title: Magnet and FACS Fetal Liver cells

city: Cambridge

first: Hojun

last: Li

state: MA

address: 500 Main St building 76

institute: Koch Institute

description: CD71/CD24low mouse fetal liver cells isolated using magnet and FACS methods and submitted for scRNAseq analysis

data_processing:
cellranger count: cellranger-4.0.0
Filtering: Filtered out cells with less than 3000 genes or more than 6500 genes, filtered out cells with more then 50000 total reads, removed cells with more then 6% mitochondrial reads, remove genes detected in less than 3 cells
Dehashing: Hashsolo algorithm (ScanPy implementation)
Count normalization: Normalization to 10^4 counts per cell, along with log transformation
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Processed count matrix, CSV: Cell by gene matrix with normalized counts
Supplementary_files_format_and_content: Contains expression matrix
Supplementary_files_format_and_content: Contains group assignemnts and batch-corrected PCA

source_name: mouse fetal liver from E14.5 pregnant mice

growth_protocol: Cells were seeded at 10,000 cells per mL of erythroid expansion media media immediately after isolation (D0). Cells were counted on days 1, 2, 3, 6, 8, and 10 and re-seeded at 50,000 cells per mL of media in fresh media on days 3 and 6.

extract_protocol: 10X 3' version 3 kit

treatment_protocol: Samples 1 and 2 were either treated with 100uM Dexamethasone or with an equivalent volument of methanol in erythroid expansion media and grown for 10 days. Cells were re-seeded at 50,000 cells per mL of media and given new media on days 3 and 6 after initial seeding.

value: CD71/CD24low cells

tag: tag

value: FACS BFU-E:TotalSeq A0951, barcode AACCTTTGCCACTGC    FACS CFU-E:TotalSeq A0952, barcode GTCCGACTAATAGCT    PE-low:TotalSeq A0953, barcode CAGGTTGTTGTCATT    PE-high:TotalSeq A0954, barcode TATTTCCACCCGGTC


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p19

status: Public on Nov 12 2021

type: genomic

city: New York

first: Gabriel

last: Sturm

state: NY

address: 40 Haven Avenue

department: Psychiatry

country: USA

institute: Columbia University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC array using standard Illumina protocol (performed at UNGC)

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting (performed at UNGC)

data_processing:
RStudio (v1.3.1056) using R (v4.0.2). Preprocessing was performed using the 'minfi' (v1.36.0) library and batch corrections using the 'sva' (v3.12.0) library. Quality control excluded 22 samples for a final total of 479 samples.
processed data file contains: ormalized Beta (Functional normalization)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Human Fibroblast (breast)

label_protocol: Standard Illumina Protocol

growth_protocol: Primary human dermal fibroblasts were obtained from distributor or in local clinic from 6 healthy and 3 Methylation_SURF1-patient donors (IRB #AAAB0483). Fibroblasts were isolated from biopsy tissue using standard centrifugation procedure. After isolation, fibroblasts were stored in 10% DMSO (Sigma-Aldrich #D4540), 90% fetal bovine serum (FBS, Life Technologies #10437036) in cryogenic tube under liquid nitrogen. To avoid freeze-shock necrosis cells were frozen gradually in an isopropanol container (Thermofisher #5100-0001) at -80°C overnight before storage in liquid nitrogen. Cells were thawed by placement in 37°C (<4min) and immediately transferred to 20ml of preheated DMEM (Invitrogen #10567022). Cells were cultured in T175 flasks (Eppendorf #0030712129) at standard 5% CO2 and atmospheric O2 at 37°C in DMEM (5.5 mM glucose) supplemented 10% FBS, 50 μg/ml uridine (Sigma-Aldrich #U6381), 1% MEM non-essential amino acids (Life Technologies #11140050), 10 μM palmitate (Sigma-Aldrich #P9767) conjugated to 1.7 μM  BSA (Sigma-Aldrich #A8806), and 0.001% DMSO (treatment-matched, Sigma-Aldrich #D4540). Cells were passaged approximately every 6 days (+/- 1 day). Brightfield microscopy images (10x, 20x magnification) were taken before each passaged using inverted phase-contrast microscope (Fisher Scientific #11350119). Cell counts, volume and death were determined at each passage using the Countess II Automated Cell Counter (ThermoFisher Scientific #A27977). Growth rates were used to determine replating density, by pre-calculating number cells needed to reach ~90% confluency (~2.5 million cells) at time of next passage. Cells were never plated below 200,000 cells or above 2.5 million cells to avoid plating artifacts of isolation or contact inhibtion, respectively. Study measurements and treatment began after 15-days of culturing post-thaw to allow for adjustment to in vitro environment. Individual cell lines were terminated after exhibiting less than one population doubling over a 30-day period. Mycoplasma testing was performed on media across the full sampleset with no detectable infection.

extract_protocol: DNA was extracted using the DNeasy kit (Qiagen cat#69506) according to the manufacturer’s protocol and quantified using QUBIT broad range kit (Thermo Fisher Scientific cat#Q32852).

treatment_protocol: Treatment conditions for healthy controls include chronic addition (dosed at every passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902), mitoNUITs; a combination of a) 2μM UK5099 (Sigma-Aldrich #PZ0160) b) 4μM Etomoxir (Sigma-Aldrich #E1905) c) 3μM BPTES t (Sigma-Aldrich #SML0601), 1nM oligomycin (Oligo, Sigma-Aldrich #75351), 5.5mM galactose (Sigma-Aldrich #G5388), 1mM 2-deoxy-d-glucose (2DG, Sigma-Aldrich #D3179), 10mM beta-hydroxybutyrate (Sigma-Aldrich #54965), 10nM MitoQ (PubChem CID:11388332), 2mM N-Acetyl-L-cysteine (NAC, Sigma-Aldrich #A7250), 1mM ⍺-ketoglutarate (⍺-KG, Sigma-Aldrich #75890), contact inhibition (allowing cells to fill up the dish and enter a quiescent state), hypoxia (3% oxygen), acute treatment (10days) of 1μg/mL 5-azacytidine (Sigma-Aldrich #A2385), and pulsated treatment (30min before each passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902).

value: Primary Human Fibroblast (breast)

tag: Sex

value: female

value: Normal

tag: treatments

tag: passage

tag: slide

tag: array

tag: well


title: Methylation_HC4_sp3_Normal_Control_ox21_p9

source_name: Primary Human Fibroblast (upper arm)

value: Primary Human Fibroblast (upper arm)

value: male

value: Control

tag: notes

value: Treatment Start


title: Methylation_HC1_sp3_Normal_Control_ox21_p8


title: HC4_sp3_Normal_DEX_ox21_p10

type: SRA

library_source: transcriptomic

data_processing:
360 samples were sent for sequencing; 9 samples did not passed intial QC (low RIN score, high DNA contamination), and 6 samples did not pass post-sequencing QC, for a final of 345 samples.
kallisto alignment v0.44.0 (Bray et al., 2016) using the hg19 genome. Sequence and annotation files were downloaded from the NCBI ftp portal for genome version GRCh37.p13
txi import using lengthScaledTPM (‘tximport’, v1.18.0)
vst normalization (‘DEseq2’, v1.30.1).
log2 transformation
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with log2 transformed vst normalized expression values for every gene and every sample
processed_cell_lifespan_RNAseq_data.csv: log2 vst normalized expression values
raw_counts_cell_lifespan_RNAseq_data.csv: raw counts as outputted by kallisto alignment
txi_transcript_abundance.csv: transcript abundances (‘tximport’, v1.18.0)
txi_transcript_count_lengthScaledTPM.csv: transcript counts length-scaled TPM (‘tximport’, v1.18.0)
txi_transcript_length.csv: transcript lengths (‘tximport’, v1.18.0)
txi_gene_abundance.csv: gene abundances (‘tximport’, v1.18.0)
txi_gene_count_lengthScaledTPM.csv: gene counts length-scaled TPM (‘tximport’, v1.18.0)
txi_gene_length.csv: gene lengths (‘tximport’, v1.18.0)

molecule: total RNA

growth_protocol: Primary human dermal fibroblasts were obtained from distributor or in local clinic from 4 healthy and 3 SURF1-patient donors (IRB #AAAB0483). Fibroblasts were isolated from biopsy tissue using standard centrifugation procedure. After isolation, fibroblasts were stored in 10% DMSO (Sigma-Aldrich #D4540), 90% fetal bovine serum (FBS, Life Technologies #10437036) in cryogenic tube under liquid nitrogen. To avoid freeze-shock necrosis cells were frozen gradually in an isopropanol container (Thermofisher #5100-0001) at -80°C overnight before storage in liquid nitrogen. Cells were thawed by placement in 37°C (<4min) and immediately transferred to 20ml of preheated DMEM (Invitrogen #10567022). Cells were cultured in T175 flasks (Eppendorf #0030712129) at standard 5% CO2 and atmospheric O2 at 37°C in DMEM (5.5 mM glucose) supplemented 10% FBS, 50 μg/ml uridine (Sigma-Aldrich #U6381), 1% MEM non-essential amino acids (Life Technologies #11140050), 10 μM palmitate (Sigma-Aldrich #P9767) conjugated to 1.7 μM  BSA (Sigma-Aldrich #A8806), and 0.001% DMSO (treatment-matched, Sigma-Aldrich #D4540). Cells were passaged approximately every 5 days (+/- 1 day). Brightfield microscopy images (10x, 20x magnification) were taken before each passaged using inverted phase-contrast microscope (Fisher Scientific #11350119). Cell counts, volume and death were determined at each passage using the Countess II Automated Cell Counter (ThermoFisher Scientific #A27977). Growth rates were used to determine replating density, by pre-calculating number cells needed to reach ~90% confluency (~2.5 million cells) at time of next passage. Cells were never plated below 200,000 cells or above 2.5 million cells to avoid plating artifacts of isolation or contact inhibtion, respectively. Study measurements and treatment began after 15-days of culturing post-thaw to allow for adjustment to in vitro environment. Individual cell lines were terminated after exhibiting less than one population doubling over a 30-day period. Mycoplasma testing was performed on media across the full sampleset with no detectable infection.

extract_protocol:
Total genomic RNA was isolated every ~11days across cellular lifespan and stored in 1ml trysol (Invitrogen cat#15596026). RNA was extracted on-column using a RNeasy kit (Qiagen cat# 74104), DNase treated according to the manufacturer’s instructions, and quantified using the QUBIT high sensitivity kit (Thermo Fisher Scientific cat#Q32852). RNA samples underwent QC on bioanalyzer and Nanodrop 2000, all samples had a RIN score >8.0 and no detectable levels of DNA. For cDNA library preparation,1,500ng of RNA at 50ng/μl was processed using Ribo-Zero Gold purification (QIAseq FastSelect -rRNA HMR Kit #334387) and NEBNext® Ultra™ II RNA Library Prep Kit (Illumina #E7770L))  (1,500ng/sample, 50ng/μl). cDNA was sequenced using paired-end 150bp chemistry on a HiSeq 4000 instrument (Illumina, single index, 10 samples/lane, Genewiz Inc), yielding  ~40 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment conditions include chronic addition (dosed at every passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902), mitoNUITs; a combination of a) 2μM UK5099 (Sigma-Aldrich #PZ0160) b) 4μM Etomoxir (Sigma-Aldrich #E1905) c) 3μM BPTES t (Sigma-Aldrich #SML0601), 5.5mM galactose (Sigma-Aldrich #G5388), 1nM oligomycin (Oligo, Sigma-Aldrich #75351), 1mM 2-deoxy-d-glucose (2DG, Sigma-Aldrich #D3179), 10mM beta-hydroxybutyrate (Sigma-Aldrich #54965), contact inhibition (allowing cells to fill up the dish and enter a quiescent state), hypoxia (3% oxygen), and acute treatment (10days) of 1μg/mL 5-azacytidine (Sigma-Aldrich #A2385).

