IL-1β (Miltenyi), 25 ng/mL IL-6 (Miltenyi), and 20 ng/mL IL-23 (R&D Systems). Media was also supplemented with 1 µg/mL anti-IFNγ antibody (Thermo Fisher) and 1 µg/mL anti IL-4 antibody (Thermo Fisher) to inhibit Th1 and Th2 polarization, respectively.  Cells were used as follows for different analyses. After 18 hours in culture, cells were collected for RNA sequencing.

tag: strain

tag: treatment

value: baseline media + polarizing cytokines

tag: genotype

tag: age

value: 8-10 weeks


title: plus Th17 WT rep3

value: WT


title: Input_T8_donor2

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

library_source: genomic

data_processing:
Reads were aligned to hg38 reference genome using Bowtie2
For each condition, peaks were called independently for each of the three donors using HOMER on the aligned reads with FDR < 0.1.
Peaks detected by both two callers were kept and labeled by the peak names generated by HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig. H3K27me3 coverage; tab-delimited, JMJD3 peaks.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood of healthy donors

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: naive CD4 T cells

tag: antibody

value: input

tag: time


title: Input_T8_donor1


title: plus Th17 WT rep1


title: Input_T0_donor3


title: plus Th17 WT rep2


title: Th17 Adcy10-/- rep 3

value: baseline media


title: Th17 WT rep3


title: Input_T8_donor3


title: Th17 Adcy10-/- rep 1


title: Th17 Adcy10-/- rep 2


title: plus Th17 Adcy10-/- rep 2


title: JMJD3_T24_donor3


title: Input_T0_donor1


title: JMJD3_T24_donor2


title: JMJD3_T24_donor1


title: Input_T0_donor2


title: Th17 WT rep2


title: IMs_TP309-6

city: 上海市

first: yang

last: he

state: 徐汇区

address: 上海市徐汇区枫林路300号植物生理生态研究所

country: China

institute: SIPPE

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Oryza sativa

source_name: rice   inflorescence meristem

growth_protocol: Plants were normally grown in paddy field.

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini Kit (Cat 74904, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: inflorescence meristem

value: wild type

tag: name


title: IMs_TP309-5

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: JMJD3_T8_donor3


title: JMJD3_T8_donor2


title: IMs_TP309-4

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th17 WT rep1


title: 3dp Glucan + LPS 2

city: Nashville

first: Cody

middle: L

last: Stothers

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University

data_processing:
Data were aligned using the STAR protocol
Aligned sequences were trimmed using QC30
Read counts were generated using featureCounts
Differentially expressed genes were identified using DESeq2. Transcripts with a log2foldchange of at least 1.0 and p-adjusted <0.05 were considered significaint
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values (CSV) file with ID, symbol, Count, FPKM, and TPM for each gene

source_name: Bone marrow-derived macrophages

growth_protocol: Femurs were harvested from mice and flushed with RPMI 1640 containing 2 mM glutamine and 25 mM HEPES (Gibco, Grand Island, New York) supplemented with 10% certified performance plus fetal bovine serum (FBS, Gibco), 1% antibiotic-antimycotic (Gibco), and 10 ng/mL mouse recombinant macrophage-colony stimulating factor (M-CSF, R&D Systems), henceforth referred to complete media. Bone marrow cell suspensions were centrifuged at 300g for 6 minutes at 4C and plated at a concentration of 5x104 cells/mL in complete media. After 7 days of differentiation, BMDM received fresh media and were treated with 5 ug/mL beta-glucan or vehicle as unstimulated controls for 24 hours.

extract_protocol:
Total RNA was isolated under an RNase-free environment, using the RNeasy Mini Kit (Qiagen, Hilden, Germany), and treated with DNase (Qiagen). Total RNA quality and concentration were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer.
mRNA Libraries were prepared using NEBNext Poly(A) selection (New England Biolabs). Sequencing was performed at paired-end 150 bp on an Illumina NovaSeq 6000 with at least 50 million reads per sample by Vanderbilt Technologies for Advanced Genomics

treatment_protocol: Macrophages were treated with beta-glucan for 4hr, 24hr, or 24hr followed by a three day rest period (3dp). 3dp or vehicle-treated macrophages were re-stimulated with LPS for 6hr.

value: Macrophage

value: 5ug/mL beta-glucan 24 hours followed by 3 days of rest and 6hr 100ng/mL LPS


title: 3dp Glucan + LPS 1


title: JMJD3_T8_donor1


title: 4hr LPS 2

value: 4hr 100ng/mL LPS


title: JMJD3_T0_donor3


title: IMs_TP309-3

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: IMs_TP309-2

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: JMJD3_T0_donor2


title: 4hr LPS 1


title: IMs_ROD1-OE-3

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: over expression


title: 3dp Glucan 1

value: 5ug/mL beta-glucan 24 hours followed by 3 days of rest


title: 3dp Glucan 2


title: C2_HepG2 treated with SPARC 800 ng/ml

type: RNA

city: Suzhou

first: Shan

last: Wan

address: Renai Road 199

department: Pathology

institute: Soochow University

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Quantile normalization was used for raw data analysis by using the R (version 3.0, https://www.r-project.org/foundation). Excel data uploaded provides the logarithm values (log2) of raw data. Fold change was caculated according to the raw data of gene expression. Filter for differentially expression of genes was set as "fold change > 1.10, and P < 0.05" by t-test (SPSS).

label: biotin

source_name: HepG2 treated with SPARC 800 ng/ml

label_protocol: standard protocol

extract_protocol: Total RNA of HepG2 cells, and HepG2 cells treated with 800 ng/ml recombinant SPARC were isolated by a NucleoSpin RNA II kit (Macherey-Nagel, Duren, Germany) and sent to GeneChem (Shanghai, China) for quality control and preparation for transcriptome analysis using an Agilent RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA).

tag: cell line

value: SPARC 800 ng/ml


title: IMs_ROD1-OE-2

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: C3_HepG2 treated with SPARC 800 ng/ml


title: JMJD3_T0_donor1


title: H3K27me3_T24_donor3

description:
H3K27me3_coverage_T24_3donors
H3K27me3_T24_new_treat_pileup.bw


title: B3_HepG2 treated with SPARC 200 ng/ml

source_name: HepG2 treated with SPARC 200 ng/ml

value: SPARC 200 ng/ml


title: C1_HepG2 treated with SPARC 800 ng/ml


title: A1_HepG2 untreated

source_name: HepG2 untreated

value: none; untreated


title: B2_HepG2 treated with SPARC 200 ng/ml


title: 24hr Glucan 2

value: 5ug/mL beta-glucan 24 hours


title: B1_HepG2 treated with SPARC 200 ng/ml


title: A3_HepG2 untreated


title: IMs_ROD1-OE-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: H3K27me3_T24_donor2


title: 24hr Glucan 1


title: H3K27me3_T24_donor1


title: IMs_rod1-3

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: variant


title: A2_HepG2 untreated


title: H3K27me3_T8_donor3

description:
H3K27me3_coverage_T8_3donors
H3K27me3_T8_new_treat_pileup.bw


title: 4hr Glucan 2

value: 5ug/mL beta-glucan 4 hours


title: IMs_TP309-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: IMs_rod1-2

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: 4hr Glucan 1


title: IMs_rod1-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Control 2

value: Vehicle


title: H3K27me3_T8_donor2

value: naive CD4 T cells


title: leaves_TP309-6

address: 上海市徐汇区枫林路300号植物生理生态研究所

source_name: rice leaves

value: leaves


title: Control 1


title: H3K27me3_T0_donor3

description:
H3K27me3_coverage_T0_3donors
H3K27me3_T0_new_treat_pileup.bw


title: H3K27me3_T0_donor2


title: Th2_KO_2_2

city: Onna son

first: Hiroki

last: Ishikawa

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

data_processing:
all raw reads were trimmed by Cutadapt 2.10.
RNA-Seq: trimmed reads were then directly mapped to the UCSC mouse genome mm10, and transcripts were quantified with Salmon 1.3.0 using default settings (k = 31).
RNA-Seq: After transcript quantification, raw feature counts of each transcript were first normalized within and between samples to obtain TPM (Transcripts Per kilobase Million).  conducted with DeSeq2
RNA-SEQ: Differential gene expression analysis was analyzed by DESeq2
ChIP-Seq: Trimmed reads were then mapped to mouse genome mm10 by calling Bowtie2 2.3.4.3 in TopHat2 2.1.1
ChIP-Seq: Peaks were called for each sample replicate using Homer 4.11 with default parameters (FDR < 0.001)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-Seq: csv files include log2FC, pvalue, qvalue for each T helper cell subset
Supplementary_files_format_and_content: ChIP-Seq: bed files include peak annotation for each antibody

source_name: Splenocytes

growth_protocol: Naïve CD4+ T cells were isolaated from mice spleen and cultured under Th0, Th1 and Th2 conditions for 48h.

extract_protocol:
RNA-Seq: QIAGEN RNAeasy. ChIP-Seq: Cell signaling SimpleChIP Plus Enzymatic Chromatin IP Kit (9005S; Cell Signaling)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-Seq, polarized cells were first stained by Zombie-NIR and viable cells were sorted by FACS. Typically, 2e+5 cells were used for one RNA-seq. For ChIP-Seq, 1e+6 cells were directly collected.

tag: polarizing condition

value: Naive CD4+ T cells


title: leaves_TP309-5

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: leaves_TP309-4

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: leaves_TP309-3

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: H3K27me3_T0_donor1


title: siJMJD3_donor3

data_processing:
RNA-seq reads were aligned to the UCSC hg38 genome using Tophat 2
Reads assigned to each gene were counted by subread with ensembl gene sets as reference.
Genes without at least 5 reads mapped in at least one sample were considered undetectable and were filtered out.
Read counts were normalized by TMM method and differential expression was calculated using R package edgeR Cut-offs imposed for differential expression analysis was set as FDR of < 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files. Output of differential gene expression analysis from EdgeR.

source_name: human naïve CD4 T cells

growth_protocol: Naïve CD4 T cells were cultured in RPMI 1640 (Gibico) supplemented with 100 U/ml Penicillin, 100 ug/ml Streptomycin and 10% FBS at 37° C with 5% CO2.

extract_protocol:
RNA for RNA-seq was isolated from purified cells using an RNeasy plus mini kit (QIAGEN) following the manufacturer’s instructions.
200 ng of purified total RNA was put into sequencing library prep, using NEBNext® Ultra™ RNA Library Prep Kit and for Illumina®NEBNext rRNA Depletion Kit (NEB). Libraries were assessed on an Agilent Bioanalyzer using a DNA chip and quantitated using the Quant-iT ds DNA BR Assay kit (Invitrogen) and a Qubit Fluorimeter (Invitrogen).

