title: Tom- LCMV-specific T cells day 8 - SI IEL - rep 2

description: Tom‒ LCMV-specific effector T cells

value: Effector memory CD8+ T cells

value: small intestine

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: Tom- LCMV-specific T cells day 8 - SI IEL - rep 1

status: Public on Aug 19 2021

type: SRA

city: Amsterdam

first: Klaas

last: van Gisbergen

state: Select one

address: Plesmanlaan 125

department: Department of Hematopoiesis

country: Netherlands

institute: Sanquin Research and Landsteiner Laboratory

description: Tom‒ LCMV-specific effector T cells

library_source: transcriptomic

data_processing:
Barcodes were removed using the fastx_barcode_splitter script from the fastx toolkit v0.0.14
Read mapping was performed using STAR(v2.5.3a) against mouse genome mm10.
Read count quantification was done with featureCounts (v1.5.2) using Ensembl’s v92 annotation with a minor modification to correct for incorrect intron/exon boundaries in Zfp683 (Hobit) locus.
Read count normalization was done using the cmp() function of EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: small intestine

growth_protocol: All mice were maintained under specific pathogen-free (SPF) conditions

extract_protocol:
SI IEL and LPL preparations were obtained from the small intestine. After removal of residual fat tissue, Peyer’s patches, and feces, small intestine tissue was cut into pieces of 1 cm and incubated in Hanks’ balanced slat solution (HBSS, Gibco) with 10% fetal calf serum (FCS), 5 mM EDTA, and 1 mM dithiothreitol (DTT) for 30 min at 37°C. After repeated vortexing, the IEL fraction was released from the tissue and isolated by filtering over a 70 μm cell strainer. Subsequently, IEL-depleted intestine pieces were washed in HBSS supplemented with 2% FCS and enzymatically digested for 30 min at 37 °C with 375 U ml-1 Collagenase Type I (Worthington) and 0.15 mg ml-1 DNase I (Roche, from bovine pancreas, grade II) in RPMI 1640 (supplemented with 10% FCS) to isolate the LPL fraction. Similarly, kidneys were cut into pieces of 1 mm3, which were enzymatically digested for 30 min at 37 °C with 750 U ml-1 Collagenase Type I (Worthington) and 0.31 mg ml-1 DNase I (Roche, from bovine pancreas, grade II) in RPMI 1640 (supplemented with 10% FCS). Single cell suspensions from the LPL fraction of small intestine, kidney, spleen, LNs and liver were prepared by mechanical disruption via passing over a 70 μm cell strainer. The isolated lymphocytes from liver, kidney, SI IEL and LPL were purified by density centrifugation on a 60% / 40% Percoll gradient (GE Healthcare). Contaminating erythrocytes were removed using red blood cell lysis buffer (155mM NH4Cl, 10mM KHCO3, 0,1mM EDTA).
Library construction was performed by Single Cell Discoveries (The Netherlands) using the CEL-Seq protocol as published in Hashimshony et al. Cel Rep 2012 (doi:j.celrep.2012.08.003).

treatment_protocol: Mice were infected intraperitoneally with 10^5 plaque-forming units (PFU) of LCMV Armstrong obtained from EVAg, or with 10^4 PFU of replication sufficient rLCMV OVA

tag: cell type

tag: tissue

tag: genotype


title: Tom- LCMV-specific TEM cells day >30 - Spleen - rep 1

description: Tom‒ LCMV-specific TEM cells

source_name: spleen

value: spleen


title: Tom+ LCMV-specific T cells day 8 - SI IEL - rep 3

description: Tom+ LCMV-specific effector T cells

value: Tissue-resident memory CD8+ T cells


title: Tom+ LCMV-specific TRM cells day >30 - Liver - rep 3

description: Tom+ LCMV-specific TRM cells

source_name: liver

value: liver


title: 160 HMEC 4p MEP rep 1

city: Duarte

first: Rosalyn

middle: W.

last: Sayaman

state: CA

address: 1500 E Duarte Rd

country: USA

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14918_160_MEP_RNA_ACTGAT

data_processing:
Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle. Real-time analysis (RTA v2.2.38) software was used to process the image analysis.
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic [Bolger et al., 2014]. The processed reads were mapped back to the human genome (hg19) using TOPHAT2 software [Kim et al., 2013].
HTSeq [Anders and Huber, 2010] and RSeQC [Wang et al., 2012] software were applied to generate the count matrices and strand information, respectively with default parameters.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix table of raw counts for 120 samples encompassing 34,623 transcripts mapped to Ensembl IDs.

organism: Homo sapiens

source_name: Human Mammary Epithelial Cells

growth_protocol: Primary HMECs were established from organoids isolated from collected breast tissue samples. HMECs were maintained and grown to 4th passage according to previously reported protocol using M87A medium containing cholera toxin and oxytocin at 0.5 ng/ml and 0.1nM, respectively [LaBarge et al., 2013, Garbe et al., 2009].

extract_protocol:
KAPA stranded mRNA-seq kit
Total RNAs were isolated from enriched LEPs and MEPs with Quick-RNA Microprep Kit (Zymo Research, R1050). For RNA-seq, isolated RNAs were submitted to Integrative Genomic Core at City of Hope (IGC at COH) for library preparation and sequencing.
RNA sequencing libraries were prepared with Kapa RNA mRNA HyperPrep Kit (Kapa Biosystems, Cat KR1352) or KAPA stranded mRNA-seq (Kapa Biosystems, Cat KK8420) according to the manufacturer's protocol. 100 ng of total RNA from each sample was used for polyA RNA enrichment. The enriched mRNA underwent fragmentation and first strand cDNA synthesis. The combined 2nd cDNA synthesis with dUTP and A-tailing reaction generated the resulting ds cDNA with dAMP to the 3’ ends.  The barcoded adaptors were ligated to the ds cDNA fragments. A 10-cycle of PCR was performed to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

treatment_protocol: LEP and MEP enrichment was performed across multiple studies (Sayaman, Miyano et al., 2021, Shalabi et al., 2021, Todhunter et al., 2021). Enrichment was conducted by FACS or EasySEP Cell Separation (Stem Cell Technologies) using well-established LEP-specific cell-surface markers: CD227 (anti-human CD227-FITC, BD Biosciences, clone HMPV) or CD133 (anti-human CD133-PE, BioLegend, clone7), and MEP-specific cell-surface marker: CD271 (anti-human CD271-APC, BioLegend, clone ME20.4). Protocols were validated and found to sort similar populations regardless of antibody combination and enrichment methodology. Breast epithelial cells were stained following standard flow cytometry protocol.