value: DEX


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p16


title: Methylation_HC1_sp3_Normal_Control_ox21_p13


title: WT Tregs Rep 1

city: Buffalo

first: Jie

last: Yu

address: 955 Main Street

department: Department of Obstetrics and Gynecology

institute: SUNY Buffalo

description: 3 mice pooled

data_processing:
Basecalling bcl2fastq v2.20.0.422 (default parameters)
Alignment hisat2 v2.1.0 (default parameters)
Quantification featureCounts v1.6.2 ("-s" "0" "-g" "gene_id" "-t" "exon")
Genome_build: Illumina igenomes UCSC/mm10
Supplementary_files_format_and_content: Processed data is tab separated output file as produced by featureCounts which is part of the subread package.

organism: Mus musculus

extract_protocol: none provided by the submitter

tag: strain

tag: tissue

value: Spleen

tag: day of infection


title: HC4_sp3_Normal_DEX_ox21_p9


title: Methylation_HC4_sp3_Normal_Control_ox21_p10


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p37


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p39


title: HC2_sp3_Normal_Control_ox21_p13


title: white pulp pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [WPMC_3]

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

description:
ex vivo isolated cells
cell type comparison

data_processing:
Read quality of sequenced libraries was evaluated with FastQC. Sequencing reads were aligned to the reference mouse genome assembly GRCm38 using STAR, and aligned reads to annotated genes were quantified with htseq-count.
Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values. Protein-coding genes with with at least 20 reads in at least two replicates were included in the analysis.
The calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression[]. Unless not otherwise mentioned genes were considered as differentially expressed at log2(foldchange) > 0.8 and an adjusted p-Value of < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM/FPKM, fold-change matrices for each replicate.

source_name: white pulp mesenchymal cell

extract_protocol:
Cells were directly FACS-sorted into RLT+ lysis buffer (Qiagen), containing 10 µl/ml β-mercaptoethanol (Roth). Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer’s instructions.
cDNA conversion was carried out using the SMART‑Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content, as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.
 Libraries were pooled and sequenced at the genome analytics facility of the Helmholtz Centre for Infection Research on Illumina HiSeq2500 using 50 bp single-end reads.

treatment_protocol: Samples represent biological replicates sorted from pooled splenic preparations from 2 three-months-old male per replicate.

tag: genotype/variation

value: wildtype&SPF-housed

tag: cell type

value: WPMC


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p34


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p30


title: HC2_sp3_Normal_Control_ox21_p12


title: WT Tregs Rep 2

description: 3 mice pooled


title: Methylation_HC4_sp3_Normal_Control_ox21_p11


title: white pulp pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [WPMC_2]


title: HC2_sp3_Normal_Control_ox21_p10


title: HC2_sp3_Normal_Control_ox21_p8


title: white pulp pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [WPMC_1]


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p26


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p18


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p20


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p16


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p23


title: HC1_sp3_Normal_Control_ox21_p13


title: Methylation_HC1_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p14

value: Treatment Start 2


title: red pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [RPMC_2]

source_name: red pulp mesenchymal cell

value: RPMC


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p30


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p32


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p34


title: red pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [RPMC_1]


title: HC1_sp3_Normal_Control_ox21_p12


title: HC1_sp3_Normal_Control_ox21_p10


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p25


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p14


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p27


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p22


title: HC1_sp3_Normal_Control_ox21_p8


title: red pulp macrophages cells isolated from wildtype specific-pathogen free mice [RPM_3]

source_name: red pulp macrophages

value: RPM


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p19


title: red pulp macrophages cells isolated from wildtype specific-pathogen free mice [RPM_2]


title: red pulp mesenchymal cells isolated from wildtype specific-pathogen free mice [RPMC_3]


title: red pulp macrophages cells isolated from wildtype specific-pathogen free mice [RPM_1]


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p34


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p27


title: endothelial cells isolated from wildtype specific-pathogen free mice [EC_1]

source_name: endothelial cells

value: EC


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p16


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p23


title: HC4_sp3_Normal_Control_ox21_p12


title: WPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [WPMC_Stat1het_3]

description:
ex vivo isolated cells
Stat1 deficiency comparison


title: endothelial cells isolated from wildtype specific-pathogen free mice [EC_2]


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p18


title: HC4_sp3_Normal_Control_ox21_p11


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p20


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p16


title: HC4_sp3_Normal_Control_ox21_p10


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p14


title: Methylation_HC2_sp2_Normal_5-azacytidine_ox21_p14


title: Methylation_HC3_sp2_Normal_Oligomycin+DEX_ox21_p11

source_name: Primary Human Fibroblast (foreskin)

value: Primary Human Fibroblast (foreskin)

value: Oligomycin+DEX


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p37

value: Primary Human Fibroblast (breast)


title: Methylation_HC2_sp2_Normal_Oligomycin+DEX_ox21_p10

value: female


title: WPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [WPMC_Stat1het_1]


title: HC4_sp3_Normal_Control_ox21_p14

value: Normal


title: WPMC isolated from Stat1 KO mice [WPMC_Stat1KO_3]


title: WPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [WPMC_Stat1het_2]


title: Methylation_HC1_sp2_Normal_5-azacytidine_ox21_p30


title: HC4_sp3_Normal_Control_ox21_p9

value: Primary Human Fibroblast (upper arm)


title: Methylation_HC1_sp2_Normal_Oligomycin+DEX_ox21_p10

value: male


title: Methylation_HC1_sp2_Normal_Oligomycin+DEX_ox21_p7


title: Methylation_HC1_sp2_Normal_Oligomycin+DEX_ox21_p13


title: HC3_sp2_Normal_Oligomycin+DEX_ox21_p10


title: endothelial cells isolated from wildtype specific-pathogen free mice [EC_3]


title: Methylation_HC3_sp2_Normal_Oligomycin_ox21_p26

value: Oligomycin


title: WPMC isolated from Stat1 KO mice [WPMC_Stat1KO_2]


title: HC3_sp2_Normal_Oligomycin+DEX_ox21_p9

value: Treatment Start


title: Methylation_HC3_sp2_Normal_Oligomycin_ox21_p23


title: Methylation_HC3_sp2_Normal_Oligomycin_ox21_p20


title: HC2_sp3_Normal_Control_ox21_p6

value: Control


title: Methylation_HC3_sp2_Normal_Oligomycin_ox21_p14


title: WPMC isolated from Stat1 KO mice [WPMC_Stat1KO_1]


title: RPMC isolated fromheterozygous Stat1 mouse (control to Stat1KO) [RPMC_Stat1het_3]


title: Methylation_HC3_sp2_Normal_Oligomycin_ox21_p11


title: HC2_sp2_Normal_Oligomycin+DEX_ox21_p6


title: HC1_sp2_Normal_Oligomycin+DEX_ox21_p12


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p37


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p34


title: RPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [RPMC_Stat1het_2]


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p25


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p22


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p19


title: HC1_sp2_Normal_Oligomycin+DEX_ox21_p9


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p16


title: RPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [RPMC_Stat1het_1]


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p10


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p31


title: HC1_sp2_Normal_Oligomycin+DEX_ox21_p6


title: RPMC isolated from Stat1 KO mice [RPMC_Stat1KO_3]


title: HC1_sp3_Normal_Control_ox21_p6


title: Methylation_HC2_sp2_Normal_Oligomycin_ox21_p7


title: HC3_sp2_Normal_Oligomycin_ox21_p34


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p22


title: RPMC isolated from Stat1 KO mice [RPMC_Stat1KO_1]


title: RPMC isolated from Stat1 KO mice [RPMC_Stat1KO_2]


title: HC3_sp2_Normal_Oligomycin_ox21_p22


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p19


title: RPMC isolated from specific-pathogen free housed mice [RPMC_SPF_3]

description:
ex vivo isolated cells
microbiota comparison

value: specific pathogen-free housed


title: RPMC isolated from specific-pathogen free housed mice [RPMC_SPF_2]


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p13


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p7


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p16


title: Methylation_HC1_sp2_Normal_Oligomycin_ox21_p10


title: HC3_sp2_Normal_Oligomycin_ox21_p10


title: HC2_sp2_Normal_Oligomycin_ox21_p38


title: Methylation_HC3_sp2_Normal_mitoNUITs+DEX_ox21_p20

value: mitoNUITs+DEX


title: RPMC isolated from specific-pathogen free housed mice [RPMC_SPF_1]


title: Methylation_HC3_sp2_Normal_mitoNUITs+DEX_ox21_p14


title: HC2_sp2_Normal_Oligomycin_ox21_p36


title: Methylation_HC3_sp2_Normal_mitoNUITs+DEX_ox21_p11


title: RPMC isolated from germ-free housed mice [RPMC_GF_1]

value: germ-free housed


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p38


title: HC2_sp2_Normal_Oligomycin_ox21_p28


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p42


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p34


title: HC3_sp2_Normal_Oligomycin_ox21_p13


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p31


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p28


title: HC2_sp2_Normal_Oligomycin_ox21_p24


title: RPMC isolated from germ-free housed mice [RPMC_GF_2]


title: HC2_sp2_Normal_Oligomycin_ox21_p18


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p19


title: Methylation_HC3_sp2_Normal_mitoNUITs+DEX_ox21_p17


title: HC2_sp2_Normal_Oligomycin_ox21_p15


title: ATAC-Seq F1648_T8d_HDAC2_deficient

city: Planegg-Martinsried

first: Andrea

last: Terrasi

address: Großhaderner Strasse 9

department: Biomedical Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

library_source: genomic

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: processed bigwig files

extract_protocol: 50 000 cells were pelleted at 500 g for 5 min at 4◦C, resuspended in 50 µl of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 0.01% digitonin) and spun at 500 g for 10 min at 4◦C to collect nuclei. Nuclei were subsequently resuspended in 50 µl Transposase mixture (25 µl 2× tagmentation buffer, 16.5 µl PBS, 0.25 µl 2% digitonin, 0.5 µl 10% Tween-20, 5.25 µl H2O, 2.5 µl Tn5 Transposase) Illumina Nextera DNA Library Preparation Kit. Reactions were incubated for 30 min at 37◦C in a thermomixer shaking at 1000 rpm and DNA purified using PCR clean-up MinElute kit (Qiagen). The transposed DNA was subsequently amplified in 50 µl reactions with custom primers. Amplified libraries were purified with the PCR clean-up MinElute kit (Qiagen) and size selected for fragments <600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.