treatment_protocol: Human naïve CD4 T cells were transfected by electroporation with 2 uM JMJD3-specific Cy3-labeled siRNA (ON-TARGETplus siRNA smartpool, GE Dharmacon) or Cy3-labeled scramble siRNA controls after isolation and incubated in culture for 16 hrs. To isolate the cells being efficiently transfected, Cy3-positive populations were sorted by flow cytometry in both siJMDJ3 and scramble transfected cells.  These populations were then activated with CD3/CD28 beads and collected at certain time points after activation for downstream experiments.

value: human naive CD4 T cells

tag: genotype/variation

value: knock-down of JMJD3 (siJMJD3)


title: siJMJD3_donor2


title: siJMJD3_donor1


title: leaves_TP309-2

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: wild type


title: leaves_TP309-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th2_WT_2_2

value: Junbfl/fl


title: leaves_ROD1-OE-3

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th2_KO_1_1


title: scrambled_donor3

value: control siRNA (scrambled)


title: Th2_WT_2_1


title: scrambled_donor2


title: leaves_ROD1-OE-2

address: 上海市徐汇区枫林路300号植物生理生态研究所

value: over expression


title: H3K27me3_T8_donor1


title: leaves_ROD1-OE-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th2_WT_1_2


title: Th2_WT_1_1


title: Th1_KO_2_2


title: leaves_rod1-2

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: scrambled_donor1


title: leaves_rod1-3

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th2_KO_2_1


title: Th1_KO_2_1


title: Th1_KO_1_2


title: leaves_rod1-1

address: 上海市徐汇区枫林路300号植物生理生态研究所


title: Th1_KO_1_1


title: Th1_WT_2_2


title: Th1_WT_2_1


title: Th1_WT_1_2


title: Th1_WT_1_1


title: Th0_KO_1_2


title: Th0_KO_1_1


title: Th2_KO_1_2


title: Th0_WT_2_2


title: A151 ODN-treated replicate array 16

city: Ankara

first: Ihsan

last: Gursel

state: Cankaya

address: Faculty of Science, Ihsan Dogramaci Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

description: Biological replicate 16 of 16 for A151 ODN-treated BALB/c splenocytes

hyb_protocol: Cy-labeled reference and sample cDNAs (7.5 ul each) were combined, denaturated by heating for 2 min at 98 C and mixed with 36 ul of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, SaltLake City, Utah). The hybridization solution containing the sample was added to the array, and was placed for 18 hrs at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Arrays were scanned and intensity values were generated using an Axon scanner and Genpix software v5.1 (Axon Instruments, Union City, CA).

data_processing: The limma v3.46.0 and the genefilter v1.72.1 packages in R v4.0.5 were used to preprocess the raw data in tabular (TSV) format. Initially, the probes with low (< 100) signal intensity, spots with low quality (flag == 0) and with small size (< 10) in an array were removed using a custom function. Identifiers for genes were replaced with the corresponding gene symbols in the annotation file downloaded together with the data sets. The background corrected data were normalized using the lowess intensity dependent normalization function normalizeWithinArrays() to adjust for differences in labeling intensities of the Cy3- and Cy5-dyes, which was then followed by the quantile normalization function normalizeBetweenArrays() to account for any heterogeneity in the statistical properties of the underlying distributions between arrays. Gene filtering was then performed using the genefilter() function, taking an inter-quantile range (IQR)-based variance filtering function as an argument to filter out probes with low (> 50%) variation across sample classes. Afterwards, empty or control wells were removed, and the corresponding expression values that are already log base 2 transformed were averaged over the probes mapping to the same gene to condense the data sets. Standard diagnostic plots were used before and after each step to decide whether further improvement is needed technically. Ultimately, the final data sets were batch corrected using the ComBat() function in the sva v3.38.0 package with a non-parametric test to fit a linear regression model to the data set for the removal of technical variation associated with the input data.

source_name: whole mouse spleen as universal reference sample

growth_protocol: 2-month-old female BALB/c mice (NCI, Frederick, MD) were housed in CBER’s specific pathogen-free facility. Spleens were surgically removed from mice under sterile conditions and dissociated in warm complete medium by gently pressing with a sterile syringe plunger. Single cell suspension were prepared in warm RPMI 1640 supplemented with 10% FBS, 50 mg/ml penicillin/streptomycin, 2 mM L-glutamine, 10 mM Hepes buffer, 0.11 mg/ml sodium pyruvate, and 0.5 mM B-mercaptoethanol.

treatment_protocol: Total RNA was extracted from spleen cell cultures using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer. 20 micrograms of total RNA was reverse-transcribed using 3 ul 10X first strand buffer (Stratagene, La Jolla, CA), 2 ul (1 ug) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 ul (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 ul 20X aminoallyl-dUTP/dNTP mix, and 3 ul 0.1 M DTT in a final volume of 30 ul at 42 C for 1 hr. A reference mouse RNA sample (Stratagene, La Jolla, CA) was processed in parallel. Both cDNA’s were purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliters of cDNA was labeled with Cy3 (for the universal reference cDNA) or Cy5 (for sample cDNA) reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M sodium bicarbonate for 90 min in the dark. Labeled cDNA was purified using MinElute PCR Purification Kits (Qiagen, Valencia, CA).

value: spleen cell culture

value: BALB/c

value: 2 months old

tag: Sex

value: female

source_name: splenocytes treated with A151 ODN

value: splenocyte cell culture

value: A151 ODN


title: A151 ODN-treated replicate array 13

description: Biological replicate 13 of 16 for A151 ODN-treated BALB/c splenocytes

label_protocol: 10 microliters of cDNA was labeled with Cy3 (for the universal reference cDNA) or Cy5 (for sample cDNA) reactive dyes (Amersham Biosciences, UK) diluted in 5 ul of DMSO plus 1.7 ul of 1 M sodium bicarbonate for 90 min in the dark. Labeled cDNA was purified using MinElute PCR Purification Kits (Qiagen, Valencia, CA).

extract_protocol: Total RNA was extracted from spleen cell cultures using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer.


title: Th0_KO_2_1


title: Colon DSS+2DG-7

city: Tokyo

first: Ikuno

last: Uehara

address: 1-1-5 Sendagi, Bunkyo

institute: Nippon medical school

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized. See hybridization protocol described in the manual of the Affymetrix GeneChip® 3'IVT Express Kit . GeneChips were washed and stained in GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: Affymetrix

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software (AGCC) and Affymetrix Expression Console Software(Expression Console)

source_name: colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA as described in GeneChip® WT Terminal Labeling Kit (Affymetorix).

growth_protocol: 8-week-old C57BL/6 female mouse

extract_protocol: RNeasy Mini Kit of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: DSS of an average molecular weight of 36,000–50,000 (MP Biomedicals) was administered to 8-week-old female C57BL/6 mice at a concentration of 2% (w/v) in drinking water. 2-DG (10 mg/mouse; Sigma-Aldrich) was injected intraperitoneally once a day.  Control mice were treated similarly, with drinking water without DSS, and intraperitoneal injection of PBS without 2-DG

tag: gender

tag: tissue

value: colon

value: DSS drinking and 2DG injection 7days


title: Colon 2-DG-7

value: 2DG injection 7days


title: Th0_WT_2_1


title: Colon Control-7

value: Mock


title: A151 ODN-treated replicate array 12

description: Biological replicate 12 of 16 for A151 ODN-treated BALB/c splenocytes


title: A151 ODN-treated replicate array 14

description: Biological replicate 14 of 16 for A151 ODN-treated BALB/c splenocytes


title: A151 ODN-treated replicate array 10

description: Biological replicate 10 of 16 for A151 ODN-treated BALB/c splenocytes


title: Dual-growing C45-4D, biological rep3

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

department: Clinical Bio-resource Research and Development

institute: Kyoto Univ Graduate School of Medicine

description: Gene expression data from from tumor spheroids cultured for 7 days from single cells

hyb_protocol: Hybridization to the GeneChip Human Gene 2.0 ST Array was performed using the GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific) (according to the protocol recommended by Thermo Fisher Scientific). Fragmented and labeled ssDNA is added to the hybridization buffer, hybridized on the GeneChip Human Gene 2.0 ST Array for 17 hours, washed and stained, fluorescently read with a scanner, and CEL with AGCC (Affymetrix GeneChip Command Console Software).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA

source_name: Single-cell orginated spheroids derived from human colerectal cancer organoids

label_protocol: Fragmentation and Labeling of Single Stranded DNA was performed using the GeneChip WT Terminal Labeling Kit (Thermo Fisher Scientific) (according to the protocol recommended by Thermo Fisher Scientific). 5.5 µg of ssDNA was fragmented using uracil DNA glycosylase (UDG) and apurinic / apyrimidinic endonuclease 1 (APE 1). The fragmented ssDNA was then biotin-labeled using terminal deoxynucleotidyl transferase (TdT) and GeneChip DNA Labeling Reagent.

growth_protocol: Spheroids were cultured for 7 days from single cells embedded in Matrigel GFR (500 cells / 7 µL of Matrigel GFR) in CTOS medium containing 10 μM Y-27632.