value: breast

tag: age

value: Not Reported

tag: chemotherapy

value: No chemo

value: Reduction Mammaplasty

value: RM

value: Myoepithelial cells

value: MEP

value: HMEC 4p

value: FACS (BD FACSVantage)

value: Mark A. LaBarge

tag: institution

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Tom+ LCMV-specific T cells day 8 - SI IEL - rep 1

description: Tom+ LCMV-specific effector T cells


title: Tom+ LCMV-specific T cells day 8 - SI IEL - rep 2

description: Tom+ LCMV-specific effector T cells


title: 215C HMEC 4p MEP rep 1

department: Population Sciences, Beckman Research Institute

institute: City of Hope Comprehensive Cancer Center

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14920_215C_MEP_RNA_CGATGT

value: Contralateral-to-Tumor

value: CLTT


title: 191L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14911_191L_LEP_RNA_CCGTCC

value: Luminal epithelial cells

value: LEP


title: 101P HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14912_101P_MEP_RNA_GTCCGC

value: Peripheral-to-Tumor

value: PTT


title: 353P HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14925_353P_LEP_RNA_GGCTAC

value: breast


title: 172L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14908_172L_MEP_RNA_AGTCAA

value: Not Reported


title: 59L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14907_59L_LEP_RNA_CTTGTA

value: No chemo


title: Tom+ LCMV-specific T cells day 8 - Kidney - rep 3

description: Tom+ LCMV-specific effector T cells

source_name: kidney

value: Tissue-resident memory CD8+ T cells

value: kidney

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: 172L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14909_172L_LEP_RNA_AGTTCC

value: Reduction Mammaplasty

value: RM


title: Tom+ LCMV-specific T cells day 8 - Kidney - rep 1

description: Tom+ LCMV-specific effector T cells


title: Tom- LCMV-specific T cells day 8 - Liver - rep 2

description: Tom‒ LCMV-specific effector T cells

value: Effector memory CD8+ T cells

value: liver


title: 101P HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14913_101P_LEP_RNA_GTGAAA

value: HMEC 4p

value: FACS (BD FACSVantage)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: 122L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14905_122L_LEP_RNA_GATCAG

value: Luminal epithelial cells

value: LEP


title: 191L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14910_191L_MEP_RNA_ATGTCA

value: Myoepithelial cells

value: MEP


title: Tom- LCMV-specific T cells day 8 - Kidney - rep 1

description: Tom‒ LCMV-specific effector T cells


title: 160 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14919_160_LEP_RNA_ATTCCT

value: breast

value: Not Reported


title: Tom+ LCMV-specific T cells day 8 - Kidney - rep 2

description: Tom+ LCMV-specific effector T cells

value: Tissue-resident memory CD8+ T cells


title: Tom- LCMV-specific T cells day 8 - Liver - rep 3

description: Tom‒ LCMV-specific effector T cells


title: Tom- LCMV-specific T cells day 8 - Kidney - rep 2

description: Tom‒ LCMV-specific effector T cells

value: kidney


title: 59L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14906_59L_MEP_RNA_GGCTAC

value: No chemo


title: Tom- LCMV-specific T cells day 8 - Liver - rep 1

description: Tom‒ LCMV-specific effector T cells

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: Tom- LCMV-specific T cells day 8 - Kidney - rep 3

description: Tom‒ LCMV-specific effector T cells


title: Tom+ LCMV-specific T cells day 8 - Liver - rep 3

description: Tom+ LCMV-specific effector T cells


title: 122L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14904_122L_MEP_RNA_CAGATC

value: Reduction Mammaplasty

value: RM


title: Tom+ LCMV-specific T cells day 8 - Liver - rep 1

description: Tom+ LCMV-specific effector T cells

value: liver


title: Tom+ LCMV-specific T cells day 8 - Liver - rep 2

description: Tom+ LCMV-specific effector T cells


title: 249P HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14903_249P_LEP_RNA_GCCAAT

value: Peripheral-to-Tumor

value: PTT

value: HMEC 4p


title: Tom- LCMV-specific T cells day 8 - Spleen - rep 3

description: Tom‒ LCMV-specific effector T cells

value: Effector memory CD8+ T cells

value: spleen


title: 237 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14901_237_LEP_RNA_CGATGT

value: Luminal epithelial cells

value: LEP

value: FACS (BD FACSVantage)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Tom- LCMV-specific T cells day 8 - Spleen - rep 2

description: Tom‒ LCMV-specific effector T cells


title: 237 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14900_237_MEP_RNA_ATTCCT

value: breast

value: Not Reported

value: Myoepithelial cells

value: MEP


title: 240L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14899_240L_LEP_RNA_ACTGAT

value: No chemo

value: Reduction Mammaplasty


title: 240L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14898_240L_MEP_RNA_GAGTGG

value: RM


title: Tom- LCMV-specific T cells day 8 - Spleen - rep 1

description: Tom‒ LCMV-specific effector T cells

value: CD45.1+/CD45.2+ heterozygous wildtype mice, containing the Hobit reporter/deleter (B6-Tg 622 (Zfp683-tdTomato-P2A-cre-P2A-DTR)) construct.


title: 124 HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14897_124_LEP_RNA_CGTACG


title: 51L HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14893_51L_LEP_RNA_GTCCGC


title: Tom+ LCMV-specific T cells day 8 - Spleen - rep 1

description: Tom+ LCMV-specific effector T cells

value: Tissue-resident memory CD8+ T cells


title: 249P HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14902_249P_MEP_RNA_ACAGTG

value: Peripheral-to-Tumor

value: PTT

value: HMEC 4p


title: Tom+ LCMV-specific T cells day 8 - Spleen - rep 2

description: Tom+ LCMV-specific effector T cells

value: spleen


title: Tom+ LCMV-specific T cells day 8 - Spleen - rep 3

description: Tom+ LCMV-specific effector T cells


title: 124 HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14896_124_MEP_RNA_GTTTCG


title: 112R HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14894_112R_MEP_RNA_GTGAAA


title: 257C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14889_257C_LEP_RNA_AGTCAA

value: Contralateral-to-Tumor

value: CLTT

value: Luminal epithelial cells

value: LEP


title: Naive HR T cells - Spleen - rep 2

description: Naive T cells

value: Naive CD8+ T cells


title: 211C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14890_211C_MEP_RNA_AGTTCC

value: breast

value: Not Reported

value: FACS (BD FACSVantage)

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Naive HR T cells - Spleen - rep 1

description: Naive T cells


title: Naive HR T cells - Spleen - rep 3

description: Naive T cells


title: Ovary-pPDL1-D0-NO.10-2

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

data_processing:
library strategy: RNA-based TCR-seq
Raw reads were analyzed from the QIAGEN GeneGlobe Data Analysis Center to estimate the abundance of reads of unique CDR3 sequence and generate TCR clonotype calls
R package tcR was used to perform all the statistical analysis for TCR repertoires
Genome_build: GRCh38
Supplementary_files_format_and_content: raw count matrix of TCR clones

source_name: experimental metastasis model of Braf-mutated melanoma

extract_protocol:
QIAGEN All Prep DNA/RNA Mini Kit and Ambion mirVana miRNA Isolation Kit
RNA-based TCR-seq; QIAGEN QIAseq Immune Repertoire RNA Library Kit

tag: treatment

value: Anti-PD-L1 lead-in

tag: molecule subtype

value: transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: Ovary-Vehicle-D0-NO.3-1

value: No


title: Ovary-pPDL1-D0-NO.10-1


title: Ovary-Vehicle-D0-NO.3-2


title: 51L HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14892_51L_MEP_RNA_CCGTCC

value: No chemo

value: Reduction Mammaplasty

value: RM

value: Myoepithelial cells

value: MEP


title: Ovary-pM+P-D3-NO.12-2


title: Ovary-pM+P-D3-NO.12-1


title: 210C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14887_210C_LEP_RNA_GGCTAC

value: Contralateral-to-Tumor

value: CLTT

value: HMEC 4p


title: 257C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14888_257C_MEP_RNA_CTTGTA


title: 210C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14886_210C_MEP_RNA_GATCAG


title: Ovary-M+P-D3-NO.1-2


title: Ovary-M+P-D3-NO.1-1


title: 247C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14884_247C_MEP_RNA_GCCAAT


title: 112R HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14895_112R_LEP_RNA_GTGGCC

value: Luminal epithelial cells

value: LEP


title: Ovary-M-D3-NO.13-2

value: Trametinib


title: 211C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14891_211C_LEP_RNA_ATGTCA

value: breast

value: Not Reported

value: FACS (BD FACSVantage)