value: pancreatic ductal adenocarcinoma cell line

tag: genotype


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p16


title: ChIP-Seq F1648_E8d_HDAC2_proficient

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files

extract_protocol: 1-2 million cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 µl Buffer-B (50 mM Tris–HCl, pH 8.0, 10 mM EDTA, 1%SDS, 1× protease inhibitors -Roche) and sonicated in a microtube (Covaris; 520045) using a Covaris S220 device to shear the chromatin to an average size of 100–500 base pairs long (settings: temperature 4◦C, duty cycle 2%, peak incident power 105 W, cycles per burst 200). Successively, lysates were diluted with 900 ul of Buffer-A (10 mM Tris–HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1× protease inhibitors-Roche) and centrifuged 10 min, 4◦C, 12000g. 150 ul of sonicated chromatin was then incubated 4h at 4◦C on a rotating wheel with 3 g of antibody conjugated to 10 l of Protein G Dynabeads (ThermoFisher). The antibody used was H3K27ac (Diagenode; Pab-174-050). Beads were washed with Buffer-A (10 mM Tris–HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1× protease inhibitors-Roche) and with Buffer-C (10 mM Tris–HCl, pH 8.0, 10 mM EDTA). Beads were re-suspended in 100 µl elution buffer (50 mM Tris–HCl, pH 8.0, 10 mM EDTA, 1% SDS) and incubated 20 min at 65◦C. Supernatant was transferred to a new tube. Crosslink reversal of immunoprecipitated DNA was carried out overnight at 65◦C. Then 100 µl TE (10 mM Tris–HCl, pH 8.0, 1 mM EDTA) was added, RNA was degraded by 4 µl RNase A (10 mg/ml) for 1 h at 37◦C and proteins were digested with 4 µl Proteinase K (10 mg/ml) at 55◦C for 2h. Finally, DNA was isolated by phenol:chloroform:Isoamyl alcohol purification followed by ethanol precipitation. Purified DNA was used as input for library preparation with MicroPlex Library Preparation Kit v2 .


title: RPMC isolated from germ-free housed mice [RPMC_GF_3]

value: RPMC


title: ATAC-Seq F1648_E8d_HDAC2_proficient


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p13


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p10


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p7


title: HC2_sp2_Normal_Oligomycin_ox21_p9


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p34


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p31


title: BP72

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

data_processing:
Salmon (v.0.91) was used to perform quasi-mapping of sequencing reads, with seqBias and gcBias corrections enabled, using a 31bp k-mer index of the GRCh38.p10 (GENCODE v.27) human reference transcripts, to estimate transcript abundance for each sample
Tximport package was used to import transcript abundance estimates from quant.sf files, generated by Salmon read mapping into R statistical programming environment for gene expression quantification. Transcript abundance estimates were collapsed to gene level gene expression counts. TXI data objects for MAYO and PITT-RCSI RNA-Seq cohort, containing unprocessed Salmon read counts, transcript per million (TPM) and gene length values were combined for subsequent downstream analysis.
Genes with little to no expression across all 90 samples were filtered if gene TPM < 0.5 in at least 10% of all samples (N=90)
Filtered gene level counts were normalized with edgeR calcNormFactors() and cpm() function, where counts per million (CPM): CPM = C * 106/N (counts (C) scaled by the library depth in million units). A log2 transformation was applied to CPM: log2(CPM +1), where 1 is a pseudocount added to prevent negative value counts. Filtered log2 CPM and TPM genes were annotated using biomaRt R package to identify protein coding genes using the ENSEMBL GRCh38 p.10 database.
In order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, filtered protein coding gene expression counts were used as input to svaseq R package for batch effect assessment. A multiple linear regression model was fit for each surrogate variable (SV), with the following independent predictors: sequencing batch ID [1,5], disease status (primary breast (P) / brain metastases (M)), estrogen receptor (ER) IHC status (ER+/ER-) and primary tumor histological subtype (DCIS, IDC, ILC, Mixed ILC/IDC). A linear model fitted using SV1 was found to be significantly associated with sequencing batch (P < 0.05; R2 ~0.70).   As such, in order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, removeBatchEffect() function in LIMMA package in R, was used with SV1, to adjust gene expression values to account for mean shifts in expression driven by the batch driven effect.
Genome_build: GRCh38.p10 (GENCODE v.27)
Supplementary_files_format_and_content: .xlsx excel spread sheet containing batch corrected log2 TMM normalized CPM proteing coding gene expression values for all 90 samples

source_name: primary breast tumor

extract_protocol: 100 ng of RNA and Illumina’s TruSeq RNA Access Library Preparation protocol

tag: cohort

value: PITT-RCSI

tag: patient id

tag: disease state

value: breast cancer

value: primary breast tumor


title: ChIP-Seq F1648_T8d_HDAC2_deficient


title: HC2_sp2_Normal_Oligomycin_ox21_p33


title: HC2_sp2_Normal_Oligomycin_ox21_p6


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p28


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p25


title: HC1_sp2_Normal_Oligomycin_ox21_p24


title: BP71


title: BM72

source_name: brain metastatic tumor

value: brain metastatic tumor


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p22

value: Primary Human Fibroblast (breast)


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p22


title: Methylation_HC2_sp2_Normal_mitoNUITs+DEX_ox21_p25

value: female


title: HC1_sp2_Normal_Oligomycin_ox21_p18

value: Normal


title: HC2_sp2_Normal_Oligomycin_ox21_p12


title: BM71


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p10


title: HC1_sp2_Normal_Oligomycin_ox21_p15


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p16


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p19


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p13


title: Methylation_HC1_sp2_Normal_mitoNUITs+DEX_ox21_p7


title: HC1_sp2_Normal_Oligomycin_ox21_p12


title: Methylation_HC3_sp2_Normal_mitoNUITs_ox21_p26

value: Primary Human Fibroblast (foreskin)

value: mitoNUITs


title: BP7


title: HC1_sp2_Normal_Oligomycin_ox21_p9

value: male

value: Oligomycin


title: BM7


title: Methylation_HC3_sp2_Normal_mitoNUITs_ox21_p23


title: Methylation_HC3_sp2_Normal_mitoNUITs_ox21_p17


title: Methylation_HC3_sp2_Normal_mitoNUITs_ox21_p11


title: HC1_sp2_Normal_Oligomycin_ox21_p6


title: Technical_replicate_sp2_Normal__ox21_p_150

value: Control


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p19


title: HC3_sp2_Normal_mitoNUITs+DEX_ox21_p31


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p16


title: BP64


title: BP68


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p13


title: Methylation_HC3_sp2_Normal_mitoNUITs_ox21_p14


title: BM68


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p10


title: HC3_sp2_Normal_mitoNUITs+DEX_ox21_p28


title: BP62


title: HC3_sp2_Normal_mitoNUITs+DEX_ox21_p22


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p37


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p31


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p28


title: 6P_RCS

extract_protocol: 100 ng of RNA and Illumina’s  TruSeq DSN library & TruSeq RNA Access Library Preparation protocol


title: HC3_sp2_Normal_mitoNUITs+DEX_ox21_p19


title: HC3_sp2_Normal_mitoNUITs+DEX_ox21_p10


title: BM62


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p7


title: 6M_RCS


title: Methylation_HC2_sp2_Normal_mitoNUITs_ox21_p22


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p40


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p13


title: BP6


title: HC4_sp3_Normal_Control_ox21_p13

value: Primary Human Fibroblast (upper arm)


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p7


title: BM6


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p30

source_name: Primary Human Fibroblast (forearm)

value: Primary Human Fibroblast (forearm)

value: DEX


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p33


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p16


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p33

value: mitoNUITs+DEX


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p30


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p19


title: BP52


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p21


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p24


title: BM52


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p29


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p27


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p18


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p21


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p24


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_DEX_ox21_p15


title: BP51


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p25


title: BM51


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p23


title: Methylation_HC1_sp2_Normal_mitoNUITs_ox21_p10


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p20


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p18


title: 5P_RCS


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p14


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p15


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p17


title: 5M_RCS


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p11


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p24


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p12


title: BP47


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p27


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p21


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p18


title: BM47


title: 4P_RCS


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p15


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_DEX_ox21_p12


title: Methylation_HC3_sp2_Normal_DEX_ox21_p23


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p6


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p33


title: Methylation_HC3_sp2_Normal_DEX_ox21_p17


title: 4M_RCS


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p30


title: Methylation_HC3_sp2_Normal_DEX_ox21_p11


title: 3P_RCS


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p24


title: Methylation_HC3_sp2_Normal_DEX_ox21_p14


title: 3M_RCS


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p21


title: Methylation_HC2_sp2_Normal_DEX_ox21_p40


title: Methylation_HC2_sp2_Normal_DEX_ox21_p42


title: Methylation_HC2_sp2_Normal_DEX_ox21_p37


title: Methylation_HC2_sp2_Normal_DEX_ox21_p34


title: BM29


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p18


title: HC2_sp2_Normal_mitoNUITs+DEX_ox21_p9


title: BP29


title: Methylation_HC2_sp2_Normal_DEX_ox21_p31


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_DEX_ox21_p26


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p15


title: Methylation_HC2_sp2_Normal_DEX_ox21_p28


title: BP25


title: Methylation_HC3_sp2_Normal_DEX_ox21_p20


title: Methylation_HC2_sp2_Normal_DEX_ox21_p25


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p12


title: Methylation_HC2_sp2_Normal_DEX_ox21_p22


title: Methylation_HC2_sp2_Normal_DEX_ox21_p19


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p9


title: 2P_RCS


title: Methylation_HC2_sp2_Normal_DEX_ox21_p13


title: HC1_sp2_Normal_mitoNUITs+DEX_ox21_p6


title: Methylation_HC2_sp2_Normal_DEX_ox21_p10


title: 2M_RCS


title: Methylation_HC2_sp2_Normal_DEX_ox21_p7


title: Methylation_HC1_sp2_Normal_DEX_ox21_p31


title: Methylation_HC1_sp2_Normal_DEX_ox21_p37


title: BP19-2


title: Methylation_HC1_sp2_Normal_DEX_ox21_p28


title: Methylation_HC1_sp2_Normal_DEX_ox21_p25


title: HC3_sp2_Normal_mitoNUITs_ox21_p19


title: HC3_sp2_Normal_mitoNUITs_ox21_p28


title: BP17


title: Methylation_HC1_sp2_Normal_DEX_ox21_p16


title: BM17


title: Methylation_HC1_sp2_Normal_DEX_ox21_p19


title: Methylation_HC1_sp2_Normal_DEX_ox21_p13


title: BM25


title: HC3_sp2_Normal_mitoNUITs_ox21_p16


title: BM19-2


title: Methylation_HC1_sp2_Normal_DEX_ox21_p10


title: Methylation_HC2_sp2_Normal_DEX_ox21_p16


title: HC3_sp2_Normal_mitoNUITs_ox21_p10


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p27


title: BM12


title: HC3_sp2_Normal_mitoNUITs_ox21_p31


title: BP12


title: Methylation_HC1_sp2_Normal_DEX_ox21_p42


title: HC2_sp2_Normal_mitoNUITs_ox21_p28


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p24


title: 1P_RCS


title: HC2_sp2_Normal_mitoNUITs_ox21_p24


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p18


title: 1M_RCS


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p21


title: HC3_sp2_Normal_mitoNUITs_ox21_p13


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p33


title: HC2_sp2_Normal_mitoNUITs_ox21_p21


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p26


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p11


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p20


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p13

value: Treatment Start


title: Template switch library from STARR-seq GP5d binary RNA, replicate 2

city: Helsinki

first: Teemu

last: Kivioja

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
sequences start with 10 bp long UMI (unique molecular identifier)
STARR-seq_TSS_flank60_motif_counts.tsv