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen, 74106) plus on-column DNAse I digestion (Qiagen, 79254) according to the manufacturer's instructions.

treatment_protocol: A hundred to a thousand CTOSs were collected and dissociated into single cells by treating with 0.25% Trypsin-EDTA and DNase I (10 μg/mL) for 10 minutes at 37°C and 1 minute at room temperature, respectively. Then, the cell suspension was gently pipetted a hundred times to promote cell dissociation and filtered through a 35 μm-cell strainer to remove cell clusters. The dissociated single cells were seeded in Matrigel GFR (500 cells / 7 µL of Matrigel GFR) and grown in CTOS medium containing 10 μM Y-27632.

value: Colorectal organoids (CTOSs)


title: Th0_WT_1_2

value: Naive CD4+ T cells


title: Th0_WT_1_1


title: A151 ODN-treated replicate array 9

description: Biological replicate 9 of 16 for A151 ODN-treated BALB/c splenocytes


title: A151 ODN-treated replicate array 8

description: Biological replicate 8 of 16 for A151 ODN-treated BALB/c splenocytes


title: Slow-growing C45-4SR, biological rep3


title: A151 ODN-treated replicate array 11

description: Biological replicate 11 of 16 for A151 ODN-treated BALB/c splenocytes


title: A151 ODN-treated replicate array 15

description: Biological replicate 15 of 16 for A151 ODN-treated BALB/c splenocytes


title: Dual-growing C45-4D, biological rep2


title: Colon DSS-7

value: DSS drinking 7days


title: A151 ODN-treated replicate array 7

description: Biological replicate 7 of 16 for A151 ODN-treated BALB/c splenocytes


title: Slow-growing C45-4SR, biological rep2


title: Slow-growing C45-4SR, biological rep1


title: A151 ODN-treated replicate array 6

description: Biological replicate 6 of 16 for A151 ODN-treated BALB/c splenocytes


title: Dual-growing C45-4D, biological rep1


title: brain_RP-9_day3

city: Taipei

first: Jian-Jong

last: Liang

state: Taiwan

address: No.128 Academia Road, Section 2

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: JEV RP-9, C57BL/6, female, 4 weeks

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Scanned images may have differences in overall brightness due to non-biological factors such as the amount of target hybridized to the array and the amount of stain applied. To minimize such non-biological differences, the arrays are normalized to achieve comparable overall intensity between arrays. The Signal values of any hybridization are multiplied by a Scaling Factor to make their median intensity equal to 500. The Scaling Factor is unique to each hybridization.

source_name: brain

label_protocol: cDNA transcription to biotin-labeled cRNA

extract_protocol: TRIzol

value: 4 weeks


title: Slow-growing C45-1, biological rep2


title: Slow-growing C45-1, biological rep3


title: brain_PBS_day3

description: PBS (control), C57BL/6, female, 4 weeks


title: brain_RP-2ms_day3

description: JEV RP2-ms, C57BL/6, female, 4 weeks


title: Mouse 632

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads were aligned against the reference genome ‘mm10'  and counted with FeatureCounts using the mm10 Ensembl GTF
Genome_build: mm10
Supplementary_files_format_and_content: count values for each sample

growth_protocol: Animals were aclimatized from 4-8 weeks and their microbiome was standardized through the mixture of bedding

extract_protocol: Liver samples were extracted for RNA using a Qiagen Rneasy Plus Minikit and sent to Novogene for analysis

treatment_protocol: Animals were oral gavaged for 3 consecutive days and tissues were harvested 24 hours following the final exposure

tag: treatment (mg/kg)

value: liver


title: spo11 null amplicon 4

first: Agnieszka

last: Lukaszewicz

state: New York

address: 1275 York Avenue

department: Developmental Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ sequencing files were analyzed using CRISPResso2 (Clement et al., 2019 Nature Biotechnology; Pinello et al., 2016 Nature Biotechnology). Reads were aligned to the reference amplicon sequence and 2.9–5.3 million paired-end reads were mapped per amplicon.
Alignments matching the target sequence for the first 20 and last 20 bases, and with one deletion >1 bp were filtered.
Genome_build: mm10
Supplementary_files_format_and_content: One txt file for each sample, containing reads with deletions. The number of deleted base pairs (n_deleted), the number of reads for each deletion event (#Reads), read frequency (%Reads), deletion start position, and sequence alignment are included. The number of additionally modified base pairs, insertions or mutations, is indicated (n_inserted, n_mutated).

source_name: spermatocytes

extract_protocol:
Based on Cole et at al., 2014 Nature Genetics and Gaysinskaya et al., 2014 Cytometry A, with modifications. DNA was isolated from testicular single-cell suspensions. Testes were decapsulated and seminiferous tubules incubated at 33 ℃ in 10 ml Gey’s Balanced Salt Solution (GBSS) with 0.5 mg/ml collagenase and 2 µg/ml DNase I for 15–20 min, shaking at 500 rpm. The tubules were washed twice with 10 ml GBSS and digested with 0.5 mg/ml trypsin in 10 ml GBSS, supplemented with 2 µg/ml DNase I, for 25–40 min at 33 ℃, shaking at 500 rpm. Trypsin was inhibited by adding 10% fetal calf serum. Cell suspension was obtained by repeated pipetting for 2 min and filtration through a 70-µm cell strainer. All of the mutant cell suspension and one-third to one-half of the wild-type cell suspension was transferred to a 15 ml tube and centrifuged for 3 min at 1550 x g. The cell pellet was resuspended by tapping the tube, followed by the addition of 600 µl lysis buffer (200 mM NaCl, 100 mM Tris-Cl pH 7.5, 5 mM EDTA, 0.5% SDS, 0.5 mg/ml Proteinase K). The lysate was transferred to a 1.5 ml Eppendorf tube and incubated overnight at 55 ℃. Genomic DNA was isolated using phenol-chloroform extraction and alcohol precipitation. Four ~580-bp overlapping amplicons of the hotspot on Chr1 were amplified using the following primer pairs: amplicon 1, Chr1_MiSeq_FW1: 5'-TCATGTCCGGTTTGGATGCC-3' and Chr1_MiSeq_RV1: 5'-CGAATCAAAGACTCCAGAAGAGG-3'; amplicon 2, Chr1_MiSeq_FW2: 5'-AGTAGCAAGAAGGGCTGGAG-3' and Chr1_MiSeq_RV2: 5'-AGAGACAGATGTGGAGGCTAAC-3'; amplicon 3, Chr1_MiSeq_FW4: 5'-CTGAATCTCTCCTGGTGTGTC-3' and Chr1_MiSeq_RV4: 5'-AGGACATTGAATGTTTTTATGGTTC-3'; amplicon 4, Chr1_MiSeq_FW5: 5'-AAACAGAAGAAGCAGTAATGCC-3' and Chr1_MiSeq_RV5: 5'-GTGTGCAACTGGGTATATTTCAG-3'. For each amplicon, PCR conditions were: 96 ℃ for 2 min followed by 22 cycles at 96 ℃ for 20 s, 59 ℃ for 30 s and 65 ℃ for 35 s. PCR was performed in a 50 µl total containing 1.5 U Taq DNA polymerase and 0.3 U Pfu Turbo DNA polymerase in the Jeffreys buffer (Cole et al., 2010 Molecular Cell) with 50 ng of testis genomic DNA. Testis DNA was derived from 3-5 different mice for each genotype and amplified independently. PCRs were carried out in 96-well plates. For each amplicon, 576 PCRs were performed with a total of 28.8 µg genomic DNA, equivalent to 9.6 million haploid genomes. PCRs were pooled, and a 1200-µl aliquot was purified and concentrated on spin columns as follows: For each 100 µl PCR aliquot, 400 µl binding buffer from the kit was added, and then the sample was applied to the column and centrifuged. This step was repeated 6 times in each of two columns before washing and elution with 37 µl elution buffer. Eluted DNA was combined from the two columns and a 15-µl aliquot was run on a 2% agarose gel to estimate DNA concentration, which was ~2 ng/µl.
The library was prepared by ligation of indexed adapter sequences using the KAPA HyperPrep Kit (Roche). Sequencing was performed using Illumina MiSeq (2 x 300-bp paired-end reads). In a single run, libraries from amplicons 1–4 were mixed with 5% PhiX DNA control library.

tag: strain background

value: testis

value: adult (2-5 months)

value: spermatocytes


title: Mouse 631

tag: strain


title: Mouse 630


title: A151 ODN-treated replicate array 4

description: Biological replicate 4 of 16 for A151 ODN-treated BALB/c splenocytes

value: spleen cell culture

value: BALB/c

tag: treatment


title: spo11 null amplicon 3

tag: genotype


title: Mouse 628


title: atm het amplicon 1

value: Atm+/-

tag: age


title: atm het amplicon 2

tag: cell type


title: A151 ODN-treated replicate array 5

description: Biological replicate 5 of 16 for A151 ODN-treated BALB/c splenocytes

value: 2 months old

value: female

value: splenocyte cell culture


title: Mouse 627


title: Slow-growing C45-1, biological rep1


title: Mouse 626


title: atm wt amplicon 3

value: Atm+/+


title: atm wt amplicon 4


title: A151 ODN-treated replicate array 3

description: Biological replicate 3 of 16 for A151 ODN-treated BALB/c splenocytes

value: A151 ODN


title: Mouse 625


title: spo11 null amplicon 2


title: Mouse 624


title: Mouse 629


title: A151 ODN-treated replicate array 2

description: Biological replicate 2 of 16 for A151 ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 28

description: Biological replicate 28 of 29 for scrambled ODN-treated BALB/c splenocytes

source_name: splenocytes treated with scrambled ODN

value: scrambled ODN


title: scrambled ODN-treated replicate array 29

description: Biological replicate 29 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 27

description: Biological replicate 27 of 29 for scrambled ODN-treated BALB/c splenocytes


title: spo11 null amplicon 1


title: Mouse 623


title: atm het amplicon 4


title: A151 ODN-treated replicate array 1

description: Biological replicate 1 of 16 for A151 ODN-treated BALB/c splenocytes


title: atm het amplicon 3


title: Mouse 619


title: Mouse 616


title: atm wt amplicon 1


title: Mouse 615


title: Mouse 614


title: atm null amplicon 4

value: Atm-/-


title: Mouse 613


title: scrambled ODN-treated replicate array 26

description: Biological replicate 26 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 25

description: Biological replicate 25 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 24

description: Biological replicate 24 of 29 for scrambled ODN-treated BALB/c splenocytes


title: mIDH1_scRNASeq_8 (7_16_4)

city: Ann Arbor

first: Maria

last: Castro

state: MI

address: 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

data_processing:
fastq files were created using Illumina NovaSeq 6000 and Cellranger v3.1
Cellranger v3.1 was also used to create the matrices of features (UMI counts linked to a gene and barcode)
Genome_build: hg38
Supplementary_files_format_and_content: Processed data is filtered and presented as a matrix for input into data analysis programs

extract_protocol:
10X Genomics Cellranger v3.1 was used to process the raw sequencing data
First, CellRanger mkfastq demultiplexed libraries that are based on sample indices, converted the barcodes and read data to fastq files. Then, using STAR, CellRanger count aligned the reads to mm10 reference genome, filtered and counted unique molecular indentifiers (UMIs). Finally, CellRanger took multiple run outputs of CellRanger count and normalized them to same sequencing depth and recalculated the matrices and analyses of the gene-barcodes on the combined data.

value: Brain Tumor

tag: celltype

value: Tumor infiltrating immune cells, primary glioma samples


title: scrambled ODN-treated replicate array 23

description: Biological replicate 23 of 29 for scrambled ODN-treated BALB/c splenocytes


title: Mouse 612


title: atm null amplicon 2


title: Mouse 610


title: mIDH1_scRNASeq_8 (7_16_3)


title: MDAMB231_rep3

first: Mihaela

last: Skobe

address: 1425 Madison Ave, Rm 15-20F

department: Oncological Sciences

institute: The Icahn School of Medicine at Mount Sinai

data_processing:
Illumina HiSeq
Paired end sequences were mapped to human genome hg38 using RNA STAR.
The resulting reads were processed by featureCounts to produce raw counts and gene lengths.
Fragments per kilobase of transcript per million (FPKM) was calculated by normalizing gene count against gene length.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated text file includes FPKM values for each sample

source_name: breast cancer

growth_protocol:
A3250 cells were cultured in high-glucose DMEM supplemented with 4 mM L-glutamine, 10% FBS, and 1X antibiotics (100 U/ml penicillin, 100 U/ml streptomycin)
MDA-MB-231 cells were cultured in RPMI 1640 (Gibco, Cat. No. 11875119) supplemented with 2 μg/ml insulin, 4 mM L-glutamine, 10% FBS and 1X antibiotics.
SUM149 cells were cultured in Ham’s F12 supplemented with 5 μg/ml insulin, 1 μg/ml hydrocortisone, 4 mM L-glutamine, 5% FBS and 1X antibiotics.