title: Brain-Vehicle-D0-NO.7


title: Ovary-M-D3-NO.13-1


title: Brain-Vehicle-D0-NO.3-1


title: Brain-Vehicle-D0-NO.3-2


title: 247C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14885_247C_LEP_RNA_CAGATC

value: Mark A. LaBarge

value: Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA


title: Control Sample 2

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

description: RNA-sequencing

data_processing:
demultiplexing with bcl2fastq v2.17.1.14
adapter trimming with cutadapt v1.18 using sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
mapping to GRCh37 (GENCODE) reference using STAR v2.6.1c
feature assignment with subread v1.6.1 featureCounts and GENCODE v33lift37 features
differential expression analysis using DESeq2 v1.32.0
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-separated text file containing rlog-normalized counts

source_name: neutrophils

extract_protocol:
Neutrophils were isolated using MACSxpress Whole Blood Neutrophil Isolation Kit in combination with MACSxpress Erythrocyte Depletion Reagent (Miltenyi Biotec, Bergisch Gladbach, Germany). For isolation of RNA, we used the RNAeasy Mini kit from Qiagen. Beta-mercaptoethanol was added to RLT buffer as mentioned in the manufacturer's protocol.
Sequencing libraries were generated using 200 ng of RNA and the TruSeq Stranded mRNA Kit according to manufacturer's instructions (Illumina, San Diego, USA).

value: neutrophils

tag: status

value: MPO wildtype

tag: condition

value: healthy


title: Brain-pPDL1-D0-NO.11-1

value: Anti-PD-L1 lead-in

value: transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: GPP Patient 2

description: RNA-sequencing

value: MPO-deficient

value: diseased


title: GPP Patient 1

description: RNA-sequencing


title: Brain-pPDL1-D0-NO.11-2


title: Control Sample 3

description: RNA-sequencing


title: Brain-pPDL1-D0-NO.10-2


title: GPP Patient 3

description: RNA-sequencing


title: Control Sample 4

description: RNA-sequencing


title: Control Sample 1

description: RNA-sequencing


title: Brain-pM+P-D3-NO.12-2


title: Brain-pM+P-D3-NO.14-1


title: Brain-pM+P-D3-NO.14-2


title: Brain-pM+P-D3-NO.12-1


title: SGC7901 cells treated with Chrysin_B1

city: Changchun

first: Dongxu

last: Wang

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

country: China

institute: Jilin University

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901B1

data_processing:
Using the HISAT2 software, the sequenced-reads were aligned to the reference sequence.
The gene expression analysis and differential gene expression analysis were determined using DEGseq and DESeq program, respectively, in HISAT2 (qValue <0.05, Fold Change >2).
Using clusterProfiler, the enrichment analysis, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, of differential expressed genes was determined.

molecule: polyA RNA

source_name: SGC7901 cells

growth_protocol: SGC-7901 cells were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Inc., Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin-streptomycin mixture (Invitrogen; Thermo Fisher Scientific, Inc.) at 37°C in a humidified environment containing 5% CO2.  confluence were cultured and pre-treated with Chrysin (Yuanye Bio-Technology, Shanghai) for 48 h.

extract_protocol:
 Total RNA of SGC-7901 cells was extracted with TRIzol Reagent (Invitrogen). To remove and purify ribosomal RNA (rRNA), we used the RiboZero Magnetic Gold Kit (Epidemiology, USA).
Then, RNA-seq (Sangon Biotech, Shanghai, China) was carried out on HiSeq2500 (Illumina, USA) to analyze raw reads, which were quality controlled by FastQC

treatment_protocol: Experiments were conducted by treating SGC-7901 cells with 40 μM of Chrysin (Yuanye Bio-Technology, Shanghai) for 48 h when they reached 80 to 90% confluence.

value: Gastric cancer cells

value: treated with 40uM Chrysin for 48h

tag: cell line


title: SGC7901 cells treated with Chrysin_B3

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901B3


title: Untreated SGC7901 cells_C3

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901c3


title: SGC7901 cells treated with Chrysin_B2

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901B2


title: Brain-M+P-D3-NO.6-2


title: Brain-M+P-D3-NO.6-1


title: Untreated SGC7901 cells_C2

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901c2


title: 71C HMEC 4p MEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14882_71C_MEP_RNA_CGATGT

value: Contralateral-to-Tumor

value: CLTT

value: Myoepithelial cells

value: MEP

value: HMEC 4p


title: 71C HMEC 4p LEP rep 1

description:
Cells isolated from finite lifespan, non-immortalized HMEC grown to 4th passage
14883_71C_LEP_RNA_ACAGTG

value: breast

value: Not Reported

value: Luminal epithelial cells

value: LEP

value: FACS (BD FACSVantage)


title: Brain-M+P-D3-NO.1-2


title: Brain-M+P-D3-NO.1-1


title: Untreated SGC7901 cells_C1

description: R19039495-NOVA20190905YMKD-2-MRNA192844CC-7901c1


title: RNAseq_Sub17_ABD_pear

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

data_processing:
The RNA-Seq samples quality was checked using the tool FastQC. After this step, a required trimming was executed reducing distortions on the “per base sequence content” at the beginning of the reads using Trimmomatic. The trimmed samples were aligned to the UCSC genome, assembly hg19, using STAR. Reads were required to be uniquely mapped using Samtools for filtering, sorting and indexing. RSeQC was used to assess quality of each sample. The RNA sequencing abundance, raw read counts and TPM values, was calculated with TPMCalculator using the default parameters. The differential gene expression analysis was executed using the Bioconductor packages Deseq2 and EdgeR. An adjusted p-value of 0.05 and a logarithmic fold change of 1.5 was used to identified differentially expressed genes.  All tools were executed using publicly available Common Workflows Language files and docker images with fixed tool versions
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include raw read count values and TPM values for each Sample

source_name: subcutaneous abdominal fat

extract_protocol:
Fat biospsies were collected, Stromal-vascular fractions were isolated from scWAT A- and GF-FAT depot, plated and cultured in aMEM suplemented with hEGF and hFGF. The preadipocyte population was enriched by depletion of the stromal-vascular fraction of endothelial cells (CD31 positive cells) using the magnetic beads technology from Stemcell technologies (Cambridge, MA). At confluence, cells were harvested and a fraction of the cells was frozen for RNA extraction. RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA)  Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Library preparation kit (Illumina Inc., San Diego, CA) as per the instructions

value: preadipocytes

tag: cell source

value: isolated from abdominal fat depot

tag: shape

value: pear


title: Brain-pPDL1-D0-NO.10-1

value: Anti-PD-L1 lead-in

value: transcripts of T cell receptor alpha, beta, gamma, and delta genes (CDR3 region)


title: Brain-M-D3-NO.8-2

value: Trametinib


title: Brain-M-D3-NO.13-2


title: RNAseq_Sub16_ABD_pear


title: Brain-M-D3-NO.8-1


title: RNAseq_Sub15_ABD_apple

value: apple


title: RNAseq_Sub16_GF_pear

source_name: subcutaneous gluteofemoral fat

value: isolated from gluteofemoral fat depot


title: RNAseq_Sub15_GF_apple


title: RNAseq_Sub14_ABD_apple


title: RNAseq_Sub14_GF_apple


title: S. enterica-MacT interactions-CerroB_rep3 [Cerro_B_3]