data_processing:
Library strategy: STARR-seq
Sequences derived from spliced transcripts were identified using the constant sequence spanning the splice site after intron removal (cutadapt program); other sequences were not processed further.
UMI sequence was removed from the 5’ end of each sequence and the last 20 bp of its random part was used to recognize the corresponding promoter from the input DNA (file avaiiable in STARR-seq random promoter-enhancer experiments part of the same study)
To accurately recognize the first base of the transcript and thus the position of the TSS, it was assumed that the template switch process had added at least 3 and at most 4 guanines to the 5’ end of the transcript. On this basis, only the RNA sequences starting with at least three Gs were used in the analysis. Each such sequence was aligned to the corresponding input DNA promoter sequence using an exact 20 bp match starting from the base to allow for the extra Gs. Finally, the Gs added by the template switch were trimmed an discordant sequences removed according to the alignment. The frequency of the four Gs instead of three was estimated from the sequences that do not have G at the fourth position in the alignment to the input. For those that did have a G also in the input sequence, removing three or four Gs was decided randomly but so that the frequency of the fourth G matched the estimate.
The two GP5d template switch libraries were processed separately and then merged so that only one transcript was kept for each input DNA promoter sequence to prevent duplicate promoter sequences.
The exact positions of the TSS at the promoters were recorded and the flanking sequences were used for further analysis.
Motifs were matched to TSS flanking promoter sequences using program MOODS and for each motif only the highest affinity match per sequence was considered. The number of matches for each motif was then counted separately at each position and strand.
Supplementary_files_format_and_content: tab-delimited text file, the columns are: name (name of the TF),   pfm (name of the motif used in the motif matching),  pos (position of the information content center of the motif in relation to TSS at +1),  strand (strand of the motif matches) ,  num (number of motif matches at this position and strand,  pfm.type (either HT-SELEX = in vitro motif from HT-SELEX experiment, promoterCore = promoter motif collected from literature or database,  deNovo = motif mined from the STARR-seq data itself, New = recently published promoter motif)

growth_protocol: GP5d cells were cultured in DMEM media supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each random promoter-enhancer binary STARR-seq experiment, a total of 250 million GP5d cells per replicate were transfected.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection.
Input library for random promoter-enhancer binary STARR-seq was constructed as described in Arnold et al. Science 2013. For generating a sequencing library using a template switch strategy, a 40-ug aliquot of isolated total RNA from the random promoter-random enhancer STARR-seq experiment in GP5d cell line was used. Briefly, TurboDNase-treated RNA was incubated at 72 C for 3 min with a custom biotinylated STARR-seq specific RT-primer and dNTPs in two reactions having 25 ng of RNA per reaction, followed by immediate chill on ice. The first strand synthesis was performed using 100 units of Superscript IV RT (Invitrogen) in 1x SS-IV RT buffer containing 10 units of RNase OUT (Invitrogen), 5 mM DTT, 6 mM MgCl2 (Sigma), 1M Betaine (Sigma) and 1 uM custom template switch oligo compatible with the custom CpG-free Illumina sequencing by incubating the reactions at 50 C for 15 min followed by 80 C for 10 min. cDNA was purified using AMPure XP beads and one cDNA reaction product was split into two for PCR amplification using KAPA HiFi master mix (Roche) together with USER enzyme (NEB) and for enrichment of STARR-seq reporter-specific template. The PCR product was purified using AMPure XP beads followed by a second PCR for a total of 5 cycles for Illumina library preparation using custom CpG-free oligos.
Illumina sequencing strategy adapted for  pCpG-free STARR-seq construct for random promoter-enhancer and template switch library using custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with random enhancer STARR-seq library using transfex (ATCC) in GP5d cells  using one ug of library per one million cells.

tag: cell line

value: GP5d  colon carcinoma cells


title: STARR-seq HepG2 random enhancers from binary STARR-seq

description: sequenced random enhancer RNA, can be connected to the promoter only through the input pairs

data_processing:
Library strategy: STARR-seq
The STARR-seq enhancer sequences derived from RNA were mapped to corresponding promoter-enhancer pairs in the input DNA by exact matches of the first 20 bases of the 150 bases long enhancer sequences.
Duplicate reads were removed by sorting the sequences four times based on 40 bases long non-overlapping subsequences from base 16 to 135 and taking only one sequence per identical subsequence at each sort step.
Promoter and enhancer sequences were filtered separately by removing 1) all adapter sequences that included some (partial) adapter sequence according to cutadapt (version 1.9.1), 2) sequences that mapped to plasmid backbone sequence using bowtie2, and 3) outlier sequences in terms of nucleotide composition (count of any nucleotide more than 3 median absolute deviations higher than the median count).
For promoter-enhancer pair analyses, the remaining promoter-enhancer pairs were collected and pairs containing highly similar sequence as promoter and enhancer were removed.
The motifs were matched to sequences using program MOODS (version 1.9.3). The matching was done separately for each strand using p-value thresholds 1e-6 (promoter analysis) and 5e-5 (promoter-enhancer pair analysis) and and strand- and sample-specific nucleotide frequencies.
In the promoter analysis, the number of motif  matches for each motif in the sequences was counted so that overlapping matches in different strands were counted only once and the fold changes between the motif match counts in RNA and  input DNA were estimated using the function PsiLFC in R package lfc.
In the promoter-enhancer pair analysis, for each motif pair, one having a binding site in the promoter, the other in the enhancer of a pair, the expected number of promoter-enhancer pairs was compared to  observed number. The expected number was calculated from the total numbers of promoter and enhancer motif sites assuming that they occur independently of each other. For each pair a p-value was calculated for the null hypothesis that the motifs occur independently using binomial test and corrected for multiple testing using Holm's method.
Supplementary_files_format_and_content: promoter only files are tab delimited text files, the columns are: name (name of the TF), pfm (motif used in the sequence matching), total.count (count of motif matches in STARR-seq RNA), input.total.count (count of motif matches in input DNA), effect (log2 fold change between STARR-seq RNA and input DNA estimated by lfc)
Supplementary_files_format_and_content: pair file (STARRseq_RandomPE_GP5d_rep1.p5e-5.pair_counts.tsv) is a tab delimited text file, the columns are: promoter.name (name of the promoter TF), enhancer.name (name of the enhancer TF),  promoter.pfm, enhancer.pfm (motifs used in the sequence matching),   promoter.count (promoter motif match count), enhancer.count (enhancer motif match count),  pair.count (count of the motif matches in the same promoter-enhancer pair),  expected.pair.count (expected count assuming that matches are independent),   pval.adj (multiple testtin adjusted p-value for pair count assuming independence of motif matches)

source_name: synthetic

growth_protocol: GP5d cells were cultured in DMEM, HepG2 cells in MEM and RPE cells with DMEM/F12  media supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each random promoter-enhancer binary STARR-seq experiment, a total of 250 million GP5d cells per replicate, and 400 million HepG2 and 480 million RPE cells  were transfected.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection followed by polyA(+) purification using direct mRNA purfication beads (ThermoFisher).
STARR-seq reporter and input library was constructed with minor modifications as described in Arnold et al. Science 2013. First strand cDNA synthesis was done with 2.5-5 ug of polyA(+) RNA and with Superscript III (Invitrogen, #18080-044) using a reporter-RNA specific primer. This was followed by RNase A treatment for 1 h at 37˚C and purification. cDNA amplification was performed with reporter-specific nested cDNA primers corresponding to the respective STARR-seq reporter construct using KAPA HiFi PCR Master mix (Roche) in the same number of reactions as done for the reverse transcription. The final PCR reactions to produce Illumina-compatible sequencing libraries were prepared from the entire amplified cDNA using KAPA HiFi PCR Master mix (Roche) as descriubed in Arnold et al. Science 2013. All purifications were done using AMPure XP beads as per manufacturer’s instruction unless otherwise mentioned.
Illumina sequencing strategy adapted for random enhancer pCpG-free STARR-seq construct  using custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with random enhancer STARR-seq library using transfex (ATCC) in GP5d cells, transfectin (Biorad) in HepG2 and FuGene HD (Promega) in RPE cells using one ug of library per one million cells.

value: HepG2 hepatocellular carcinoma cells


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p14

tag: Sex


title: Methylation_HC1_sp2_Normal_DEX_ox21_p7

tag: treatments


title: HC2_sp2_Normal_mitoNUITs_ox21_p12

tag: passage


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p11

tag: slide


title: HC2_sp2_Normal_mitoNUITs_ox21_p9


title: STARR-seq GP5d random enhancer, replicate 2

data_processing:
Library strategy: STARR-seq
150 bases long STARR-seq RNA and input DNA paired-end reads were combined using the FLASH program (version 1.2.11, options --min-overlap=130--max-overlap=134 -x 0.25 -z -t 4) and only combined sequences of length 170 were chosen
Duplicate reads were removed by sorting the sequences four times based on 45 bases long non-overlapping subsequences from base 6 to 165 and taking only one sequence per identical subsequence at each sort step.
The motifs were matched to sequences using program MOODS (version 1.9.3). The matching was done separately for each strand using p-value thresholds 1e-6 and and strand- and sample-specific nucleotide frequencies.
The number of motif  matches for each motif in the sequences was counted so that overlapping matches in different strands were counted only once.
Fold changes between the motif match counts in RNA and  input DNA were estimated using the function PsiLFC in R package lfc.
Supplementary_files_format_and_content: tab delimited text files, the columns are: name (name of the TF),  pfm (motif used in the sequenc matching),  total.count (count of motif matches in STARR-seq RNA), input.total.count (count of motif matches in input DNA),  effect (log2 fold change between STARR-seq RNA and input DNA estimated by lfc)

growth_protocol: GP5d cells were cultured in DMEM and HepG2 cells in MEM media with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each random enhaner STARR-seq experiment, a total of 250 million GP5d cells per replicate were transfected.

treatment_protocol: The cells were transfected with random enhancer STARR-seq library using transfex (ATCC) in GP5d cells and transfectin (Biorad) in HepG2 cells using one ug of library per one million cells.