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit, as recommended by the manufacturer.
RNA-Seq libraries were prepared for sequencing by Genewiz

treatment_protocol: Tumor cells were harvested for RNA-Seq analysis at 50% confluency under standard culture conditions, no treatment.

value: breast cancer


title: wtIDH1_scRNASeq_4 (7_12_4)


title: atm null amplicon 1


title: atm wt amplicon 2


title: Mouse 611

value: liver


title: MDAMB231_rep2


title: mIDH1_scRNASeq_7 (7_16_2)


title: scrambled ODN-treated replicate array 20

description: Biological replicate 20 of 29 for scrambled ODN-treated BALB/c splenocytes


title: Mouse 607


title: scrambled ODN-treated replicate array 21

description: Biological replicate 21 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 22

description: Biological replicate 22 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 17

description: Biological replicate 17 of 29 for scrambled ODN-treated BALB/c splenocytes


title: mIDH1_scRNASeq_7 (7_16_1)


title: scrambled ODN-treated replicate array 19

description: Biological replicate 19 of 29 for scrambled ODN-treated BALB/c splenocytes


title: Mouse 606


title: SUM149_rep3

source_name: inflammatory breast cancer

value: inflammatory breast cancer


title: wtIDH1_scRNASeq_4 (7_12_3)


title: scrambled ODN-treated replicate array 18

description: Biological replicate 18 of 29 for scrambled ODN-treated BALB/c splenocytes


title: Mouse 605


title: scrambled ODN-treated replicate array 16

description: Biological replicate 16 of 29 for scrambled ODN-treated BALB/c splenocytes


title: mIDH1_scRNASeq_6 (4_30_2)


title: SUM149_rep2


title: Mouse 604


title: Mouse 609


title: mIDH1_scRNASeq_6 (4_30_1)


title: mIDH1_scRNASeq_5 (3_20_2)


title: Mouse 603


title: MDAMB231_rep1


title: scrambled ODN-treated replicate array 15

description: Biological replicate 15 of 29 for scrambled ODN-treated BALB/c splenocytes


title: A3250_rep3


title: scrambled ODN-treated replicate array 13

description: Biological replicate 13 of 29 for scrambled ODN-treated BALB/c splenocytes


title: mIDH1_scRNASeq_5 (3_20_1)


title: A3250_rep2


title: Mouse 601


title: mIDH1_scRNASeq_4 (3_18_2)


title: HSPC_rep3 Tn5 NakedDNA

city: Tianjin

first: Kuangyu

last: Yen

address: Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
All reads were trimmed via Trimmomatic version 0.33.0 using the NexteraPE adapter sequence
Trimmed reads were aligned to the mm10 or hg38 genome assembly using Bowtie2 version 2.2.7 with default parameters
Mapped reads were de-duplicated using Picard version 2.9.0 and filtered using samtools version 1.7 with the parameter "-F 780 -q 30"
Processed reads on the forward strand were shifted by +4bp and reads on the reverse strand were shifted by -5bp to get the centers of each Tn5 insertion event (insertion sites)
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: bed files contain the single-base Tn5 insertion sites information. the 5th column indicate Tn5 insertion frequency, the 6th indicate the strand information

source_name: bone marrow

growth_protocol: E14 cells were maintained in 0.2% gelatin (Sigma)-coated plates 2i medium, which consisted of DMEM/F12 supplemented with Neurobasal medium, serum-free N2B27 medium supplemented with 10uM MEK inhibitor PD0325901 and 30uM GSK3 inhibitor CHIR99021 (both from Selleckchem), 2% KnockOutTM serum replacement (Gibco), 0.002% BSA (Gibco), 1mM MTG (Gibco), 1,000 U/ml LIF (Millipore), 0.1mM non-essential amino acid (NEAA) and 2 mM GlutaMAX Supplement (Gibco). Mouse HSPCs were cultured in IMDM (Gibco) supplemented with 15% FBS (Gibco), 10 ng/ml mIL-6, 10 ng/mL mIL-3, 50 ng/ml SCF, 20 ng/ml thrombopoietin (TPO, PeproTech) and 10 ng/ml Flt3 ligand (Flt3-L, PeproTech). The K562 cells were cultured in RPMI-1640 (Giboco) supplemented with 10% FBS.

extract_protocol:
DNA was purified with QIAamp DNA Mini Kit (QIAGEN) and 50ng DNA was used for the following procedure.
The DNA was added with a 50ul Transposition reaction mix (5 μL TTE Mix V50, 10 μL 5 X TTBL and use ddH2O from Vazyme TD501) and followed with incubation at 55C for 10 min. After tagmentation, VAHTS DNA Clean Beads were used to stop the reaction, and DNA was purified for final library construction (TruePrepTM DNA Library Prep Kit V2 for Illumina).

value: Normal HSPCs


title: SUM149_rep1


title: mIDH1_scRNASeq_4 (3_18_1)


title: wtIDH1_scRNASeq_3 (7_12_2)


title: HSPC_rep1 Tn5 NakedDNA


title: wtIDH1_scRNASeq_3 (7_12_1)


title: RNA primary BM-MSC serum type 2 diabetes rep 2

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
Sequencing reads were mapped to the human genome (GRCh38) using STAR (Dobin A, et al., Bioinformatics 29:15-21) and default settings.
Tag counts were summarized at the gene level using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Differentially expressed genes were determined by DESeq2 (Love M I,  et al. 2014. Genome Biology 15: 550).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts and DESeq2 processed rlog and normalized counts and adjusted p-values and log-2-fold changes comparing all three conditions against each other.

source_name: BM-MSC

growth_protocol: Cells were cultured in standard culture conditions in alpha-MEM containing 10% FBS and 100 U/ml penicillin P/S.

extract_protocol:
RNA was extracted in TRIzol.
cDNA libraries were constructed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA

treatment_protocol: Cells were plated at a density of 20000 cells/cm2. Osteogenic induction media alpha-MEM medium containing 100 U/ml penicillin, 5% FBS plus 5% serum pooled from two lean, obese or type 2 diabetes subjects,  10 mM beta-glycerophosphate, 10 nM dexamethasone, 50 microg/ml vitamin C  and 10mM vitamin D3. Media was changed every other day and RNA was harvested on day 10.

value: plastic adherent bone marrow stromal progenitor

value: 10 days osteogenic differentiation + serum from type 2 diabetes subject


title: RNA primary BM-MSC serum type 2 diabetes rep 1


title: HSPC_rep2 Tn5 NakedDNA


title: RNA primary BM-MSC serum obese rep 2

value: 10 days osteogenic differentiation + serum from obese subjects


title: scrambled ODN-treated replicate array 10

description: Biological replicate 10 of 29 for scrambled ODN-treated BALB/c splenocytes

value: spleen cell culture

value: BALB/c


title: wtIDH1_scRNASeq_2 (6_27_2)


title: scrambled ODN-treated replicate array 14

description: Biological replicate 14 of 29 for scrambled ODN-treated BALB/c splenocytes

value: 2 months old

value: female


title: scrambled ODN-treated replicate array 11

description: Biological replicate 11 of 29 for scrambled ODN-treated BALB/c splenocytes

value: splenocyte cell culture


title: scrambled ODN-treated replicate array 7

description: Biological replicate 7 of 29 for scrambled ODN-treated BALB/c splenocytes


title: A3250_rep1


title: wtIDH1_scRNASeq_2 (6_27_1)


title: Mouse 602


title: scrambled ODN-treated replicate array 12

description: Biological replicate 12 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 8

description: Biological replicate 8 of 29 for scrambled ODN-treated BALB/c splenocytes


title: wtIDH1_scRNASeq_1 (3_07_2)


title: RNA primary BM-MSC serum lean rep 2

value: 10 days osteogenic differentiation + serum from lean subjects


title: RNA primary BM-MSC serum lean rep 1


title: wtIDH1_scRNASeq_1 (3_07_1)


title: SP1-ERT2-3HA ChIP-seq 4OHT 60min

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to the custom genome containing hg38 and sacCer3 assembly using bowtie2 using parameter --sensitive.
PCR duplicates were removed using picard MarkDuplicates and mapped reads with low quality score (less than 30) were excluded using samtools.
Peaks calling was performed with MACS2 using input from each expetiment as a reference with the following setting: -q 0.01.
bedGraph files were created by MACS2 pileup.
Values in bedGraph were normalized to reference-adjusted reads per million (RRPM) calculated as deviding human ChIP-seq score by total yeast mapped read number.
bedGraph files were converted to bigWig by UCSC bedGraphToBigWig program.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig, Scores represent Reference-adjusted RPM

growth_protocol: K562 cells expressing SP1-ERT2-3HA were routinely cultured in phenol-red free IMDM containing 10% FBS.

extract_protocol:
Protein-DNA complexes were isolated with HA antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645).

treatment_protocol: Cells were treated with EtOH or 100nM 4OHT.