city: Beltsville

first: Serajus

last: Salaheen

state: Maryland

address: 10300 Baltimore Ave., Bldg. 173,, BARC-East

department: ARS

institute: USDA

description: processed data file: Read_Count_Cerro.txt

data_processing:
Data demultiplexed using the BCL2FastQ v2.15.0.4
Reads were trimmed and sequencing adapters were removed using Trimmomatic V 0.36 (leading 20, trailing 20, sliding 4:20, min len 36)
Removed reads that mapped to the bovine genome using STAR v2.7.2b
Sequencing reads were then mapped to serovar-specific S. enterica reference genomes using Bowtie 2 v2.3.2 using the following parameters --very-sensitive-local --no-unal  --minins 150 --maxins 1000 --fr --no-mixed --no-discordant
Reads that originated from S. Dublin strains were mapped to S. enterica serovar Dublin strain USMARC-69838 chromosome and plasmid pSDU1-USMARC-69838 (GenBank accession numbers: NZ_CP032449.1, NZ_CP032450.1). Reads that originated from S. Cerro strains were mapped to S. enterica serovar Cerro strain CFSAN001588 chromosome and plasmids pCFSAN001588_001 and pCFSAN001588_002 (GenBank accession numbers: NZ_CP012833.1, NZ_CP012834.1, NZ_CP012835.1)
The number of reads that were uniquely mapped to coding sequences of reference was calculated using featureCounts from the Subread package v2.0.1 using parameters -t CDS -g ID -Q 10 -s 2 -p -B -P -d 150 -D 1000
Genome_build: NZ_CP032449.1, NZ_CP032450.1, NZ_CP012833.1, NZ_CP012834.1, NZ_CP012835.1
Supplementary_files_format_and_content: tab-delimited text files that include matrix table with raw gene counts for every gene and every sample

organism: Salmonella enterica

source_name: Salmonella enterica total RNA

extract_protocol:
MAC-T cells were infected with S. enterica strains for 2 h. The infected MAC-T cells were lysed in ice cold RNA stabilization solution, and bacterial pellets were harvested using centrifugation. Total RNA was extracted from bacterial pellets Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research, Irvine, CA). Total RNA was treated with the MICROBEnrich™ Kit (Invitrogen) to eliminate/reduce MAC-T cell RNA contaminants. RNA samples were treated with DNAse.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: serovar

value: Cerro

tag: host cell-line

value: MAC-T

tag: strain identifier

value: B

value: Infection of MAC-T for 2 h


title: S. enterica-MacT interactions-CerroB_rep2 [Cerro_B_2]


title: S. enterica-MacT interactions-CerroB_rep1 [Cerro_B_1]


title: RNAseq_Sub13_GF_apple


title: S. enterica-MacT interactions-CerroA_rep2 [Cerro_A_2]

value: A


title: RNAseq_Sub12_GF_pear


title: RNAseq_Sub12_ABD_pear


title: S. enterica-MacT interactions-CerroA_rep1 [Cerro_A_1]


title: RNAseq_Sub13_ABD_apple


title: S. enterica-MacT interactions-DublinB_rep3 [Dublin_B_3]

description: processed data file: Read_Count_Dublin.txt

value: Dublin


title: S. enterica-MacT interactions-CerroA_rep3 [Cerro_A_3]


title: RNAseq_Sub17_GF_pear


title: RNAseq_Sub11_ABD_apple


title: S. enterica-MacT interactions-DublinB_rep2 [Dublin_B_2]


title: RNAseq_Sub11_GF_apple


title: RNAseq_Sub10_GF_apple


title: S. enterica-MacT interactions-DublinA_rep3 [Dublin_A_3]


title: RNAseq_Sub10_ABD_apple


title: S. enterica-MacT interactions-DublinB_rep1 [Dublin_B_1]


title: Brain-M-D3-NO.13-1


title: S. enterica-MacT interactions-DublinA_rep2 [Dublin_A_2]


title: RNAseq_Sub9_GF_apple


title: S. enterica-MacT interactions-DublinA_rep1 [Dublin_A_1]


title: RNAseq_Sub9_ABD_apple


title: RNAseq_Sub8_ABD_apple


title: RNAseq_Sub8_GF_apple


title: RNAseq_Sub5_GF_apple


title: RNAseq_Sub7_ABD_pear


title: RNAseq_Sub6_GF_pear


title: RNAseq_Sub7_GF_pear


title: RNAseq_Sub4_GF_apple


title: RNAseq_Sub5_ABD_apple


title: RNAseq_Sub6_ABD_pear


title: RNAseq_Sub3_ABD_apple


title: Nr2f1_het3_induced

city: Paris

first: Daniel

last: Holoch

state: Cedex 05

address: 26 rue d'Ulm

department: Genetics and Developmental Biology Unit

country: France

institute: Institut Curie, Centre de Recherche

data_processing:
Adapter trimming (Trim Galore! 0.4.4 wrapper with default settings)
Discard reads aligning to complete mouse rRNA sequence (Bowtie 2.2.9)
Alignment to mouse genome (Tophat 2.1.1 & Bowtie 2.2.9)
Gene counts (FeatureCounts 1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.txt files contain gene counts
Supplementary_files_format_and_content: read_counts.txt files contain wild-type and mutant read counts for targeted experiments

source_name: Immortalized mouse embryonic fibroblast line B

growth_protocol: MEF cells were grown in DMEM supplemented with 10% FCS, 100 mM nonessential amino acids, 2 mM L-glutamine.

extract_protocol:
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions
Targeted amplification of Nr2f1 from cDNA with addition of Illumina adapters

value: c-myc-immortalized mouse embryonic fibroblasts

tag: genotype/treatment

value: Heterokaryon (of DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction and DD-dCas9-VPR; Nr2f1-mutant, untreated), during transient induction

tag: fraction

value: total RNA


title: Foxa1_het7-12_washout

extract_protocol:
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions
Targeted amplification of Foxa1 from cDNA with addition of Illumina adapters

tag: cell type

value: Heterokaryon (of DD-dCas9-VPR; sgRNA-Foxa1, after transient induction and DD-dCas9-VPR; Foxa1-mutant, untreated), after transient induction


title: Foxa1_het7-12_induced

value: Heterokaryon (of DD-dCas9-VPR; sgRNA-Foxa1, after transient induction and DD-dCas9-VPR; Foxa1-mutant, untreated), during transient induction


title: Foxa1_het7-5_induced


title: Nr2f1_het9_mock

value: Heterokaryon of DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction and DD-dCas9-VPR; Nr2f1-mutant, untreated


title: Foxa1_het7-12_mock

value: Heterokaryon of DD-dCas9-VPR; sgRNA-Foxa1, after transient induction and DD-dCas9-VPR; Foxa1-mutant, untreated


title: Foxa1_WT_ON_mut_OFF

value: DD-dCas9-VPR; sgRNA-Foxa1, after transient induction and DD-dCas9-VPR; Foxa1-mutant, untreated


title: Nr2f1_het9_washout

value: Heterokaryon (of DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction and DD-dCas9-VPR; Nr2f1-mutant, untreated), after transient induction


title: Nr2f1_het9_induced


title: Foxa1_WT_ON_mut_ON

value: DD-dCas9-VPR; sgRNA-Foxa1, after transient induction and DD-dCas9-VPR; Foxa1-mutant; sgRNA-Foxa1, after transient induction


title: Foxa1_het7-5_washout


title: RNAseq_Sub4_ABD_apple

value: preadipocytes

value: isolated from abdominal fat depot

value: apple


title: RNAseq_Sub3_GF_apple

value: isolated from gluteofemoral fat depot


title: RNAseq_Sub1_GF_pear

value: pear


title: Nr2f1_het3_washout


title: RNAseq_Sub2_GF_pear


title: Nr2f1_WT_ON_mut_ON

value: DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction and DD-dCas9-VPR; Nr2f1-mutant; sgRNA-Nr2f1, after transient induction