title: Methylation_SURF1_3_sp2_Methylation_SURF1_Mutation_Control_ox21_p15

tag: array


title: STARR-seq HepG2 random enhancer

source_name: STARR-seq HepG2 random enhancer


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p27

tag: well


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p24


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p21


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p18


title: HC2_sp2_Normal_mitoNUITs_ox21_p18


title: STARR-seq RPE random enhancers from binary STARR-seq

value: RPE  retinal pigment epithelium cells


title: Technical_replicate_sp2_Normal__ox21_p_110


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p15


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p10

tag: notes


title: GP5d genomic input library

data_processing:
Library strategy: STARR-seq
Demultiplexed Illumina STARR-seq RNA and input DNA paired-end reads (trimmed to common length 2 x 37 bp) were aligned to the human genome using bowtie2 (version 2.2.4, option --maxins 1000)
Mapped read pairs were deduplicated using picard (version 2.9.0) and paired-end reads that had mapping quality <20 or mapped in a discordant orientation were discarded using samtools (version 0.1.19)
MACS2 (version 2.1.1) was used to call peaks in paired-end mode (-f BAMBE) using input DNA as control
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 narrowPeak files

source_name: GP5d  colon carcinoma cells

growth_protocol: GP5d cells were cultured in DMEM and HepG2 cells in MEM media with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each genomic STARR-seq experiment, 500 million GP5d cells and 350 million HepG2 cells were used for transfection.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection followed by polyA(+) purification using direct mRNA purfication beads (ThermoFisher).
STARR-seq reporter and input library was constructed with minor modifications as described in Arnold et al. Science 2013. First strand cDNA synthesis was done with 2.5-5 ug of polyA(+) RNA and with Superscript III (Invitrogen, #18080-044) using a reporter-RNA specific primer. This was followed by RNase A treatment for 1 h at 37˚C and purification. cDNA amplification was performed with reporter-specific nested cDNA primers corresponding to the respective STARR-seq reporter construct using KAPA HiFi PCR Master mix (Roche) in the same number of reactions as done for the reverse transcription. The final PCR reactions to produce Illumina-compatible sequencing libraries were prepared from the entire amplified cDNA using KAPA HiFi PCR Master mix (Roche) as descriubed in Arnold et al. Science 2013. All purifications were done using AMPure XP beads as per manufacturer’s instruction unless otherwise mentioned.
Illumina sequencing strategy adapted for CpG-free custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with genomic STARR-seq library using transfex (ATCC) in GP5d cells and Transfectin (Biorad) in HepG2 cells and one ug of library was used per one million cells.

tag: treatment

value: no treatment


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p17


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p9


title: Methylation_SURF1_1_sp2_Methylation_SURF1_Mutation_Control_ox21_p12


title: STARR-seq HepG2 genomic, replicate 2

source_name: HepG2 hepatocellular carcinoma cells

value: non-methylated


title: BM64

value: PITT-RCSI

value: breast cancer

tag: tissue

value: brain metastatic tumor


title: HC1_sp2_Normal_mitoNUITs_ox21_p33

value: Primary Human Fibroblast (breast)

value: Normal

value: mitoNUITs


title: Methylation_HC3_sp2_Normal_Control_ox21_p32

value: Primary Human Fibroblast (foreskin)

value: male

value: Control


title: Methylation_SURF1_2_sp2_Methylation_SURF1_Mutation_Control_ox21_p7

value: Primary Human Fibroblast (forearm)


title: Methylation_HC3_sp2_Normal_Control_ox21_p34


title: Methylation_HC3_sp2_Normal_Control_ox21_p23


title: STARR-seq HepG2 genomic, replicate 1


title: HC1_sp2_Normal_mitoNUITs_ox21_p21


title: STARR-seq GP5d genomic, p53 null, CpG-methylated

description: TP53-null GP5d cell line was generated by targeting exon 4 of the TP53 gene using CRISPR-Cas9 genome editing.

value: CpG-methylated


title: HC2_sp2_Normal_mitoNUITs_ox21_p15

value: female


title: HC2_sp2_Normal_mitoNUITs_ox21_p6


title: Methylation_HC3_sp2_Normal_Control_ox21_p17


title: STARR-seq GP5d genomic, p53 null


title: STARR-seq GP5d random enhancer, replicate 1

value: GP5d  colon carcinoma cells


title: HC1_sp2_Normal_mitoNUITs_ox21_p18


title: Methylation_HC3_sp2_Normal_Control_ox21_p14


title: Methylation_HC3_sp2_Normal_Control_ox21_p11


title: STARR-seq GP5d genomic, CpG-methylated


title: HC1_sp2_Normal_mitoNUITs_ox21_p30


title: HC1_sp2_Normal_mitoNUITs_ox21_p9


title: STARR-seq GP5d genomic


title: HC1_sp2_Normal_mitoNUITs_ox21_p12


title: HC1_sp2_Normal_mitoNUITs_ox21_p27


title: Methylation_HC3_sp2_Normal_Control_ox21_p20


title: Methylation_HC2_sp2_Normal_Control_ox21_p34


title: Methylation_HC3_sp2_Normal_Control_ox21_p6


title: Methylation_HC2_sp2_Normal_Control_ox21_p28


title: Methylation_HC2_sp2_Normal_Control_ox21_p25


title: HC1_sp2_Normal_mitoNUITs_ox21_p6


title: Methylation_HC2_sp2_Normal_Control_ox21_p22


title: MHC-IIlo TAM incubated with lactate Biological replicate 4

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIlo TAM_4 + LAC

data_processing:
The preprocessing of the RNA sequencing data was done by Trimmomatic.  Adapters were cut off, and reads were trimmed when the quality dropped below 20. Reads with a length < 35 were discarded.
Reads were mapped to the mouse reference genome GRCm38.82 via STAR and counted via FeatureCounts
The two runs were aggregated by summing the counts per gene and per sample.  We removed 32825 genes, for which all samples have less than 1 counts-per-million and performed correction for GC-content,library size and RNA composition using the EDASeq package from Bioconductor
Genome_build: GRCm38.82
Supplementary_files_format_and_content: comma-delimited text file with raw counts for each gene and each sample
Supplementary_files_format_and_content: comma-delimited text file with FPKM values for each sample (normalized filtered counts)

source_name: Tumor-associated macrophage

growth_protocol: To assess gene expression in freshly sorted MHC-IIhi/MHC-IIlo TAMs, 3.10^4 cells were sorted. To assess how gene expression in MHC-IIhi/MHC-Iilo TAMs is altered by lactate, 2.5.10^5 sorted MHC-IIhi/MHC-IIlo TAMs were cultured for 24h with or without 20mM sodium L-lactate.

extract_protocol:
3.10^4 freshly sorted MHC-IIhi/MHC-IIlo TAMs were directly sorted in 500ul RLT buffer (Qiagen) containing 1% 2-mercaptoethanol. 2.5.10^5 sorted MHC-IIhi/MHC-IIlo TAMs were cultured for 24h with or without 20mM sodium L-lactate. After 24h the cells were lysed by adding 175ul RLT buffer to the wells of the cell culture plate. The final volume was adjusted up to 350ul RLT buffer. RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) and RNA sequencing was performed using a NextSeq sequencer (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The incubated MHC-IIhi/MHC-IIlo TAMs were treated for 24h with or without 20mM sodium L-lactate.

tag: strain

value: WT

value: 3LL-R subcutaneous tumor tissue

value: Tumor-associated macrophage


title: Methylation_HC2_sp2_Normal_Control_ox21_p19


title: HC3_sp2_Normal_DEX_ox21_p31

value: DEX


title: MHC-IIlo TAM incubated with lactate Biological replicate 2

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIlo TAM_2 + LAC


title: MHC-IIlo TAM incubated with lactate Biological replicate 5

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIo TAM_5 + LAC


title: Methylation_HC2_sp2_Normal_Control_ox21_p16


title: MHC-IIlo TAM incubated with lactate Biological replicate 3

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIlo TAM_3 + LAC


title: Methylation_HC3_sp2_Normal_Control_ox21_p9

value: Treatment Start


title: Methylation_HC3_sp2_Normal_Control_ox21_p8


title: Methylation_HC2_sp2_Normal_Control_ox21_p13


title: Methylation_HC2_sp2_Normal_Control_ox21_p7


title: Methylation_HC2_sp2_Normal_Control_ox21_p5


title: Methylation_HC2_sp2_Normal_Control_ox21_p10


title: Methylation_HC2_sp2_Normal_Control_ox21_p31


title: HC1_sp2_Normal_mitoNUITs_ox21_p15


title: MHC-IIlo TAM incubated with lactate Biological replicate 1

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIlo TAM_1 + LAC


title: HC3_sp2_Normal_DEX_ox21_p25


title: HC3_sp2_Normal_DEX_ox21_p22


title: MHC-IIhi TAM incubated with lactate Biological replicate 5

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIhi TAM_5 + LAC


title: HC3_sp2_Normal_DEX_ox21_p19


title: MHC-IIhi TAM incubated with lactate Biological replicate 4

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIhi TAM_4 + LAC


title: Methylation_HC1_sp2_Normal_Control_ox21_p42


title: Methylation_HC2_sp2_Normal_Control_ox21_p1


title: Methylation_HC2_sp2_Normal_Control_ox21_p3


title: HC3_sp2_Normal_DEX_ox21_p16


title: Methylation_HC1_sp2_Normal_Control_ox21_p37


title: MHC-IIhi TAM incubated with lactate Biological replicate 3

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIhi TAM_3 + LAC


title: Methylation_HC1_sp2_Normal_Control_ox21_p34


title: Methylation_HC1_sp2_Normal_Control_ox21_p31


title: HC3_sp2_Normal_DEX_ox21_p13


title: HC3_sp2_Normal_DEX_ox21_p10


title: Methylation_HC1_sp2_Normal_Control_ox21_p25


title: Methylation_HC1_sp2_Normal_Control_ox21_p22


title: Methylation_HC1_sp2_Normal_Control_ox21_p28


title: MHC-IIhi TAM incubated with lactate Biological replicate 2

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIhi TAM_2 + LAC


title: MHC-IIhi TAM incubated with lactate Biological replicate 1

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated with 20mM sodium L-lactate for 24h
MHC-IIhi TAM_1 + LAC


title: MHC-IIlo TAM incubated without lactate Biological replicate 5

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIo TAM_5 - LAC


title: HC2_sp2_Normal_DEX_ox21_p36


title: MHC-IIlo TAM incubated without lactate Biological replicate 4

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIlo TAM_4 - LAC


title: Methylation_HC1_sp2_Normal_Control_ox21_p19


title: Methylation_HC1_sp2_Normal_Control_ox21_p16


title: Methylation_HC1_sp2_Normal_Control_ox21_p13


title: HC2_sp2_Normal_DEX_ox21_p41


title: HC2_sp2_Normal_DEX_ox21_p33


title: MHC-IIlo TAM incubated without lactate Biological replicate 3

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIlo TAM_3 - LAC


title: Methylation_HC1_sp2_Normal_Control_ox21_p6


title: Methylation_HC1_sp2_Normal_Control_ox21_p7


title: HC2_sp2_Normal_DEX_ox21_p30


title: MHC-IIlo TAM incubated without lactate Biological replicate 2

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIlo TAM_2 - LAC


title: Methylation_HC1_sp2_Normal_Control_ox21_p10


title: MHC-IIlo TAM incubated without lactate Biological replicate 1

description:
MHC-IIlo TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIlo TAM_1 - LAC