tag: chip antibody

value: HA (F-7) (sc-7392, Santa Cruz)


title: SP1-ERT2-3HA ChIP-seq 4OHT 30min


title: RNA primary BM-MSC serum obese rep 1


title: scrambled ODN-treated replicate array 5

description: Biological replicate 5 of 29 for scrambled ODN-treated BALB/c splenocytes

value: scrambled ODN


title: PB_Prdm14

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer 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 bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Mean of Transcripts Per Million(meanTPM) were calculated using a standard protocol from GENERGY BIO company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of GENERGY BIO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: 46c mouse  embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. MGI2000 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

value: embryo

tag: expression


title: SP1-ERT2-3HA ChIP-seq 4OHT 20min


title: WT + AOM + Spd T (4910-AG-26)

first: Alain

middle: P

last: Gobert

address: 2215B Garland Ave

institute: VUMC

data_processing:
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts of each gene for each sample

growth_protocol: Age-matched (8-12 weeks) male C57BL/6 and C57BL/6 Smox–/– mice were house-bred in our animal facility.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (BioLabs, Inc.)

treatment_protocol: Intraperitoneal injection of 12.5 mg/kg AOM followed by 3 cycles of 4% DSS for 5 days beginning at day 5, 26, and 47. Spermidine (14 mM) was given in drinking water for 56 days

tag: colitis status

value: Colitis

tag: tumor status

value: tumor

value: WT

value: AOM + Spd

value: colon


title: Smox + AOM + T (4910-AG-30)

value: Smox

value: AOM


title: WT + AOM + Spd T (4910-AG-27)


title: PB_Flag

description: flag.txt

source_name: 46c mouse embryonic stem cells

value: Flag


title: Smox + AOM + Spd NT (4910-AG-24)

value: no tumor


title: Smox + AOM + T (4910-AG-28)


title: WT + AOM + Spd T (4910-AG-25)


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons (RNA-Seq) Replicate 2

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
total RNA - rRNA depleted
HypothalamusESC_rnaseq_tpm_perReplicate.csv
HPvsHN.DE_rnaseq_edgeR.txt
ESCvsHN.DE_rnaseq_edgeR.txt

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end sequences were aligned to reference genome using STAR (v2.6.0c)
Read counts were calculated using HTSeq-count (v0.6.1). with parameter settings -f bam -r pos -s reverse -t exon -m intersect. Reads were mapped to a curated annotation consisting of GencodeV19 with lincRNA and sno/miRNA annotation from the UCSC Tabler Browser.
Genes located on mitochondiral genomes or annotated as rRNA were excluded from analysis
Differential analysis was performed using edgeR (v3.16.5). Raw reads per genes features were converted to CPM (read Counts Per Million mapped reads). The gene features with median value of less than 0.7 CPM (10 ~ 18 reads per gene feature) across all samples were filtered from differential analysis. The trimmed mean of M-values (TMM) method were used to calculate normalization scaling factors. The differentially expressed genes between ESCs, HPs, and HNs were identified with thresholds of FDR < 0.05 and absolute log2FC > 1.
TPM values were calculated for all genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: WiCell

growth_protocol: Human ESC H9 (W09; WiCell) were seeded on Matrigel plates (16 million cells/148 cm2) in DMEM KO medium supplemented with 15% KnockOut Serum Replacement, 0.1mM MEM Non-Essential Amino Acids, 2mM GlutaMAX, 0.06 mM 2-Mercaptoethanol) with FGF-Basic (20 ng/ml media), and 10 mM Rock inhibitor.

extract_protocol:
RNA was isolated from each sample using TRIzol Reagent. RNA was then purified using the Direct-zol RNA Miniprep Kit and depleted of contaminating genomic DNA using DNAse I. Purified RNA was then checked for quality on the Bioanalyzer 2100 using the Nano RNA Chip and samples with a RIN number above 7 were used for RNA-seq library synthesis.
RNA samples were depleted of rRNA using the QIAseq FastSelect RNA Removal Kit then processed into libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Quality and quantity of the libraries was measured using the Bioanalyzer 2100 DNA chip and Qubit Fluorometer. Libraries were pooled and sequenced on the NovaSeq 6000 platform using paired-end 51bp reads at the Center for Spatial and Functional Genomics at CHOP.

treatment_protocol: ESC were untreated. Upon confluency, cells were cultured in ESC medium without FGF-Basic and Y-27632, but supplemented with Shh (100 ng/ml), Purmorphamine (2 μM), 10 μM SB431542, and 2.5 μM LDN193289. From days 5 to 8, ESC medium was gradually replaced with neuroprogenitor medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, 0.2 μM ascorbic acid, 0.16% glucose). At day 9, cells were switched into neuronal differentiation medium (DMEM/F-12 supplemented with 0.1 mM MEM Non-Essential Amino Acids, N-2 Supplement, B-27 Supplement minus Vitamin A, 0.2 μM ascorbic acid, 0.16% glucose containing 10 μM DAPT). On day 12, cells were collected with TrypLE Express Enzyme at 37°C for 7 min and washed twice including filtration through pre-wetted 40 μm Corning Sterile Cell Strainer. The hypothalamic progenitor cell pellet was then resuspended with neuronal differentiation medium containing 10 μM Y-27632 for plating on 148 cm2 dishes coated with Poly-L-Ornithine solution (0.01%) and laminin (4 μg/ml) at a seeding density of 16 million cells/148 cm2. After 4 hours (once the cells had completely attached to the plate), the medium was changed to neuronal differentiation medium supplemented with 10 μM DAPT. On day 15, the neuronal differentiation medium was supplemented with 20 ng/ml BDNF (Peprotech Cat # 450-02) until collection on day 27.

tag: esc line

value: Hypothalamic Neuron

tag: age (differentiation protocol)

tag: sample origin

value: human ESC H9


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons  (RNA-Seq) Replicate 3

department: Center for Spatial and Functional Genomics


title: SP1-ERT2-3HA ChIP-seq 4OHT 15min

tag: cell line


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (RNA-Seq) Replicate 3

description:
total RNA - rRNA depleted
HypothalamusESC_rnaseq_tpm_perReplicate.csv
ESCvsHP.DE_rnaseq_edgeR.txt
HPvsHN.DE_rnaseq_edgeR.txt

value: Hypothalamic Progenitor


title: Smox + AOM + Spd NT (4910-AG-23)

tag: tissue


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (RNA-Seq) Replicate 2


title: atm null amplicon 3

city: New York

value: Atm-/-

value: testis

value: adult (2-5 months)

value: spermatocytes


title: scrambled ODN-treated replicate array 6

description: Biological replicate 6 of 29 for scrambled ODN-treated BALB/c splenocytes

value: spleen cell culture

value: BALB/c

value: 2 months old

tag: Sex

value: female

value: splenocyte cell culture

value: scrambled ODN


title: Smox + AOM + Spd NT (4910-AG-22)

value: Colitis

value: Smox

value: AOM + Spd

value: colon


title: scrambled ODN-treated replicate array 3

description: Biological replicate 3 of 29 for scrambled ODN-treated BALB/c splenocytes


title: scrambled ODN-treated replicate array 4

description: Biological replicate 4 of 29 for scrambled ODN-treated BALB/c splenocytes


title: SP1-ERT2-3HA ChIP-seq 4OHT 5min

value: HA (F-7) (sc-7392, Santa Cruz)


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (RNA-Seq) Replicate 1

value: human ESC H9


title: scrambled ODN-treated replicate array 2

description: Biological replicate 2 of 29 for scrambled ODN-treated BALB/c splenocytes


title: SP1-ERT2-3HA ChIP-seq 4OHT 2.5min


title: WT + AOM + Spd NT (4910-AG-20)

value: no tumor

value: WT


title: WT + AOM + Spd NT (4910-AG-21)


title: SP1-ERT2-3HA ChIP-seq EtOH


title: Embryonic Stem Cells (RNA-Seq) Replicate 2

description:
total RNA - rRNA depleted
HypothalamusESC_rnaseq_tpm_perReplicate.csv
ESCvsHP.DE_rnaseq_edgeR.txt
ESCvsHN.DE_rnaseq_edgeR.txt

value: Embryonic Stem Cell


title: input DNA 60 min


title: Embryonic Stem Cells (RNA-Seq) Replicate 3


title: SP1-ERT2-3HA ChIP-seq 4OHT 10min


title: WT + AOM + Spd NT (4910-AG-19)


title: Smox + AOM NT (4910-AG-18)

value: AOM


title: scrambled ODN-treated replicate array 1

description: Biological replicate 1 of 29 for scrambled ODN-treated BALB/c splenocytes


title: Embryonic Stem Cells (RNA-Seq) Replicate 1


title: input DNA 30 min


title: Smox + AOM NT (4910-AG-17)


title: input DNA 20 min


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons(Capture C) Replicate 2

description:
HypothalamicNeurons_1frag_chicagoRes.ibed
HypothalamicNeurons_4frag_chicagoRes.ibed

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from three replicates from ESCs, HPs, and HNs were pre-processed using the HICUP pipeline (v0.5.9) with the default parameters. Reads were aligned to hg19 using bowtie2. We called call significant promoter interactions using the read count from promoters included in our reference bait.
Significant interactions were called CHiCAGO (v1.1.8) with default parameters except for bin-size set to 2,500. In addition to our analysis per individual DpnII fragment (1frag), we also called interactions by binning four fragments, which improves detection of long-distance interactions. Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial baitmap and .rmap files where four DpnII fragments were concatenated. Interactions with a CHiCAGO score > 5 in at least one cell type in either 1-fragment or 4-fragment resolution were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: ibed

growth_protocol: Human ESC H9 were seeded on Matrigel plates (16 million cells/148 cm2) in DMEM KO medium supplemented with 15% KnockOut Serum Replacement, 0.1mM MEM Non-Essential Amino Acids, 2mM GlutaMAX, 0.06 mM 2-Mercaptoethanol) with FGF-Basic (20 ng/ml media), and 10 mM Rock inhibitor.

extract_protocol:
For each library, 107 fixed cells were thawed at 37ºC, followed by centrifugation at RT for 5 mins at 14,000 rpm. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 μL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 μL in dH2O.
Both samples underwent a pre-digestion incubation with the addition of 0.3% SDS, 1x NEBuffer DpnII, and dH2O for 1hr at 37ºC in a Thermomixer shaking at 1,000rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After the pre-digestion incubation, 10 μL of DpnII (was added only to each sample tube, and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digestion continued overnight. The next day, another additional 10 µL of DpnII was added and the incubation continued for another 2-3 hours. 100 μL of each digestion reaction was then removed, pooled into one 1.5 mL tube. The remaining samples were heat inactivated at 65°C for 20 min at 1000 rpm in a Thermomixer, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 μL of T4 DNA ligase (HC 30U/uL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a Thermomixer. The next day, an additional 2 µL of T4 DNA ligase was spiked into each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K along with the pre-digestion and digestion controls. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation at -20°C. The 3C libraries were centrifuged at 3000 rpm for 45 min at 4°C 14,000 rpm, to pellet the samples. DNA pellets were resuspended in 70% ethanol and again centrifuged as described above. The 3C library pellets were resuspended in 300 μL dH2O and stored at −20°C. 10 μg of isolated DNA from 3C libraries of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp.  After shearing, DNA was purified using AMPure XP beads. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C probe set.
Promoter Focused Capture C

value: Hypothalamic Neuron

tag: restriction enzyme

value: DpnII


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons (Capture C) Replicate 3


title: input DNA 15 min


title: Low-quality Egg, sample 8

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

description:
16-LQ8
cRNA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits).