title: RNAseq_Sub2_ABD_pear


title: Foxa1_het7-5_mock


title: Nr2f1_het3_mock


title: RNAseq_Sub1_ABD_pear


title: D7 (chronic timepoint) 5OPRU+TGFB, Donor 3

city: New York

first: Christina

last: Leslie

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
SEQC pipeline described in Azizi et al Cell 2018 was used for pre-processing of raw data and count matrix generation
Additional gene/cell filters were applied manually as described in the methods of the manuscript
Seurat v2.3.4 was used for clustering and differential expression analyses
Genome_build: hg19
Supplementary_files_format_and_content: Seurat object RDS containing raw and normalized count matrices, UMAP coordinates
Supplementary_files_format_and_content: Cell-level metadata for all cells in Seurat object

source_name: MAIT cells

extract_protocol:
Healthy donor PBMCs were obtained with written informed consent at Sloan Kettering Institute, MSKCC, Rockefeller University or ATCC. De-identified blood samples were processed according to the protocols approved by the Institutional Review Board of MSKCC and Rockefeller University.  PBMCs were isolated from peripheral blood using Ficoll-Prep (GE Healthcare) or cell preservation tubes (CPT; Becton Dickinson) according to the manufacturer’s instructions and cryopreserved using 90% fetal bovine serum (Gibco) 10% DMSO (Sigma Aldrich) and stored in liquid N2 prior to thawing for in vitro assays.  PBMCs were cultured for 15 hrs or 7 days in RPMI (GIBCO) supplemented with 10% (v/v) heat inactivated FBS, penicillin/streptomycin (100 U/mL), L-glutamine (2 mM), sodium pyruvate (1 mM), nonessential amino acids (0.1 mM), HEPES buffer (10 mM) and 2-mercaptoethanol (50 M) (from GIBCO or Sigma Aldrich) at 37oC 5% CO2 in 96 well plates in the presence of IL2 (GIBCO 100 IU/mL or Roche 1 ng/mL).  Additional conditions included 1 ng/mL TGF (GIBCO).  2 M 5-A-RU was added directly to 50 M methylglyoxal to form 5-OP-RU on Day 1 for in vitro stimulation assays.  5-amino-6-D-ribitylaminouracil  (5-A-RU) was synthesized as previously described (Li et al., 2018), resuspended in 200 M aliquots, cryopreserved, and thawed as needed.  CD3/CD28 beads (Gibco; #11161D) were incubated with PBMCs at a 1:2 bead:cell ratio for scRNA-seq and flow cytometric validation assays.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood MAIT cells

tag: time point

value: D7 (chronic timepoint) 5OPRU+TGFB

tag: donor

value: Donor 3


title: human melanocyte  PM treated-2

city: Seoul

first: Sang Ho

last: Oh

address: 50-1 Yonsei-ro

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and Quantile nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: human melanocyte

growth_protocol: Human melanocytes were isolated from human foreskin and cultured in M254 medium with human melanocyte growth supplements, respectively. Cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: Primary human epidermal melanocytes were treated with particulate matter (5 μg/cm2) and incubated for 24 h

tag: tissue

value: Foreskin

value: primary human melanocytes

value: treated with particulate matter


title: D7 (chronic timepoint) resting IL2+TGFB, Donor 3

value: D7 (chronic timepoint) resting IL2+TGFB


title: D7 (chronic timepoint) anti-CD3/CD28, Donor 3

value: D7 (chronic timepoint) anti-CD3/CD28


title: human melanocyte  con-2

value: media only


title: human melanocyte PM treated-1


title: liver_D_TLST_2 [1_Exiqon_19713609]

type: RNA

city: Hannover

first: Asha

last: Balakrishnan

state: Lower saxony

address: carl neuberg str. 1

department: Gastroenterology, Hepatology, and Endocrinology

institute: Hannover Medical School (MHH)

hyb_protocol: The Hy3TM-labeled samples and a Hy5TM-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNATM microRNA Array 7'th (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria).

scan_protocol: Slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using quantile normalization method, which we have found produces the best between-slide normalization to minimize the intensity-dependent differences between the samples.

source_name: liver, late stage, Dox on, group D

label_protocol: 700 ng total RNA from sample and reference was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA was extraccted from liver or liver tumor tissues, as per the group. Quality was subsequently assessed on an Agilent 2100 Bioanalyzer.

tag: strain background

value: FVBn

tag: genotype/variation

value: double transgenic LAP-Tta/TRE-c-MYC (LT2/MYC:conditional doxycycline-regulatable transgenic c-Myc driven mouse model of liver cancer)

tag: Sex

value: Male

tag: tumor stage

value: late stage_regressing

value: doxycycline

value: Liver


title: D7 (chronic timepoint) 5OPRU, Donor 3

value: D7 (chronic timepoint) 5OPRU


title: liver_C_ULST_4 [1_Exiqon_19713602]

label: miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM

source_name: liver, late stage, group C

value: late stage_developing


title: D7 (chronic timepoint) anti-CD3/CD28+TGFB, Donor 2

value: Blood MAIT cells

value: Donor 2


title: D7 (chronic timepoint) 5OPRU+TGFB, Donor 2

value: D7 (chronic timepoint) 5OPRU+TGFB


title: liver_D_TLST_1 [1_Exiqon_19713606]

tag: treatment


title: liver_C_ULST_2 [1_Exiqon_19713595]


title: Nr2f1_WT_ON_mut_OFF

value: c-myc-immortalized mouse embryonic fibroblasts

value: DD-dCas9-VPR; sgRNA-Nr2f1, after transient induction and DD-dCas9-VPR; Nr2f1-mutant, untreated

value: total RNA


title: D1 (acute timepoint) anti-CD3/CD28, Donor 3

value: D1 (acute timepoint) anti-CD3/CD28

value: Donor 3


title: liver_D_TLST_4 [1_Exiqon_19713596]


title: D1 (acute timepoint) resting IL2, Donor 3

value: D1 (acute timepoint) resting IL2


title: D1 (acute timepoint) 5OPRU, Donor 3

value: D1 (acute timepoint) 5OPRU


title: liver_C_ULST_3 [1_Exiqon_19713608]

value: FVBn

value: double transgenic LAP-Tta/TRE-c-MYC (LT2/MYC:conditional doxycycline-regulatable transgenic c-Myc driven mouse model of liver cancer)


title: liver_C_ULST_1 [1_Exiqon_19713591]

value: Male


title: D7 (chronic timepoint) resting IL2, Donor 3

value: D7 (chronic timepoint) resting IL2


title: D7 (chronic timepoint) 5OPRU, Donor 2


title: liver_D_TLST_2 [0_Exiqon_19713609]

value: late stage_regressing

value: doxycycline

value: Liver


title: liver_C_ULST_3 [0_Exiqon_19713608]

value: late stage_developing


title: D7 (chronic timepoint) anti-CD3/CD28, Donor 2

value: Blood MAIT cells

value: D7 (chronic timepoint) anti-CD3/CD28

value: Donor 2


title: D7 (chronic timepoint) resting IL2+TGFB, Donor 2

value: D7 (chronic timepoint) resting IL2+TGFB


title: D7 (chronic timepoint) resting IL2, Donor 2


title: D7 (chronic timepoint) anti-CD3/CD28+TGFB, Donor 3


title: liver_D_TLST_1 [0_Exiqon_19713606]


title: human melanocyte  con-1

value: Foreskin

value: primary human melanocytes

value: media only


title: liver_C_ULST_4 [0_Exiqon_19713602]


title: D1 (acute timepoint) resting IL2, Donor 2

value: D1 (acute timepoint) resting IL2


title: D1 (acute timepoint) 5OPRU, Donor 2

value: D1 (acute timepoint) 5OPRU


title: liver_D_TLST_4 [0_Exiqon_19713596]