title: Methylation_HC6_sp1_Normal_a-ketogluturate_ox21_p14

value: a-ketogluturate


title: HC2_sp2_Normal_DEX_ox21_p27


title: Methylation_HC1_sp2_Normal_Control_ox21_p1


title: Methylation_HC6_sp1_Normal_a-ketogluturate_ox21_p17


title: Methylation_HC6_sp1_Normal_a-ketogluturate_ox21_p12


title: Methylation_HC6_sp1_Normal_a-ketogluturate_ox21_p10


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p20


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p26


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p18


title: MHC-IIhi TAM incubated without lactate Biological replicate 4

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIhi TAM_4 - LAC


title: HC2_sp2_Normal_DEX_ox21_p18


title: MHC-IIhi TAM incubated without lactate Biological replicate 3

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIhi TAM_3 - LAC


title: MHC-IIhi TAM incubated without lactate Biological replicate 2

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIhi TAM_2 - LAC


title: HC2_sp2_Normal_DEX_ox21_p12


title: Methylation_HC1_sp2_Normal_Control_ox21_p3


title: HC2_sp2_Normal_DEX_ox21_p15


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p9


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p13


title: Methylation_HC5_sp1_Normal_NAC+DEX_ox21_p20

value: NAC+DEX


title: Freshly sorted MHC-IIlo TAM Biological replicate 5

description:
Freshly sorted MHC-IIloTAMs from subcutaneous 3LL-R tumors
MHC-IIlo TAM_5


title: HC2_sp2_Normal_DEX_ox21_p24

value: Primary Human Fibroblast (breast)


title: Methylation_HC5_sp1_Normal_NAC+DEX_ox21_p18

value: Normal


title: Methylation_HC5_sp1_Normal_NAC+DEX_ox21_p16


title: HC2_sp2_Normal_DEX_ox21_p21


title: MHC-IIhi TAM incubated without lactate Biological replicate 1

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIhi TAM_1 - LAC


title: Methylation_HC5_sp1_Normal_NAC+DEX_ox21_p13


title: HC2_sp2_Normal_DEX_ox21_p6


title: Freshly sorted MHC-IIlo TAM Biological replicate 4

description:
Freshly sorted MHC-IIloTAMs from subcutaneous 3LL-R tumors
MHC-IIlo TAM_4


title: HC1_sp2_Normal_DEX_ox21_p36


title: Methylation_HC6_sp1_Normal_NAC_ox21_p14

value: NAC


title: MHC-IIhi TAM incubated without lactate Biological replicate 5

description:
MHC-IIhi TAM sorted from subcutaneous 3LL-R tumors and incubated without lactate for 24h
MHC-IIhi TAM_5 - LAC


title: Methylation_HC6_sp1_Normal_NAC_ox21_p10


title: Freshly sorted MHC-IIlo TAM Biological replicate 3

description:
Freshly sorted MHC-IIloTAMs from subcutaneous 3LL-R tumors
MHC-IIlo TAM_3


title: HC1_sp2_Normal_DEX_ox21_p33


title: Methylation_HC5_sp1_Normal_a-ketogluturate_ox21_p16


title: 4T1Br_Mouse_Model

city: San Francisco

first: Hugo

last: Gonzalez

state: California

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

data_processing:
After sequencing attemping 50,000 counts per cell captured by the 10X chip, Cell Ranger count pipeline (Version 3.0.2 from 10X Genomics) was used to map the FASTQ files to the human genome GRCh38, which generates a gene vs cell expression matrix (See Matrix.mtx.gz and Metrics_Summary.csv files).
The LogNormalized_Data was generated for each sample using the Seurat NormalizeData function. Briefly, counts for each cell are divided by the total counts for that cell and multiplied by the scale.factor 10000. This is then natural-log transformed using log1p
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix
Supplementary_files_format_and_content: Features for downstream processing
Supplementary_files_format_and_content: Single Cell barcodes for downstream processing
Supplementary_files_format_and_content: Cell Ranger Quality Metrics per each sample
Supplementary_files_format_and_content: Normalized Expression per each sample
Supplementary_files_format_and_content: Annotations of the Cell types described in the study.

source_name: Mouse Breast Cancer Cell Line

extract_protocol: Single-cell libraries were generated via the Chromium Controller and the Single Cell Reagent Kit 3’ v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions

tag: type of tumor

value: Experimental Brain Metastasis

value: Breast Cancer Brain Metastasis


title: Freshly sorted MHC-IIlo TAM Biological replicate 2

description:
Freshly sorted MHC-IIloTAMs from subcutaneous 3LL-R tumors
MHC-IIlo TAM_2

tag: cell type


title: HC1_sp2_Normal_DEX_ox21_p30

value: male


title: IRF8R294C 3

city: NEW DELHI

first: Prafullakumar

last: Tailor

state: DELHI

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39 (Ensembl  database: Mus_musculus.GRCm39.dna.primary_assembly.fa; Mus_musculus.GRCm39.103.gtf ) whole genome using  HISAT2 aligner (v.2.1.0) with default parameters.
Raw read counts were determined using HTSeq-count (v.0.12.4), and further raw read counts were normalized via DESeq2 (v.1.30.1)  by following the methods described in Love M.I., Huber W. and Anders S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15:550.
Genome_build: GRCm39 (Ensembl Mus_musculus)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Splenic pDC

extract_protocol:
CD11c+B220+SiglecH+ pDCs were sorted through flow cytometry from low density DC enriched fraction from spleen of IRF8WT and IRF8R294C mice and immediately lysed in RNAiso Plus. RNA was extracted using Qiagen Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

tag: genotype

value: IRF8 R294C

tag: age

value: 8-12 weeks


title: Methylation_HC5_sp1_Normal_NAC_ox21_p18

value: Primary Human Fibroblast (forearm)


title: HC2_sp2_Normal_DEX_ox21_p9

source_name: Primary Human Fibroblast (breast)

value: female


title: HC1_sp2_Normal_DEX_ox21_p27


title: IRF8R294C 2


title: Freshly sorted MHC-IIlo TAM Biological replicate 1

description:
Freshly sorted MHC-IIloTAMs from subcutaneous 3LL-R tumors
MHC-IIlo TAM_1

value: WT

value: 3LL-R subcutaneous tumor tissue


title: Methylation_HC5_sp1_Normal_NAC+DEX_ox21_p9


title: Freshly sorted MHC-IIhi TAM Biological replicate 5

description:
Freshly sorted MHC-IIhi TAMs from subcutaneous 3LL-R tumors
MHC-IIhi TAM_5

value: Tumor-associated macrophage


title: IRF8R294C 1


title: Methylation_HC5_sp1_Normal_NAC_ox21_p13


title: Methylation_HC5_sp1_Normal_NAC_ox21_p16


title: HC1_sp2_Normal_DEX_ox21_p24

value: DEX


title: Methylation_HC5_sp1_Normal_NAC_ox21_p9


title: Methylation_HC5_sp1_Normal_NAC_ox21_p20


title: Freshly sorted MHC-IIhi TAM Biological replicate 2

description:
Freshly sorted MHC-IIhi TAMs from subcutaneous 3LL-R tumors
MHC-IIhi TAM_2


title: Freshly sorted MHC-IIhi TAM Biological replicate 4

description:
Freshly sorted MHC-IIhi TAMs from subcutaneous 3LL-R tumors
MHC-IIhi TAM_4


title: HC1_sp2_Normal_DEX_ox21_p21


title: HC1_sp2_Normal_DEX_ox21_p15


title: IRF8WT 1

value: IRF8 WT


title: Methylation_HC5_sp1_Normal_MitoQ+DEX_ox21_p25

value: MitoQ+DEX


title: IRF8WT 3


title: Freshly sorted MHC-IIhi TAM Biological replicate 1

description:
Freshly sorted MHC-IIhi TAMs from subcutaneous 3LL-R tumors
MHC-IIhi TAM_1


title: HC1_sp2_Normal_DEX_ox21_p18

value: Primary Human Fibroblast (breast)


title: HC1_sp2_Normal_DEX_ox21_p12

value: Normal


title: IRF8WT 2


title: BS-seq_G9a_GLP_DKO_ExE

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

institute: Technical University Munich

data_processing:
The RNA-seq data were aligned to the mm10 reference genome using the STAR aligner (Dobin et al., 2013) (STAR version 2.5.0 c: –outFilterMultimapNmax 1). The read counts for every RefSeq isoform (RefSeq gene annotation (downloaded February 2018) were determined using the htseq-count pythonphyton script (Anders et al., 2015) (version 0.6.1) and further normalized in R. The Allelome.PRO approach was used to calculate allele-specific expression from the RNA-seq data as outlined in (Andergassen et al., 2015). Briefly, the Allelome.PRO pipeline uses strain-specific single-nucleotide polymorphisms (SNPs) to assign RNA-seq reads to the corresponding allele in F1 crosses. To obtain allele-specific ratios and scores from a single replicate, we slightly modified the Allelome.PRO pipeline and uploaded the modified version on SourceForge (https://sourceforge.net/projects/allelomepro/).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: ExE

growth_protocol: Embryos were generated as previously described (Wang et al., 2013). Briefly, BDF1 strain female mice (age 6–8 weeks, Jackson Labs) were superovulated by serial Pregnant Mare Serum Gonadotropin (5 IU per mouse, Prospec Protein Specialists) and human chorionic gonadotropin (5 IU, Millipore) injections 46 h apart. The following day, MII stage oocytes were isolated in M2 media supplemented with hyaluronidase (Millipore) and stored in 25 μl drops of pre-gassed KSOM with half-strength concentration of amino acids (Millipore) under mineral oil (Irvine Scientific). Zygotes were generated by piezo-actuated intracytoplasmic sperm injection (ICSI. See (Grosswendt et al., 2020)) using thawed CAST strain sperm in batches of 30–50 oocytes and standard micromanipulation equipment, including a Hamilton Thorne XY Infrared laser, Eppendorf Transferman NK2 and Patchman NP2 micromanipulators, and a Nikon Ti-U inverted microscope. Zygotes for whole genome bisulfite sequencing were generated by natural mating with BDF1 males. For the reciprocal cross, BDF1 males were naturally mated to CAST females and screened for copulation plugs, after which E6.5 stage embryos were isolated accordingly, with the date of the copulation plug score day E0.5. For zygotic disruption, pronuclear stage 3 (PN3) zygotes were injected with 200 ng μl−1 Cas9 mRNA and a 100 ng μl−1 equimolar ratio of 3–4 sgRNAs targeting different exons of an epigenetic regulator gene locus (designed using ChopChop (Labun et al., 2016) and the IDT CRISPR–Cas9 guide RNA checker, as previously described in (Smith et al., 2017)). We designed the gRNA to avoid CAST SNPs to ensure that the gRNAs are equally effective between the alleles. Injections utilized the same microinjection setup and Piezo-actuated injection of front-filled 6-7 μm injection needles. At around 84 h after fertilization, cavitated blastocysts were transferred into the uterine horns of pseudopregnant CD-1 strain females (25–35g, Charles River) generated by mating with vasectomized SW strain males (Taconic), which results in a 24 h offset in gestational time to accommodate implantation, after which animals were monitored for 5 days for embryo isolation at E6.5.