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Sander lucioperca

source_name: Low-quality egg

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)” Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: For the study cultured, grown in recirculating aquaculture system (RAS) with fully controlled environmental conditions pikeperch broodstock (at Asialor fish farm, Pierrevillers, France) was used. The RAS was equipped with UV sterilizers, biological filtration and drum filter ensuring appropriate solids removal. The oxygen levels was always >80% of the saturation, ammonia in the range between 0.2–1.1 mg L−1 and nitrite between 0.05–0.70 mg L-1. The temperature (within a range of 8–23°C, ±0.5°C) and photoperiod (±1 min) was controlled automatically. The fish were already spawned 3 times before the study was conducted, meaning they were fully “functional” spawners. In order to promote annual gonadal cycle the fish were exposed to annual fluctuation in photo-thermal program described in earlier studies so that the fish were exposed to wintering period (period with temperature below 10°C) for 4 months. Fish were fed throughout the year at a rate between 0.2-1% of biomass, depending on the temperature and apparency in satiation with compound feed (50% protein, 11% fat, 10% moisture, 1.55% crude fiber, 1.35% phosphorus, 9.5% ash, and 17.9% nitrogen‐free extract; Le Gouessant, France).

extract_protocol: Total RNA from the 50 mg of eggs (approx. 50 eggs) was extracted using Total RNA Mini kit (Cat. No. 031‐25; A&A Biotechnology, Gdynia, Poland) following manufacturer’s protocol. Next, the genomic DNA from the samples was removed using Clean-Up RNA Concentrator (Cat. No. 039-100C; A&A Biotechnology, Gdynia, Poland) according to manufacturer’s protocol. The concentration of RNA obtained was measured with NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). Quality of the RNA was verified with 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA). All the samples had RIN (RNA integrity number) values higher than 9.5.

treatment_protocol: In total, 60 males and 60 females were reproduced following the standardized methods. For induction of ovulation and spermiation human chorionic gonadotropin (hCG; Chorulon, Intervet, France) was injected to each fish intraperitoneally at a dose of 250 and 500 IU kg-1 for males and females, respectively. Next, the fish were periodically monitored for ovulation by checking the ripeness of the fish by gentle pressure of the abdomens. When particular female was found to ovulate the eggs were collected into individual sealable, dry, plastic container and kept at temperature between 8-10°C for less than 30 min prior to further procedures. Sperm was collected into dry disposable syringes between 5 and 7 days following hormonal stimulation and was stored at 4°C prior to use (not longer than 15 min), as it is practiced in commercial production. Each egg batch collected was aliquoted into 3 portions. Portion 1 was sub-portioned into individually labelled cryotubes and immediately after snap frozen in liquid nitrogen (later stored at -80°C prior to proteomic and transcriptomic analysis). Second portion was subjected to pre-selection procedure (as described further). Portion 3 was subjected to fertilization in order to asses the egg quality indices. During the controlled reproduction photoperiod was set to 14 h of light per day (provided with neon tubes) and the temperature was halted at 12°C from the day of injection until the end of the experiment. Before each manipulation (catheterization, ovulation control, gametes collection, etc.) fish were anesthetized with MS-222 (150 mg L-1; Sigma-Aldrich).

value: Egg

tag: egg quality

value: Low


title: Smox + AOM NT (4910-AG-16)

tag: treatment


title: Low-quality Egg, sample 6

description:
14-LQ6
cRNA


title: input DNA 10min


title: WT + AOM NT (4910-AG-15)

tag: genotype


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons(Capture C) Replicate 1


title: Low-quality Egg, sample 7

description:
15-LQ7
cRNA


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells(Capture C) Replicate 3

description:
HypothalamicProg_1frag_chicagoRes.ibed
HypothalamicProg_4frag_chicagoRes.ibed

value: Hypothalamic Progenitor


title: Low-quality Egg, sample 1

description:
10-LQ2
cRNA


title: WT + AOM NT (4910-AG-14)


title: Low-quality Egg, sample 2

description:
13-LQ5
cRNA


title: input DNA 2.5min


title: High-quality Egg, sample 7

description:
7-HQ7
cRNA

source_name: High-quality egg

value: High


title: High-quality Egg, sample 5

description:
5-HQ5
cRNA


title: input DNA 5min


title: scrambled ODN-treated replicate array 9

description: Biological replicate 9 of 29 for scrambled ODN-treated BALB/c splenocytes

value: spleen cell culture

tag: strain

value: BALB/c

tag: age

value: 2 months old

value: female

value: splenocyte cell culture

value: scrambled ODN


title: WT + AOM NT (4910-AG-13)

value: Colitis

value: colon


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells(Capture C) Replicate 2

tag: cell type

value: human ESC H9


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells(Capture C) Replicate 1


title: Smox + Spd (4910-AG-12)

value: no colitis

value: no tumor

value: Smox

value: Spd


title: input DNA 0min

tag: chip antibody

value: HA (F-7) (sc-7392, Santa Cruz)


title: High-quality Egg, sample 2

description:
2-HQ2
cRNA

value: Egg


title: Smox + Spd (4910-AG-11)


title: Embryonic Stem Cells(Capture C) Replicate 3

description:
HumanESCells_1frag_chicagoRes.ibed
HumanESCells_4frag_chicagoRes.ibed

value: Embryonic Stem Cell

value: DpnII


title: ATAC-seq_HCT116OxR

city: Ji'nan

first: lian

middle: qing

last: jiao

state: Shandong Province

address: 247 Beiyuan Road

institute: the Second Hospital of Shandong University

data_processing:
Raw data were stored in FASTQ format, including the base sequence and  corresponding quality information. Adaptor-polluted or low-quality reads were then  filtered out to get the clean data
Clean data were mapped to reference genome by Bowtie2, and visualized by IGV
The enrichment analysis of  GO term (http://geneontology.org/) or KEGG pathway (http://www.kegg.jp/) was  based on hypergeometric test with the threshold q value < 0.05, to find the significant  enrichment of detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks corresponding  to the open region in genome were detected by MACS2

source_name: HCT116 cells

extract_protocol:
Around 50,000 living cells were taken for each library preparation. The cells were  lysed in 1 × Lysis Buffer to get the nuclei
TruePrep DNA Library Prep Kit for Illumina was used to construct the transposase-treated libraries

value: Colorectal cancer

value: HCT116 cells

value: Oxaliplatin-resistant


title: High-quality Egg, sample 3

description:
3-HQ3
cRNA

value: High


title: Embryonic Stem Cells(Capture C) Replicate 2


title: Smox + Spd (4910-AG-10)

city: Nashville


title: WT + Spd (4910-AG-9)

value: WT


title: WT + Spd (4910-AG-8)


title: Embryonic Stem Cells(Capture C) Replicate 1


title: Input_HCT116OxR

data_processing:
Reads were aligned to the hg19 human genome with Bowtie2 2.1.0
MACS2 2.1.1 was used for peak calling (p value threshold = 10-5) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: all the locally  enriched peaks were determined by MACS2 2.1.1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols


title: Input_HCT116

value: Oxaliplatin-unresistant


title: Mouse5-O

type: genomic

city: Rochester

first: Yang

last: Zhao

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

hyb_protocol: Cy3 and Cy5 labeling, hybridization, and scanning (iScan, Illumina), were performed.

data_processing: DNAm levels (β values) were determined by calculating the ratio of intensities between methylated (signal A) and unmethylated (signal B) sites.

source_name: Fibroblasts

growth_protocol: Fibroblasts were maintained at 37 °C incubator in an atmosphere of 5% CO2 and 3% O2 on treated polystyrene culture dishes (Corning) in EMEM media (ATCC) with 15% (vol/vol) fetal bovine serum (FBS).

extract_protocol:
Genomic DNA was extracted using a Zymo Quick-DNA Miniprep Plus Kit.
Bisulfite conversion of DNA samples were performed using the Zymo EZ DNA Methylation Kit.

treatment_protocol: No treatment

value: overproliferated

value: Fibroblasts


title: WT + Spd (4910-AG-7)

value: colon


title: H3K27me3_HCT116OxR


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons  (ATAC-Seq) Replicate 6

description:
HNvsHP.DE_atacseq_edgeR.txt
HNvsESC.DE_atacseq_edgeR.txt
HypothalamusESC_atac_counts_fpkm.txt

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Prior to differential analysis peaks were filtered to remove peaks not identified in at least half of replicates using bedtools intersect (v2.25.0). A consensus set of peaks was generated by taking the union of peaks defined in the three stages of differentiation
Read counts for the consensus set of peaks were normalized using csaw v1.8.1. OCRs with maximium median value of less than 1.2 CPM (~10-50 reads per OCR) across all replicates were filtered prior to differential analysis.
Differential analysis was performed using the glmQLFit implmented in edgeR v 3.16.5 using the normalization factors calculated with csaw. Differential OCRs were identified with thresholds of FDR < 0.05 and log2 fold change > 1.
FPKM values were calculated from reads mapped to consensus OCRs and bigWig files were generated from the duplicate filtered bam files using the R packages GenomicAlignments (v1.10.1) & rtracklayer(1.34.2)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for each replicate as well as a tab-deliminated file containing OCR locations, raw counts and fpkm, as well as results from each differential comparison

extract_protocol:
A total of 50,000 cells were centrifuged at 550g for 5 min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 g for 10 min at 4°C. The tagmented DNA was then purified using the Qiagen MinElute kit and eluted in 10.5 μL Elution Buffer.
Ten microliters of purified tagmented DNA was PCR amplified using the Nextera Indexing Kit for 12 cycles to generate each library. The PCR reaction was subsequently purified using 1.8x AMPure XP beads, and concentrations were measured by Qubit Fluorometer.  Quality of completed libraries was assessed on a Bioanalyzer 2100 high sensitivity DNA Chip.  Libraries were paired-end sequenced at the Center for Spatial and Functional Genomics on the Novaseq 6000 platform (50 bp read length).