value: FVBn


title: liver_C_ULST_1 [0_Exiqon_19713591]

value: double transgenic LAP-Tta/TRE-c-MYC (LT2/MYC:conditional doxycycline-regulatable transgenic c-Myc driven mouse model of liver cancer)


title: D7 (chronic timepoint) anti-CD3/CD28+TGFB, Donor 1

value: Donor 1


title: D7 (chronic timepoint) 5OPRU, Donor 1

value: D7 (chronic timepoint) 5OPRU


title: D7 (chronic timepoint) anti-CD3/CD28, Donor 1


title: liver_C_ULST_2 [0_Exiqon_19713595]

value: Male


title: liver_D_TLST_3 [1_Exiqon_19713592]

value: late stage_regressing

value: doxycycline


title: D7 (chronic timepoint) resting IL2+TGFB, Donor 1


title: trmD_KO_RNAseq

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
The linker was trimmed using Skewer. Reads were aligned using Bowtie and allowing two mistmatches. Reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 2.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell cultures

growth_protocol: Cultures with the pClpXP plasmid were diluted into fresh LB + Ara media three times to induce ClpPX expression. In the third cycle, a 500 mL culture was grown from OD600 = 0.1 to 0.3 at 37 C and harvested by filtration. Cultures with the pTrm5 plasmid were diluted into fresh MOPS complete synthetic media + Glc media to repress Trm5 expression. In the third cycle, a 300 mL culture was grown from OD600 = 0.1 to 0.3 at 37 C and harvested by filtration.

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. The lysis buffer contained Cm (pClpPX samples) or 150 mM MgCl2 (pTrm5 samples) to arrest translation. Lysates were clarified and ribosomes were pelleted prior to digestion of mRNA with MNase. After digestion, 70S monosomes were purified over a sucrose gradient.
Ribosome footprints and total RNA fragments 15-45 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

tag: genotype

tag: plasmids

tag: molecule subtype

value: mRNA


title: D7 (chronic timepoint) 5OPRU+TGFB, Donor 1

value: Blood MAIT cells

value: D7 (chronic timepoint) 5OPRU+TGFB


title: liver_D_TLST_3 [0_Exiqon_19713592]

value: Liver


title: trmD_WT_RNAseq


title: trmD_KO_FP

data_processing:
Library strategy: ribosome profiling
The linker was trimmed using Skewer. Reads were aligned using Bowtie and allowing two mistmatches. Reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 2.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

value: mRNA:ribosome footprints


title: trmD_control_RNAseq2

value: pClpPX


title: D1 (acute timepoint) 5OPRU, Donor 1


title: D1 (acute timepoint) anti-CD3/CD28, Donor 1

value: D1 (acute timepoint) anti-CD3/CD28


title: trmD_degron_FP2

value: trmD_degron (YALAA)


title: FAP_H_G62

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

data_processing:
mRNA sequences were aligned with Bowtie 1.1.2 on hg19 and quantified with RSEM 1.2.21 using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited RSEM output with expected counts, TPM, FPKM values

source_name: colonic normal mucosa from FAP patient

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). RNA was quantified using Qubit (Life Technologies) and RNA quality was assessed with the Agilent 2100 Bioanalyzer to select samples with RNA integrity numbers (RIN) ≥8 for analysis.
Sample preparation, library construction, and sequencing was performed at the DNA Analysis Facility Core at MD Anderson

tag: subject status

value: patient with Familial Adenomatous Polyposis (FAP)

value: colonic normal mucosa


title: trmD_degron_RNAseq2


title: FAP_H_G60


title: trmD_control_FP2


title: D1 (acute timepoint) resting IL2, Donor 1

value: D1 (acute timepoint) resting IL2


title: D1 (acute timepoint) anti-CD3/CD28, Donor 2

value: Donor 2


title: FAP_H_G49


title: trmD_degron_RNAseq1


title: trmD_control_RNAseq1


title: trmD_control_FP1


title: D7 (chronic timepoint) resting IL2, Donor 1

value: D7 (chronic timepoint) resting IL2

value: Donor 1


title: FAP_H_G1


title: HBEC Input rep2

city: BOSTON

first: Boting

last: Ning

state: Massachusetts

address: 72 E Concord St

institute: BOSTON UNIVERSITY

description: ChIP-seq data from control human bronchial epithelial cells, using IgG control.

library_source: genomic

data_processing:
FASTQ files were aligned to the human genome (hg19) using Bowtie2 (v2.3.4.1)
Redundant reads were removed using samtools (v1.7)
Peaks were called using MACS2 (v2.1.2) with q-value cutoff of 0.05.
Genome_build: hg19

molecule: genomic DNA

source_name: Human Bronchial Epithelial Cells

growth_protocol: Human bronchial epithelial cells were cultured in PneumaCult-Ex Plus.

extract_protocol:
Harvested chromatin was sonicated using the Bioruptor UCD-200 for 2 cycles of 10 min (max power 30 s on 30 s off). After sonication, chromatin was incubated with designated amount of antibody at 4 °C overnight. Immunoprecipitated complexes were collected by Protein A/G Magnetic beads (Pierce, 8802).
Sample  integrity  and  purity were detected by Agilent Technologies 2100 bioanalyzer. DNA was 3' adenylated and PCR amplified. dsDNA products were heat denatured and circularized by splint oligo for formating the ssCircularDNA library.

treatment_protocol: Cells were cross-linked in 1mM EGS in PBS for 30min followed by a 1% formaldehyde treatment for 10 min.

value: Human Bronchial Epithelial Cells

tag: chip antibody

value: Input Control


title: FAP_H_G40


title: trmD_WT_FP


title: FAP_H_G26


title: BAT preadipocyte differentiation day 0 replicate2

city: Xinyang

first: pengpeng

last: Zhang

state: Henan

address: No.237 Nanhu Road Shihe District

institute: Xinayang Normal University

data_processing:
Quality control of sequences was examined with FastQC version 0.11.9. The clean data were obtained using the Fastp version 0.20.1 to remove reads with adapters, reads containing poly-N and reads with low quality.
The clean reads were subjected to mapping with Mus musculus mm9 reference genome by HISAT2 version 2.2.0.
circRNA was indentified by CIRI2
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw circRNA counts for every gene and every sample

source_name: inguinal BAT

growth_protocol: Primary BAT SVF cells were isolated using collagenase digestion as we previously described. Briefly, the inguinal BAT were collected from 6-week-old mice. Adipose tissue was cut into small pieces and digested with 1.5 mg ml-1 collagenase at 37 ℃ for 30-50 min. The digestions were terminated with DMEM containing 20% FBS, and filtered through 100-μm and 70-μm cells trainer to remove tissue debris. Cells were then centrifuged at 450g for 8 min and SVF cells pellet was resuspend. SVF cells were cultured in growth medium containing 20 % FBS, high glucose DMEM, at 37 ℃ with 5% CO2, culture medium was changed every 2 days.