extract_protocol:
At E6.5, animals were euthanized and the uterine horn removed. Purified epiblast and ExE were isolated according to Ref. (Chenoweth and Tesar, 2010) with a few modifications. Briefly, E6.5 embryos were removed from deciduae and transferred to independent 25 μL drops of M2 media. Using a glass flame-pulled capillary, Reichart’s membrane was reflected, and the embryo carefully bisected along the epiblast, ExE boundary. Then, each Epiblast/ExE pair was transferred into an individual drop of dissociation medium containing 0.5% trypsin and 2.5% pancreatin in PBS (w/v, Sigma). Embryos were cultured with slow orbital rotation at 4ºC for 15 minutes, after which they were transferred into new M2 drops. After ~5 minutes of resting, Epiblast and ExE were passed through a slightly narrower flame-pulled glass capillary to remove the visceral endoderm without disrupting the target tissue. Finally, each tissue was serially washed in 0.1% BSA in PBS prior to snap freezing in lysis buffer.
Approximately 300-600 cells were collected from E6.5 embryos and directly transferred to 2.6 µl of Lysis Buffer (Takara Bio USA, Inc.) followed by snap-freezing at -80°C in preparation for cDNA synthesis using the SMART-Seq v4 assay. Full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and sequencing libraries prepared using the Nextera XT DNA library preparation kit (Illumina). The resulting libraries were evaluated using a 4200 TapeStation (Agilent Technologies) and quantified by qPCR. Libraries were pooled and sequenced on an Illumina NovaSeq SP or S1 flow cell using paired-end, 50 bp reads. The E6.5 ExE ∆G9a-Glp sample was isolated and processed into WGBS libraries using the Accel-NGS Methyl-seq kit as described in (Grosswendt et al., 2020) and sequenced on an Illumina NovaSeq using paired-end, 150 bp reads.

value: ExE (Extraembryonic Ectoderm)

tag: background


title: Methylation_HC5_sp1_Normal_MitoQ+DEX_ox21_p18


title: Fetal liver with Cite-Seq

description: CD71/CD24low cells mouse feta liver cells isolated using magnet and FACS methods and tagged with CITEseq antibodies

source_name: mouse fetal liver from E14.5 pregnant mice

value: CD71/CD24low cells

tag: tag

value: CD117 oligo:  TGCATGTCATCGGTG  CD71 oligo: ACCGACCAGTAGACA


title: Methylation_HC5_sp1_Normal_MitoQ+DEX_ox21_p16

value: male


title: HC1_sp2_Normal_DEX_ox21_p9


title: TauPS2APP [SAM24401891]

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Single-cell RNA sequencing data were processed with an in-house analysis pipeline as described (https://www.sciencedirect.com/science/article/pii/S2211124719317656). Reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.
For each sample, L001 and L002 denote the sequencing lane. I1 refers to the index. R1 and R2 indicate read 1 and 2, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary file TsneCoordinatesAndClusterAssignments.txt contains sample ID and genotype for each cell, as well as tSNE coordinates, SingleCellExperiment clusters and biological interpretations of SingleCellExperiment clusters. As described in the manuscript, interpretations "Neuron" and "Neuron-Reelin" were combined for differential expression analysis. Cells with expression of two or more cell types were labled as "Double-positive"

source_name: Hippocampus

extract_protocol:
Single cell suspensions were processed using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) and Chromium Next GEM Chip G Single Cell Kit (10X Genomics, PN-1000120) following manufacturer’s user guide. Cell-RT mix was prepared to aim 1,000 cells per sample and applied to Chromium™ Controller for GEM generation and barcoding. Then, samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles), and library construction according to the user guide. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626). Libraries were sequenced by Novaseq (Illumina) following 10X Genomics sequencing specification.
cDNAs and libraries were prepared according to manufacturer instructions (10X Genomics)

tag: genotype/variation


title: Methylation_HC5_sp1_Normal_MitoQ+DEX_ox21_p13

tag: Sex


title: PS2APP [SAM24401890]


title: HC1_sp2_Normal_DEX_ox21_p6

tag: treatments


title: Methylation_HC6_sp1_Normal_MitoQ+DEX_ox21_p17

tag: passage


title: Viral_2-2

description:
RCM_viralInfected_2.txt.txt.gz
MCMVinfected_2

data_processing:
Raw base call (BCL) files were demultiplexed to generate Fastq files using the cellranger mkfastq pipeline within Cell Ranger 3.0.3 (10x Genomics). Whole transcriptome Fastq files were processed using the standard cellranger pipeline within Cell Ranger 3.0.3 (10x genomics) against the merged genomes of GRCm38 (Ensembl v90) and MCMV (BAC derived wild type Smith strain, Accession Identifier: NC_004065). The expected cell parameter was set to 10,000 for all libraries. Briefly, cellranger count performs alignment, filtering, barcode counting, and UMI counting to obtain read count matrices (RCM). In total four RCMs were obtained, with two independent experiments performed for both virally infected and steady-state condition.
RCMs were further processed via R (version 3.6.2) using Seurat (version 3.1.5) and uwot (version 0.1.8). Cells with at least 1000 detected genes and < 7.5% mitochondrial reads were retained in the analysis. Analysis was performed in a stepwise manner to successively identify and focus on RPSC, WPSC and Pv/VSMC. Genes were included if they were expressed in at least 1 % of the cells.
Initially, the four RCMs were merged using FindIntegrationAnchors(list(experimental_batches), anchor.features = 1000, dims = 1:15, k.filter = 200, k.anchor = 10) and IntegrateData(). Data was scaled and regressed against the variables percent mitochondrial UMIs, percent ribosomal protein UMIs, percent viral UMIs and the total number of UMIs per cell. PCAs were computed using default settings. Uniform Manifold Approximation and Projection (UMAP) dimensional reduction via RunUMAP() and FindNeighbors() were performed using the first 15 PCA dimensions as input features.  FindClusters() was computed at resolution 0.4. In total 50401 cells with 16426 detected genes were processed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read-count matrices for each replicate.

source_name: splenic stroma

extract_protocol:
Single surface-decorated CD45-/+ITGB1hiCD31- cells were sorted by FACS ARIA II sorter (BD) and collected in PBS containing 0.04% w/v BSA at a densitiy of 400 cells/μl. Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and
Single Cell 3’ reagent kit v3 for reverse transcription, cDNA amplification and library construction (10xGenomics).
Sequencing was performed in paired-end mode (2 × 75 cycles) using NextSeq 500 sequencer (Illumina) to attain approximately 35,000 reads per single cell.

treatment_protocol: Five-months-old C57BL/6Jrj female mice were i.p. injected with 10exp6 pfu of bacterial artificial chromosome–derived mCMV (pSM3fr-MCK-2 full-length; J Virol. 2011; 85(19):10346-53) or MOCK and sacrificed 24 hours p.i. Cells were sorted from pooled splenic preparations from 3 mice per condition.

tag: sample type

value: ex vivo isolated cells


title: NonTg [SAM24401889]

value: NonTg


title: Methylation_HC5_sp1_Normal_MitoQ+DEX_ox21_p9

data_processing:
RStudio (v1.3.1056) using R (v4.0.2). Preprocessing was performed using the 'minfi' (v1.36.0) library and batch corrections using the 'sva' (v3.12.0) library. Quality control excluded 22 samples for a final total of 479 samples.
processed data file contains: ormalized Beta (Functional normalization)

extract_protocol: DNA was extracted using the DNeasy kit (Qiagen cat#69506) according to the manufacturer’s protocol and quantified using QUBIT broad range kit (Thermo Fisher Scientific cat#Q32852).

tag: slide

tag: array


title: Viral_2-1


title: Viral_1-2

description:
RCM_viralInfected_1.txt.txt.gz
MCMVinfected_1


title: Technical_replicate_sp2_Normal__ox21_p_70

data_processing:
360 samples were sent for sequencing; 9 samples did not passed intial QC (low RIN score, high DNA contamination), and 6 samples did not pass post-sequencing QC, for a final of 345 samples.
kallisto alignment v0.44.0 (Bray et al., 2016) using the hg19 genome. Sequence and annotation files were downloaded from the NCBI ftp portal for genome version GRCh37.p13
txi import using lengthScaledTPM (‘tximport’, v1.18.0)
vst normalization (‘DEseq2’, v1.30.1).
log2 transformation
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with log2 transformed vst normalized expression values for every gene and every sample
processed_cell_lifespan_RNAseq_data.csv: log2 vst normalized expression values
raw_counts_cell_lifespan_RNAseq_data.csv: raw counts as outputted by kallisto alignment
txi_transcript_abundance.csv: transcript abundances (‘tximport’, v1.18.0)
txi_transcript_count_lengthScaledTPM.csv: transcript counts length-scaled TPM (‘tximport’, v1.18.0)
txi_transcript_length.csv: transcript lengths (‘tximport’, v1.18.0)
txi_gene_abundance.csv: gene abundances (‘tximport’, v1.18.0)
txi_gene_count_lengthScaledTPM.csv: gene counts length-scaled TPM (‘tximport’, v1.18.0)
txi_gene_length.csv: gene lengths (‘tximport’, v1.18.0)

extract_protocol:
Total genomic RNA was isolated every ~11days across cellular lifespan and stored in 1ml trysol (Invitrogen cat#15596026). RNA was extracted on-column using a RNeasy kit (Qiagen cat# 74104), DNase treated according to the manufacturer’s instructions, and quantified using the QUBIT high sensitivity kit (Thermo Fisher Scientific cat#Q32852). RNA samples underwent QC on bioanalyzer and Nanodrop 2000, all samples had a RIN score >8.0 and no detectable levels of DNA. For cDNA library preparation,1,500ng of RNA at 50ng/μl was processed using Ribo-Zero Gold purification (QIAseq FastSelect -rRNA HMR Kit #334387) and NEBNext® Ultra™ II RNA Library Prep Kit (Illumina #E7770L))  (1,500ng/sample, 50ng/μl). cDNA was sequenced using paired-end 150bp chemistry on a HiSeq 4000 instrument (Illumina, single index, 10 samples/lane, Genewiz Inc), yielding  ~40 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Control


title: SURF1_3_sp2_SURF1_Mutation_DEX_ox21_p36

value: Primary Human Fibroblast (forearm)


title: Viral_1-1


title: Methylation_HC6_sp1_Normal_MitoQ_ox21_p10

value: female

value: MitoQ

tag: well


title: Steady_2-2

description:
RCM_steadyState_2.txt.txt.gz
SteadyState_2

tag: treatment


title: SURF1_3_sp2_SURF1_Mutation_DEX_ox21_p26


title: Methylation_HC6_sp1_Normal_MitoQ_ox21_p17


title: PS2APP [SAM24401887]


title: NonTg [SAM24401886]


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p25


title: SURF1_3_sp2_SURF1_Mutation_DEX_ox21_p20


title: Steady_2-1


title: SURF1_3_sp2_SURF1_Mutation_DEX_ox21_p23


title: TauPS2APP [SAM24401885]


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p20


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p33


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p18


title: Freshly sorted MHC-IIhi TAM Biological replicate 3

description:
Freshly sorted MHC-IIhi TAMs from subcutaneous 3LL-R tumors
MHC-IIhi TAM_3

value: WT

tag: tissue

value: 3LL-R subcutaneous tumor tissue


title: Steady_1-1

description:
RCM_steadyState_1.txt.txt.gz
SteadyState_1

tag: strain


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p16


title: NonTg [SAM24401883]


title: PS2APP [SAM24401884]


title: TauPS2APP [SAM24401888]