tag: cell stage

value: Hypothalamic Neuron

value: human ESC H9


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons  (ATAC-Seq) Replicate 4


title: Smox (4910-AG-6)

tag: colitis status

value: no colitis

value: no tumor

value: Smox

value: control


title: H3K27me3_HCT116


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons  (ATAC-Seq) Replicate 3


title: Smox + AOM + T (4910-AG-29)

value: Colitis

tag: tumor status

value: tumor

value: AOM


title: High-quality Egg, sample 1

description:
1-HQ1
cRNA

value: Egg


title: Smox (4910-AG-5)


title: Mouse5-Y

scan_protocol: Cy3 and Cy5 labeling, hybridization, and scanning (iScan, Illumina), were performed.

value: young


title: Mouse4-Y

label_protocol: Cy3 and Cy5 labeling, hybridization, and scanning (iScan, Illumina), were performed.


title: Mouse4-O


title: Mouse3-O


title: ATAC-seq_HCT116

value: Colorectal cancer

value: HCT116 cells


title: H3K27ac_HCT116OxR

value: Oxaliplatin-resistant


title: Mouse3-Y


title: Mouse1-O

value: overproliferated


title: Mouse2-O

value: Fibroblasts


title: Smox (4910-AG-4)

value: colon


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons (ATAC-Seq) Replicate 1

value: Hypothalamic Neuron

tag: esc line


title: H3K27ac_HCT116

value: Oxaliplatin-unresistant


title: Mouse2-Y


title: Embryonic Stem Cell dervived Hypothalamus-like Neurons (ATAC-Seq) Replicate 2

tag: age (differentiation protocol)

value: human ESC H9


title: Mouse1-Y


title: H3K4me3_HCT116OxR


title: WT (4910-AG-3)

value: no colitis

value: no tumor

value: WT


title: WT (4910-AG-2)

value: control


title: WT (4910-AG-1)


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells  (ATAC-Seq) Replicate 4

description:
HNvsHP.DE_atacseq_edgeR.txt
HPvsESC.DE_atacseq_edgeR.txt
HypothalamusESC_atac_counts_fpkm.txt

value: Hypothalamic Progenitor


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (ATAC-Seq) Replicate 3


title: H3K4me3_HCT116


title: H3K4me1_HCT116OxR


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (ATAC-Seq) Replicate 2


title: mIDH1_scRNASeq_2 [Run_2961 B2]

data_processing:
fastq files were created using Illumina NovaSeq 6000 and Cellranger v3.1
Cellranger v3.1 was also used to create the matrices of features (UMI counts linked to a gene and barcode)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is filtered and presented as a matrix for input into data analysis programs

source_name: Brain Tumor

tag: celltype

value: mIDH1 Tumor cells symptomatic stage


title: mIDH1_scRNASeq_1 [Run_2961 B1]


title: Hi-C_HCT116OxR

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
The BWA package was used to map the  sequences against the human reference genome with the parameter -n 0. Mapped  reads with MAPQ quality scores ≥20 were chosen for further analysis.
We applied the ICE  method to normalize the interaction matrix for different resolutions
If a region between two adjacent boundaries was less than 400 kb, the region was  marked as a TAD boundary
The Juicer pipeline’s HiCCUPS was applied for discovery of locally enriched  peaks
Genome_build: hg19
Supplementary_files_format_and_content: all the locally  enriched peaks were determined by HiCCUPS

extract_protocol:
The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols


title: H3K4me1_HCT116


title: Embryonic Stem Cells (ATAC-Seq) Replicate 4

description:
HPvsESC.DE_atacseq_edgeR.txt
HNvsESC.DE_atacseq_edgeR.txt
HypothalamusESC_atac_counts_fpkm.txt

value: Embryonic Stem Cell


title: Embryonic Stem Cells (ATAC-Seq) Replicate 3


title: Hi-C_HCT116


title: mIDH1_scRNASeq_2 [Run_2943 B3]

tag: genotype/variation

value: Brain tumor

value: Tumor infiltrating immune cells, symptomatic stage


title: Embryonic Stem Cell dervived Hypothalamic Progenitor-like Cells (ATAC-Seq) Replicate 1


title: mIDH1_scRNASeq_1 [Run_2943 B1]

tag: tissue


title: Embryonic Stem Cells (ATAC-Seq) Replicate 2


title: wtIDH1_scRNASeq_1 [Run_2943 A1]


title: Embryonic Stem Cells (ATAC-Seq) Replicate 1


title: RNA-seq_HCT116

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
Reads mapped to the exon regions of each gene were counted by featurecouts (Subread-1.5.1; Bioconductor) and FPKMs were calculated. Genes differential expressed between groups were identified using the edgeR package
A corrected P-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
HCT116 cells were further purified from Pancreatic cancer tissue  .mRNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer

value: HCT116 cells


title: BMR5-Y

organism: Nannospalax ehrenbergi

value: Wild-caught

value: young


title: BMR5-O

value: overproliferated

value: Fibroblasts


title: BMR4-Y


title: RNA-seq_HCT116OxR

value: Oxaliplatin-resistant


title: BMR4-O


title: wtIDH1_scRNASeq_2 [Run_2943 A2]


title: BMR3-Y


title: BMR2-Y


title: Gudjonsson_018_018_029036

status: Public on Sep 30 2021

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

value: Skin

tag: disease state

value: Psoriasis


title: Gudjonsson_019_019_029037

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: BMR3-O


title: BMR1-Y


title: BMR1-O


title: BMR2-O


title: Gudjonsson_017_017_029035


title: Gudjonsson_020_020_029038


title: Gudjonsson_022_022_029040


title: Gudjonsson_015_015_029033


title: Gudjonsson_021_021_029039


title: Gudjonsson_016_016_029034


title: Gudjonsson_010_010_029028


title: Gudjonsson_012_012_029030


title: Gudjonsson_014_014_029032


title: Gudjonsson_007_007_029025


title: Gudjonsson_008_008_029026


title: Gudjonsson_011_011_029029


title: Gudjonsson_013_013_029031


title: Gudjonsson_003_003_029021


title: Gudjonsson_002_002_029020


title: Gudjonsson_009_009_029027


title: Gudjonsson_006_006_029024


title: Gudjonsson_005_005_029023


title: Gudjonsson_001_001_029019


title: Gudjonsson_024_176


title: Gudjonsson_022_174


title: P30

city: San Francisco

first: Corey

last: Harwell

state: CA

address: 35 Medical Center way

department: Neurology

institute: University of California, San Francisco

description: P30 (i.e., F30 and M30)

data_processing:
The raw fastq files uploaded here were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. In brief, each NextSeq run results in 16 fastq files (4 lanes x 4 reads per lane). The read files have the following content, also as described in the documentation for inDrops.py (github/indrops):   *_R1_001.fastq.gz   : contains the 3' UTR cDNA read  *_R2_001.fastq.gz   : contains the first half of the cell barcode  *_R3_001.fastq.gz   : contains the library index for demultiplexing libraries  *_R4_001.fastq.gz   : contains the second half of the barcode and the UMI.
All  subsequent processing steps from fastq files to count matrices were performed using a custom pipeline for inDrops data analysis (github.com/indrops).  The following steps are provided as an overview on the internal workings of inDrops.py.
inDrops.py first filters reads based on information present in read files 2, 3 and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the inDrops.py custom pipeline are given in the yaml files.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.88) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene.
Genome_build: GRCm38.88
Supplementary_files_format_and_content: cd_norm: Gene Expression Matrix of count data normalized by total counts in each cell; matrix.tsv:  Raw cell/counts tables each sample;  seurat_metadata.csv: Metadata for individual cells: cell barcode, assigned cell type and other metadata for establishing clusters.

source_name: septum from postnatal brains, from both male (M30) and female (F30) animals

extract_protocol:
RNA was isolated within the droplets according to the inDrops protocol (Klein et al. Cell 2015, Zilionis et al. Nature Protocols 2017).
polyA RNA captured via inDrops platform
2 libraries of approximately 3000 cells were collected from each biological replicate: pools from animals from the same litter for embryonic and early postnatal stages (E11 - 3 litters, 35 embryos total; E14 - 3 litters, 33 embryos total; E17 - 2 litters, 8 embryos total; P3 - 2 litters, 4 pups total), or individual animals for later postnatal stages (P10 - one male and one female pup from the same litter; P30 - two male and two female animals from the same litter). inDrops library preparation was performed as previously described (Klein et al. Cell 2015, Zilionis et al. Nature Protocols 2017) Libraries were sequenced on the Illumina NextSeq system.
custom inDrops single-cell RNA-Seq

value: CD-1 (strain code 022, Charles River)

tag: gender

value: pooled male and female

value: septum


title: Wild-type rep2 IP

city: Chicago

first: Bryan

middle: T

last: Harada

state: IL

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

data_processing:
Library strategy: m6A-seq
HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome and transcriptome (mm10).
The m6A peaks identification and differential methylation analysis were performed using MeRIPtools.
Differential gene expression was calculated using DESeq2 (version 1.18.1) using the sequencing reads from input samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing the DESeq2 output for the differential expression analysis
Supplementary_files_format_and_content: tab-delimited text files listing significant m6A peaks identified in each condition

source_name: Liver

extract_protocol:
Total hepatic RNA was isolated with TRIzol reagent.  Polyadenylated RNA was enriched using a Dynabeads mRNA purification kit (Sigma, # MRN10).  The mRNA was fragmented using a Bioruptor ultrasonicator (Diagenode) with 30s on/off for 30 cycles.  m6A-IP was performed using the Epimark N6-methyladenosine enrichment kit (New England Biolabs).
Library preparation was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit according to previously published protocols(Dominissini et al., 2012)

treatment_protocol: WT and METTL14Alb mice were i.p injected with Tm (2mg/kg) for 24 hours.