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’ instructions.  To enrich circRNA, the rRNA and linear RNA were removed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When the cells reached 90 % confluence, they were induced to adipogenic differentiation with induction medium, which contains DMEM, 10% FBS, 2.85 mM insulin, 0.3 mM dexamethasone and 0.63mM 3-isobutyl-methylxanthine for 4 days. Then the medium was switched to differentiation medium which contains DMEM, 10% FBS, 200 nM insulin and 10 nM T3 for another 4 days to induce the mature of adipocytes.

value: BAT preadipocyte

tag: strain

tag: time

value: proliferation

value: inguinal BAT


title: hNS1 proliferation rep1

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome GRCh38 using STAR
Measures of gene level expression with HT-Seq raw read counts.
Differential expression analysis was performed using DESeq2 v. 1.10.1
Genome_build: GRCh38
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 (DESeq2) for every gene and every sample

source_name: human fetal forebrain-derived

growth_protocol: Human stem cell (HSC) medium supplemented with 20 ng/ml epidermal growth factor (EGF; PetroPech) and 20 ng/ml basic fibroblast growth factor (FGF2; PetroPech)

extract_protocol:
RNeasy Mini extraction kit (Qiagen, Valencia, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were proliferated in an incubator set to 37 °C and 5% CO2. Cultures were differentiated on poly-L-lysine- (10–30 μg/ml; Sigma) coated plastic or glass coverslips, by withdrawal of growth factors (EGF and FGF2) and addition of 0.5% heat-inactivated fetal bovine serum (FBS) for 4 days.

tag: cell line

tag: develomental stage


title: hNS1 proliferation rep2


title: HBEC TEAD rep2

description: ChIP-seq data from human bronchial epithelial cells treated, using TEAD antibody.

tag: cell type

value: TEAD


title: BAT preadipocyte differentiation day 8 replicate1

value: post differentiation day8


title: FAP_H_G31


title: hNS1 differentiation rep2

value: differentation day4


title: BAT preadipocyte differentiation day 4 replicate1

value: post differentiation day4


title: Arid5a-/-_MEFs_w_IL-6_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Arid5a-/- MEFs with IL-6 treatment (100 ng/ml) for 24 h

data_processing:
Sequencing was performed on an Illumina HiSeq3000 platform in a 100-base paired-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (GRCm38.p6) using HISAT2.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Arid5a-/- MEFs with IL-6 treatment

extract_protocol:
An RNeasy Mini Kit (Qiagen) was used to isolate total RNA.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: Mouse Embryonic Fibroblast


title: Arid5a-/-_MEFs_w_IL-6_rep2


title: hNS1 differentiation rep1


title: FAP_H_G16


title: HBEC TEAD rep1


title: FAP_H_G54


title: FAP_H_G4


title: HBEC Input rep1


title: hNS1 proliferation rep3


title: Arid5a-/-_MEFs_wo_IL-6_rep2

description: Arid5a-/- MEFs without IL-6 treatment for 24 h

source_name: Arid5a-/- MEFs without IL-6 treatment


title: PARK2-PD1 rep3 line DN PDS14

city: Boston

first: Ksenia

middle: S

last: Anufrieva

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD3dn_3

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic (v. 0.35).
Trimmed RNAseq reads were quantified against Homo Sapiens GRCh38.13  genome annotation at the transcript level using Salmon (v.1.4). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data files format and content: tab-delimited tsv files include TPM values for every gene and every sample

source_name: terminally differentiated neurons

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. Neural progenitors were cultivated in DMEM/F12 containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential amino acids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1%  N2 supplement (“Life Technologies”, USA), 10 µM SB431542 (“Stemgent”, USA), and 80 ng recombinant Noggin (“Peprotech”, USA). Neurons were cultivated in DMEM/F12 containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies”, USA), 100 ng/ml recombinant Shh, 20 ng/ml recombinant FGF8, purmorphamine 2 µM all from (“Peprotech”, USA) for 10 days, and in DMEM/F12, containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco”, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U/ml; 50 µg/ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies”, USA), 5 µM forskolin (“Stemgent”, USA),  20 ng/ml BDNF, 20 ng/ml GDNF, 200 µM ascorbic acid all from (“Peprotech”, USA) for 24 days.

extract_protocol:
Total RNA was isolated from neural progenitors using RNeasy Micro Kit (Qiagen, USA) followed by treatment with DNAse I (Qiagen, USA). The reaction was purifed with PureLink RNA Mini Kit (ThermoFisher, USA). RNA quality was checked by 2100 bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol. Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
Library preparation was performed with NEB Next Ultra II Directional RNA Library Prep (NEB, USA) according to the manufacturer’s protocol.

treatment_protocol: To obtain neural progenitors from iPSCs, the culture medium was replaced with a neuronal differentiation medium containing a cocktail of factors that stimulates differentiation in the neuronal direction. After 10-14 days of culturing, neural rosettes with specific “ridges” formed by iPSCs were mechanically transferred to a 24-well plate with extremely low adhesion, where neurospheres were formed. After 3-5 days, neurospheres were collected and treated with 0.05% trypsin. Thereafter, neurospheres were resuspended in DMEM with 10% FBS, then resuspended in growth medium for neural progenitors (DMEM/F12 containing 2% serum replacement (Gibco, USA), 1 mM non-essential amino acids (Paneco, Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“Paneco”, Russian Federation), 1% N2 supplement (“Life Technologies” , USA), 10 μM SB431542 (Stemgent, USA), and 80 ng recombinant Noggin (Peprotech, USA), and transferred to Petri dishes coated with Matrigel. For differentiation into dopaminergic neurons, the neural progenitors were cultivated with DMEM/F12 containing 2% serum replacement (Gibco, USA), 1 mM non-essential aminoacids (Paneco, Russian Federation), 2 mM L-glutamine (ICN Biomedicals Inc ”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“ Paneco ”, Russian Federation), 1% В27 supplement (“ Life Technologies ”, USA), 100 ng / ml recombinant Shh, 20 ng / ml recombinant FGF8, purmorphamine 2 µM all from (“Peprotech”, USA) for 10 days, and in DMEM / F12, containing 2% serum replacement (“Gibco”, USA), 1 mM non-essential aminoacids (“Paneco” , Russian Federation), 2 mM L-glutamine (“ICN Biomedicals Inc”, USA), penicillin-streptomycin (50 U / ml; 50 µg / ml) (“Paneco”, Russian Federation), 1% В27 supplement (“Life Technologies ”, USA), 5 µM forskolin (“ Stemgent ”, USA), 20 ng / ml BDNF, 20 ng / ml GDNF, 200 µM ascorbic acid all from (“ Peprotech ”, USA) for 24 days.

value: neurons presumably dopaminergic

value: PARK2:heterozygous deletion of 2 exon

tag: disease

value: Parkinson's disease


title: BAT preadipocyte differentiation day 8 replicate2

tag: tissue


title: BAT preadipocyte differentiation day 0 replicate1


title: PARK2-PD1 rep2 line DN PDS14

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD3dn_2


title: PARK2-PD1 rep1 line DN PDS14

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD3dn_1


title: BAT preadipocyte differentiation day 4 replicate2


title: hNS1 differentiation rep3


title: PN2_rna_muscle

city: Basel

first: Grégoire

middle: M

last: Vernaz

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

description: Total RNAseq from adult tissue

data_processing:
RNAseq reads were mapped to MZ_UMD2a and gene expression values were calculated using kallisto (see SUPP methods)
WGBS reads were mapped to mapped to SNP-corrected genomes (based on MZ_UMD2a) and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see SUPP Methods). Methylation at CG sites with ≥5 ≤100 non-clonal seq reads averaged across 50bp-long non-slidding windows per species were performed to produce bw files.
Species-specific high-confidence SNP-corrected genome (fa file) was generated for each of the species studied in this study by using published whole genome sequencing dataset (Malinsky et al 2018); see Methods.
DMRs were called using DSS (see SUPP Methods). P<0.05, minimal overall methylation difference across any DMR between any species was >25% (d25pc), ≥4 CpG, ≥50bp and pvalue<0.05 (p005). For DMR calling, all CG sites were used independent of sequencing coverage following DSS recommandations (improved DMR calling).
Genome_build: Maylandia zebra MZ_UMD2a  and SNP-corrected genomes
Supplementary_files_format_and_content: tpm for RNAseq (tsv) generated using kallisto, mCG/CG (bigwig) generated using bismark, SNP-corrected genomes (fa)