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p13


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p28

value: DEX


title: NonTg [SAM24401880]


title: Steady_1-2


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p22


title: PS2APP [SAM24401881]


title: Methylation_HC6_sp1_Normal_Pulsated_DEX_ox21_p14


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p19


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p16


title: Th17 cells + inhibitor + IgG

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
Library strategy: CUT&RUN
Trimmomatic (version 0.39)
bowtie2 (version 2.3.5.1)
deeptools (version 3.3.1)
macs2 (version 2.2.7.1)
DiffBind (version 2.16.2)
Genome_build: mm10
Supplementary_files_format_and_content: Called peaks in macs2 format

growth_protocol: CD4 cells were isolated by negative selection from spleens and lymph nodes of 8 week old C57BL/6 mice and activated on anti-CD3 and anti-CD28 antibody coated plates with cytokines to promote Th17 and Treg differentiation. Cells were cultured for 72 hours before collection.

extract_protocol:
CUT&RUN
KAPA Hyper Prep

treatment_protocol: Cells were treated with either DMSO (vehicle) or 500nM DS18561882 (MTHFD2i) for 72 hours.

value: inhibitor

tag: antibody

value: IgG


title: Methylation_HC6_sp1_Normal_Pulsated_DEX_ox21_p12


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p13


title: Th17 cells + inhibitor + anti-H3K27me3_C

tag: cell type


title: Methylation_HC6_sp1_Normal_Pulsated_DEX_ox21_p10


title: Methylation_HC5_sp1_Normal_MitoQ_ox21_p9


title: SURF1_3_sp2_SURF1_Mutation_DEX_ox21_p14


title: SURF1_2_sp2_SURF1_Mutation_DEX_ox21_p10


title: Methylation_HC5_sp1_Normal_Pulsated_DEX_ox21_p18


title: Methylation_HC5_sp1_Normal_Pulsated_DEX_ox21_p20


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p32


title: Th17 cells + DMSO + IgG

value: DMSO


title: Th17 cells + inhibitor + anti-H3K27me3_A


title: CLDX n3 (JE285), MOLM14 ARAC treatment

type: RNA

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

description: MOLM14 cell line xenografts (CLDXs)

hyb_protocol: cRNA products were randomly fragmented and labeled prior hybridization onto Affymetrix GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were preprocessed using TAC sofware with GC correction followed by RMA.

label: biotin

label_protocol: 100 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 703174 Rev.2 )

growth_protocol: 2x106 MOLM-14 cells were injected into mice for a Cell Line Derived Xenograft (CLDX). The tumor grow for 10 days before treatment.

extract_protocol: After one week of treatment, mice bone marrow and spleen were collected. Then viable bone marrow human AML cells (CD45+CD33+AnnexinV-) were sorted and RNA-seq was processed.

treatment_protocol: The treatment consisting in 5 days of AraC treatment (30 mg/kg) by intra-peritoneal injection, in association with 7 days of venetoclax treatment (100 mg/kg) by oral gavage.

tag: cell line

tag: batch

tag: idhstatus

value: ARAC


title: CLDX n2 (JE280), MOLM14 WT VEN+ARAC treatment

description: MOLM14 cell line xenografts (CLDXs)


title: CLDX n3 (JE285), MOLM14 VEN+ARAC treatment

description: MOLM14 cell line xenografts (CLDXs)


title: CLDX n3 (JE285), MOLM14 CTL treatment

description: MOLM14 cell line xenografts (CLDXs)

value: CTRL


title: CLDX n2 (JE280), MOLM14 WT ARAC treatment

description: MOLM14 cell line xenografts (CLDXs)


title: CLDX n2 (JE280), MOLM14 WT CTL treatment

description: MOLM14 cell line xenografts (CLDXs)


title: Th17 cells + DMSO + anti-H3K27me3_A


title: Th17 cells + DMSO + anti-H3K27me3_C


title: CLDX n1 (JE278), MOLM14 R132H VEN+ARAC treatment

description: MOLM14 cell line xenografts (CLDXs)


title: Methylation_HC6_sp1_Normal_DEX_ox21_p17

value: Normal


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p26


title: Methylation_HC5_sp1_Normal_Pulsated_DEX_ox21_p16


title: Th17 cells + inhibitor + anti-H3K27me3_B


title: Methylation_HC5_sp1_Normal_Pulsated_DEX_ox21_p13


title: Th17 cells + DMSO + anti-H3K27me3_B


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p23


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p14


title: Treg cells + inhibitor + IgG

source_name: Treg

value: Treg


title: Treg cells + inhibitor + anti-H3K27me3_C


title: Methylation_HC5_sp1_Normal_DEX_ox21_p27

value: male


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p17


title: Treg cells + inhibitor + anti-H3K27me3_B


title: Methylation_HC5_sp1_Normal_DEX_ox21_p23


title: Technical_replicate_sp2_Normal__ox21_p_50

value: Primary Human Fibroblast (breast)


title: Treg cells + inhibitor + anti-H3K27me3_A


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p11


title: Methylation_HC5_sp1_Normal_DEX_ox21_p18


title: Treg cells + DMSO + IgG


title: HC3_sp2_Normal_Control_ox21_p31

source_name: Primary Human Fibroblast (foreskin)

value: Primary Human Fibroblast (foreskin)


title: Methylation_HC5_sp1_Normal_DEX_ox21_p16


title: CLDX n1 (JE278), MOLM14 R132H ARAC treatment

description: MOLM14 cell line xenografts (CLDXs)


title: CLDX n1 (JE278), MOLM14 R132H CTL treatment

description: MOLM14 cell line xenografts (CLDXs)


title: Treg cells + DMSO + anti-H3K27me3_C


title: HC3_sp2_Normal_Control_ox21_p25

value: Control


title: Methylation_HC5_sp1_Normal_DEX_ox21_p13

value: Primary Human Fibroblast (forearm)


title: Treg cells + DMSO + anti-H3K27me3_A


title: 33_III_ExE_Eed

data_processing:
The RNA-seq data were aligned to the mm10 reference genome using the STAR aligner (Dobin, A. et al. 2013, Bioinformatics, STAR version 2.5.0 c: –outFilterMultimapNmax 1). The read counts for every RefSeq isoform (RefSeq gene annotation (downloaded February 2018) were determined using the htseq-count phyton script (Anders, S. et al. 2015 Bioinformatics, version 0.6.1) and further normalized in R. The Allelome.PRO approach was used to calculate allele-specific expression from the RNA-seq data as outlined in Andergassen D. et al. 2015 NAR. Briefly, the Allelome.PRO pipeline uses strain-specific single-nucleotide polymorphisms (SNPs) to assign RNA-seq reads to the corresponding allele in F1 crosses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

value: ExE (Extraembryonic Ectoderm)

tag: age

tag: background

tag: genotype

value: {delta}Eed

value: M

tag: embryo


title: HC3_sp2_Normal_Control_ox21_p16

tag: Sex

tag: treatments

tag: passage


title: 32_III_ExE_Eed


title: Methylation_HC6_sp1_Normal_Control_ox21_p17

value: female

tag: slide

tag: array


title: HC3_sp2_Normal_Control_ox21_p10


title: HC3_sp2_Normal_Control_ox21_p22


title: Methylation_HC5_sp1_Normal_DEX_ox21_p9

value: DEX

tag: well


title: Methylation_HC6_sp1_Normal_Control_ox21_p12


title: Treg cells + DMSO + anti-H3K27me3_B

tag: treatment


title: Methylation_HC6_sp1_Normal_Control_ox21_p14


title: 31_I_epi_Eed

source_name: Epiblast

tag: tissue

value: Epiblast


title: HC2_sp2_Normal_Control_ox21_p36


title: Methylation_HC6_sp1_Normal_Control_ox21_p10


title: 31_III_ExE_Eed

value: F


title: 32_I_epi_Eed


title: HC3_sp2_Normal_Control_ox21_p13


title: Methylation_HC6_sp1_Normal_Control_ox21_p5


title: 30_I_epi_Eed


title: Methylation_HC6_sp1_Normal_Control_ox21_p7


title: Methylation_HC5_sp1_Normal_Control_ox21_p25


title: HC2_sp2_Normal_Control_ox21_p30


title: HC2_sp2_Normal_Control_ox21_p33


title: 30_III_ExE_Eed


title: HC2_sp2_Normal_Control_ox21_p27


title: SURF1_1_sp2_SURF1_Mutation_DEX_ox21_p29


title: HC3_sp2_Normal_Control_ox21_p19


title: 26_III_ExE_Eed


title: HC2_sp2_Normal_Control_ox21_p24


title: Methylation_HC5_sp1_Normal_Pulsated_DEX_ox21_p9


title: 26_I_epi_Eed


title: CAGE-GP5d

data_processing:
The 5' ends of the GP5d CAGE reads contain a 3-bp barcode (ATC) followed by a 6 bp constant sequence (CAGCAG). In addition to removing these, the next 2 bp that were mostly Gs, according to a FastQC quality control report, were discarded. The reads were aligned to a combined Phi X 174 + hg19 reference genomes using bwa aln (version 0.7.15-r1142-dirty) with parameters ‘-t 8 -B 11 -q 30’.
Only the reads mapping to hg19 with MAPQ 30 or higher were extracted and duplicates were removed with samtools rmdup (version 1.3.1).
The strand specific 5'-end coverages of the mapped reads were computed with bedtools genomecov (version 2.27.1).
The active promoters were discovered from the mapped CAGE reads by clustering the 5'-ends of the reads with paraclu software. In total, paraclu called 7365 clusters (peaks) from the GP5d CAGE data fulfilling the following criteria: 1) Cluster is supported by more than 9 unique reads. 2) Cluster cannot be longer than 200 bp. 3) Remove clusters where the maximum 5’ end density per base divided by the baseline density is less than 2. 4) Remove any cluster that is contained within a larger cluster.
Genome_build: hg19
Supplementary_files_format_and_content: Strand specific 5'-end coverages in .genomecov files, columns are: chromosome, position, 5'-end coverage. Paraclu filtered clustering output, columns are: chromosome, strand, start, end, sites, sum of values, min d, max d

source_name: GP5d cell line

growth_protocol: GP5d cells were cultured in DMEM with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
Total RNA was isoated and CAGE library was prepared essentially as described in Takahashi et al. Nature Protocols 2012.
CAGE library preparation protocol as described in Takahashi et al. Nature Protocols 2012.
Illumina library preparation adapted for CAGE

treatment_protocol: Untreated

value: colon cancer cell line


title: HC2_sp2_Normal_Control_ox21_p21


title: 25_III_ExE_Eed


title: Methylation_HC5_sp1_Normal_Control_ox21_p6

source_name: Primary Human Fibroblast (forearm)


title: Methylation_HC5_sp1_Normal_Control_ox21_p13


title: 25_I_epi_Eed


title: Methylation_HC5_sp1_Normal_Control_ox21_p9


title: 24_III_ExE_Eed


title: Methylation_HC5_sp1_Normal_Control_ox21_p4


title: Tumor_RNA

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using STAR (v2.7.0f)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Kidney

extract_protocol:
Beckman Coulter FormaPure Total DNA & RNA extraction
Agilent RNA Direct

tag: condition

value: Tumor

value: kidney


title: Methylation_HC5_sp1_Normal_Control_ox21_p20

value: Normal


title: HC2_sp2_Normal_Control_ox21_p9


title: Methylation_HC5_sp1_Normal_Control_ox21_p16


title: 23_III_ExE_Eed


title: 24_I_epi_Eed


title: Normal.kidney_RNA