value: Tunicamycin

value: Liver

tag: antibody

value: anti-m6A (NEB E1610S)


title: Gudjonsson_004_004_029022


title: Gudjonsson_021_173


title: Gudjonsson_019_171


title: Gudjonsson_015_167


title: Gudjonsson_023_175


title: Gudjonsson_016_168


title: Wild-type rep1 IP

tag: treatment


title: Gudjonsson_018_170


title: Gudjonsson_012_164


title: Gudjonsson_014_166


title: Gudjonsson_020_172


title: Knockout rep2 input

data_processing:
HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome and transcriptome (mm10).
The m6A peaks identification and differential methylation analysis were performed using MeRIPtools.
Differential gene expression was calculated using DESeq2 (version 1.18.1) using the sequencing reads from input samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing the DESeq2 output for the differential expression analysis
Supplementary_files_format_and_content: tab-delimited text files listing significant m6A peaks identified in each condition

tag: genotype


title: Knockout rep1 IP


title: Wild-type rep2 input


title: Knockout rep1 input


title: Wild-type rep1 input


title: Knockout rep2 IP


title: GSCLC_S4

first: Yukihiro

last: Yabuta

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: PBAT

data_processing:
The genome sequences of the pseudo-autosomal region (PAR) on the chromosome Y in GRCm38.p6, chrY:90745845-91644698 were replaced with Ns and the genes in this region were deleted from the reference to avoid a “mapped multi” call at the mapping step.
Read data processing of the methylation levels was performed as described previously (Shirane et al., 2016).  In brief, all reads were processed with Trim-Galore v0.4.1 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)/cutadapt v1.9.1 (http://cutadapt.readthedocs.io/en/stable/guide.html) with the “--clip_R1 4”, “--trim1” and “-a AGATCGGAAGAGC” options.
Output reads were mapped onto the mouse genome, GRCm38.p6, using Bismark v0.22.1/Bowtie2 v2.3.4.1 with the "--pbat" option.   All CpG sites with a read depth of between 4 and 200 were used for the bigWig files.
Genome_build: GRCm38.p6

source_name: GSC-like cells

growth_protocol: Generation and Culture of Reconstituted Testes (rTestis)  To isolate E12.5 mouse male gonads (fetal testes), pregnant ICR females were sacrificed by cervical dislocation, and the embryos were isolated in chilled Dulbecco's Modified Eagle Medium (DMEM) (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 10 mM HEPES (GIBCO, #15630-106), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Fetal testes were identified by their appearance, and the mesonephroi were dissected out with tungsten needles.  The isolated fetal testes were dissociated into single cells, and endogenous mouse germ cells were selected out by magnetic-activated cell sorting (MACS).  Compared to FACS, MACS requires much less time and less physical stress to collect the cells for the rTestis formation.  The mPGCLCs (10,000 cells/well) and the fetal testes somatic cells (when using frozen stocks, 20,000 cells/well) (total 30,000 cells/well) were mixed and plated on the wells of a Nunclon Sphera 96-well Microplate (#174925; Thermo Fisher Scientific) and cultured under a floating condition in GK10+FR10 medium (GK10, 10 μM forskolin and 10 μM rolipram).  After a period of 2 days for the floating culture, using a glass capillary, the rTestes were transferred onto ThinCert™Cell Culture Inserts for 24-Well Plates (Greiner #662610) soaked in alpha-Minimum Essential Medium (GIBCO, #32561-037) containing 10% FCS (Hyclone), 55 μM 2-mercaptoethanol (GIBCO, 21985-023), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Half the medium was changed every two days.  All rTestes were cultured for a gas-liquid interphase culture at 37℃ under an atmosphere of 5% CO2 in air.    Derivation of GSCLCs from rTestis  For the derivation of GSCLCs, VR+; CD9-APC+ cells in rTestes (m14) were sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ).  For deriving GSCLCs from all VR+; CD9-APC+ cells/rTestis, 24-well culture dishes (Falcon, #353047) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, seeded with mouse embryonic feeders (MEF) for at least 6 h prior to the plating of mPGCLC-derived cells, and then VR+; CD9-APC+ cells (derived from 1 rTestis)/well were seeded and cultured with GSCs/GSCLCs medium.  For deriving GSCLCs from single VR+; CD9-APC+ cells, 96-well culture dishes (Falcon, #353072) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, then seeded with MMC-treated MEF for at least 6 h prior to the plating of an mPGCLC-derived cell.  A single VR+; CD9-APC+ cell was then seeded using a FACS Automated Cell Deposition Unit (ACDU) system and cultured with GSCs/GSCLCs medium.The GSC/GSCLC medium was as described previously (Kanatsu-Shinohara et al., 2003), with some modifications (Ishikura et al., 2016).  StemPro-34 SFM (GIBCO, #10639011) was supplemented with StemPro supplement (GIBCO, #10639011), 0.1 mM 2-mercaptoethanol (GIBCO, 21985-023), 1% FCS (Hyclone), 1 × minimal essential medium (MEM) Vitamin Solution (GIBCO, # 11120-052), 5.0 mg/mL AlbuMAXⅠ (GIBCO, #11020-021), 0.1 mM NEAA (GIBCO, #11140-050), 1 mM sodium pyruvate (GIBCO, 11360-070), 100 U/mL penicillin, 0.1 mg/mL streptomycin (GIBCO, #15070), 2 mM GlutaMAX (GIBCO, #35050-061), 1 × Insulin-Transferrin-Selenium (ITS-G) (GIBCO, #41400045), 10 ng/mL bFGF Recombinant Human Protein (Life Technologies, #13256029), 20 ng/mL GDNF Rat Recombinant (RSD, #512GF050), 20 ng/mL EGF Mouse Recombinant Carrier-free (RSD, #2028EG200), and 1000 U/mL LIF (Merk, ESG1107).  Half the medium was changed every two or three days.  All GSCs/GSCLCs were cultured at 37℃ under an atmosphere of 5% CO2 in air."  "Isolation of Germ Cells  To isolate germ cells for the RNA-seq analysis, ICR females were crossed with C57BL/6N; mvh-RFPTg/Tg males.  The embryonic gonads/postnatal testis fragments at E12.5–P7.5 were dissociated into single cells by incubating with 0.05% Trypsin-EDTA (GIBCO, #15400-054) for 10 min at 37℃, and were quenched with an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, #15070).  Large clumps of cells were removed using a nylon cell strainer (FALCON, #352350), and cells were centrifuged at 1,200 rpm for 5 min.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, 1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037), and sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ)    Fluorescence-activated Cell Sorting (FACS)  The d4 floating aggregates of EpiLCs and d4c5 mPGCLCs were incubated in TrypLE express for 10 min at 37℃, with periodical pipetting, and the dissociates were quenched with a 5 × volume of DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037) and DNase I (Sigma, DN25), followed by pipetting to generate a single cell suspension.  After centrifugation at 1,200 rpm for 5 min, the supernatant was discarded.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, #15260037), the cell suspension was filtered through a nylon cell strainer (FALCON, #352350), and BV+ d4 mPGCLCs or BV+; SC+ d4c5 mPGCLCs were sorted by a flow cytometer (BD Biosciences, FACSAria III) and collected in the GK10+FR10 medium.  The rTestes at various culture periods were peeled off from the cell insert membrane using a P1000 pipette tip and incubated in 0.25% Trypsin-EDTA in PBS (GIBCO, #15400-054) for 5~15 min, with periodical intermittent pipetting, and the dissociates were quenched by an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, 35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  The resultant cell pellet was resuspended with PBS containing 0.1% BSA fraction V (Life Technologies, # 15260037), and large clumps of cells were removed using a nylon cell strainer (FALCON, #352350).  The BV+; SC+ and Ddx4/mvh-RFP-positive (BV+; SC+; VR+) cells (mPGCLC-derived cells in rTestes: m0, m3, m5, m7, m10), VR+ and CD9-APC-positive (VR+; CD9-APC+) cells (mPGCLC-derived cells in rTestes: m12, m14), and VR+ cells in embryonic gonads/postnatal testes were sorted by the FACSAria III (BD Biosciences) cell sorter, and were collected in CELLOTION (Nippon Zenyaku Kogyo, CB051).  For RNA/DNA extraction, the sorted cells were centrifuged at 500G for 10 min, and the cell pellets were frozen down by liquid N2, and preserved at −80℃.

extract_protocol:
The sample preparations from GSCLCs were performed essentially as described previously (Ishikura et al., 2016) (see Fluorescence-activated Cell Sorting (FACS)).  15,000 cells of GSCLCs (GSCLC_S1, GSCLC_S2, GSCLC_S3, GSCLC_S4) were sorted and the genomic DNA was extracted with NucleoSpin ® Tissue XS (MACHEREY-NAGEL, U0901).  For the bisulfite treatment, the whole elute of the genomic DNA extraction containing 0.45 ng of unmethylated λ phage DNA was treated with an EZ DNA Methylation‐Gold Kit (ZYMO RESEARCH,  D5005) according to the manufacturer's instructions.
Sequence libraries were generated with a post-bisulfite adaptor tagging method (http://www.crest-ihec.jp/english/epigenome/index.html; Miura et al., 2012; Shirane et al., 2016).  Some reagents were replaced as follows: Phusion Hot Start High‐Fidelity DNA Polymerase (Thermo Fisher Scientific, F540S) was replaced with Phusion Hot Start II DNA Polymerase (Thermo Fisher Scientific, F549S); Agencourt AMPure XP was replaced with an AxyPrep MAG PCR Clean‐Up Kit (Corning, MAG‐PCR‐CL‐250).  The sequencing was performed on an Illumina HiSeq 2500 platform with the TruSeq SR Cluster Kit ‐cBot‐HS and TruSeq SBS Kit ‐HS (Illumina).
library strategy: Post-bisulfite adaptor-tagging (PBAT)

value: Germ cells derived from ESCs

tag: strain

value: B6C3(Cg) x C57BL/6


title: Hippocampus microvessels, LDL-R -/- mice fed with control diet (CD)

city: Davis

first: Saivageethi

last: Nuthikattu

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

description:
Gene expression data of hippocampus microvessels from male LDL-R -/- mice fed with control diet (CD)
LDLR KO CD

hyb_protocol: Following fragmentation and labeling, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on the Mouse Gene 2.0 ST Array using Affymetrix WT array hybridization protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Analyses of gene expression levels were performed with Transcriptome Analysis Console software version 3.1.0.5.

source_name: Male Mice brain hippocampus microvessels

label_protocol: 125 pg of total RNA was used to prepare cRNA according to Affymetrix's GeneChip® WT Pico Kit protocol. Biotinylated sscDNA (5.5 ug) were prepared from 20 ug of cRNA.

growth_protocol: Male mice were housed in single cages in a temperature- and humidity-controlled environment with a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from the laser-captured hippocampal brain microvessels from each of the four experimental groups using an Arcturus PicoPure™ RNA Isolation Kit according to the manufacturer’s instructions.

treatment_protocol: Five-week-old LDL-R-/- and wild type (WT) male mice were fed a chow (control diet, CD) or western diet (WD) for 8 weeks.

value: male

value: B6.129S7-Ldlr tm1Her/J

value: LDL-R -/-

tag: diet

value: control

value: brain hippocampus microvessels