organism: Pundamilia nyererei

source_name: homogenised adult skeletal muscle

extract_protocol:
total RNA extracted using phenol/chlorophorm approach (see SUPP methods)
ribosomal RNA depletion (RiboZero Illumina) followed by Illumina RNAseq stranded library kit, according to manusfacturer's instructions

value: skeletal muscle

value: male

tag: type

value: tank reared


title: trmD_degron_FP1

value: trmD_degron (YALAA)

value: pClpPX

value: mRNA:ribosome footprints


title: PN3_rna_muscle

description: Total RNAseq from adult tissue


title: Sample_47

city: Los Angeles

first: Alice

last: Mouton

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_47

data_processing:
The alignment of the samples was performed on STAR 2.5.3 (Dobin et al., 2013) using the mouse genome (mm10).
Differential expression analysis was performed using the LIMMA package (R version 3.5.3) (Ritchie et al., 2015).
For each tissue (adipose and heart), we filtered out reads with low counts (CPM < 0.5) and explored the data to check for outliers and batch effects. The remaining genes and samples were normalized using TMM (trimmed mean of M-values) in the edgeR package (Robinson and Oshlack, 2010) in R.
Voom with quality weight in Limma  (Law et al., 2014; Ritchie et al., 2015). We then performed a pairwise comparison between Control vs HFCD, HFCD vs HFCD+FMD and Control vs HFCD+FMD.
Genome_build: mm10
Supplementary_files_format_and_content: norm counts
Supplementary_files_format_and_content: raw counts

source_name: Adipose

growth_protocol: mice maintained in a pathogen-free environment and housed in clear shoebox cages in groups with constant temperature and humidity and 12 h/12 h light/dark cycle and with access to water at all times

extract_protocol:
RNeasy Mini Kit following instructions (Qiagen).
KAPA RNA Hyper+RiboErase HMR kit (Roche)

treatment_protocol: mice were fed ad libitum either a commercial high fat and high calorie diet (HFCD) (60% calories from fat) or a control diet (10% calories from fat), or a HFCD diet combined once every 4 weeks with cycles of a 5 day FMD (HFCD+FMD). Starting at cycle 6, the 5 day FMD was followed by 2 days of a control diet before the switch to HFCD.

tag: age

value: 22 months

value: HFCD 11CYCLES RF4 days


title: Hashtag-HTO

city: Tel Aviv

first: Eldad

middle: David

last: Shulman

address: Kelechkin 35

country: Israel

institute: Tel Aviv University

description:
10x Genomics single cell 3' v2
polyA HTO

data_processing:
Cell barcodes and UMIs were quantified using the Cell Ranger pipeline with default parameters (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Genome_build: mm10
Supplementary_files_format_and_content: barcodes, features, MTX

source_name: cochlear immune

extract_protocol:
To prepare single cell suspension, cochleae from n=6 mice per experimental condition were pooled and digested in 1xAccutase (Stem Cell Technology) for 20 min in 37°C, washed with staining buffer containing 1% fetal bovine serum (FBS) in PBS, centrifuged at 400g for 5 min at 4°C and plated in a 96-well plate. The cells were blocked with CD16/CD32 (1:200, Thermo Fisher Scientific) and stained with live dead cell marker using Aqua Live/Dead stain kit (1:1000, Amcyan) in the presence of RNAse inhibitor (1:400, Promega) in PBS for 15 min. After subsequent wash, the cells obtained from each condition were stained with a 1:1 mixture of CD45-PE (1:200, 30F11, Biolegend) and a corresponding TotalSeq antibody (Biolegend) in staining buffer containing RNase inhibitor (1:400) for 30 min. The following antibodies were used for each condition: TotalSeqTM A0301-Hashtag1 antibody (M1/42, 30F11) for Sham treated cells, TotalSeqTM A0302-Hashtag2 antibody (M1/42, 30F11) for 3d, TotalSeqTM A0303-Hashtag3 antibody (M1/42, 30F11) for 7d and TotalSeqTM A0304-Hashtag4 antibody (M1/42, 30F11) for 14d post noise. CD45 positive living cells were sorted on BDFACS ARIA III (BD Biosciences) in 500 µL collecting buffer containing RNase free 1% BSA (Thermo Fischer Scientific) and RNAse inhibitor (1:400). The cells were centrifuged at 400g for 5 min at 4°C and resuspended in 50 µL collecting buffer
Chromium single cell 3´reagent kit v3 (10x Genomics) was used according to the manufacturer’s instructions

value: cochlear  immune cells


title: WT_MEFs_w_IL-6_rep1

description: WT MEFs with IL-6 treatment (100 ng/ml) for 24 h

source_name: WT MEFs with IL-6 treatment


title: Hashtag-RNA

description:
10x Genomics single cell 3' v2
polyA RNA


title: PARK2-PD1 rep2 line DN PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD2dn_2

value: PARK2:homozygous deletion of 8 exon


title: Sample_48

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_48

value: 21 months


title: PN3_rna_liver

description: Total RNAseq from adult tissue

source_name: homogenised adult liver tissue

value: liver

tag: Sex

value: tank-reared


title: PARK2-PD1 rep3 line DN PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD2dn_3


title: WT_MEFs_wo_IL-6_rep1

description: WT MEFs without IL-6 treatment for 24 h

source_name: WT MEFs without IL-6 treatment

value: Mouse Embryonic Fibroblast


title: Sample_45

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_45

value: 20 months


title: Sample_44

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_44


title: Sample_46

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_46


title: PN1_rna_muscle

description: Total RNAseq from adult tissue


title: Sample_38

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_38

value: HFCD+FMD 11CYCLES RF4 days


title: WT_MEFs_w_IL-6_rep2


title: Arid5a-/-_MEFs_wo_IL-6_rep1


title: PARK2-PD1 rep1 line DN PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD2dn_1

value: neurons presumably dopaminergic

value: Parkinson's disease


title: PARK2-PD1 rep2 line DN PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD1dn_2

value: PARK2:2 exon (del 202-203 AG), 1 intron (splicing mutation IVS1+1G/A)


title: Sample_43

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_43


title: PN2_rna_liver

description: Total RNAseq from adult tissue

value: male


title: AS1_mC_liver_run2

description:
WGBS from adult tissue
AS_l_n2_50bpmean_SNPcorr.bw

organism: Aulonocara stuartgranti

extract_protocol:
Genomic DNA extracted using phenol/chlorophorm approach (see SUPP methods)
DNA strand-specific library using methylated adaptor (NEB) followed by bisulfite conversion (Imprint, Sigma), according to manusfacturer's instructions. WGBS libraries contain lambda genome spike-in control (0.2% w/w).

value: wild-caught


title: AS1_mC_liver_run1


title: Sample_33

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_33

value: CNTR 11CYCLES RF4 days


title: norma2 rep2 line DN HD 1.1S

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma2dn_2

value: normal

value: healthy


title: Sample_30

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_30

source_name: Heart

value: HFCD 11CYCLES RF4 days


title: PARK2-PD1 rep3 line DN PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD1dn_3


title: WT_MEFs_wo_IL-6_rep2

description: WT MEFs without IL-6 treatment for 24 h


title: Sample_41

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_41


title: PN1_rna_liver

description: Total RNAseq from adult tissue


title: RL2_rna_muscle

description: Total RNAseq from adult tissue

organism: Rhamphochromis longiceps

value: skeletal muscle


title: Sample_28

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_28


title: Sample_40

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_40


title: Sample_27

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_27


title: norma1 rep2 line DN RG2L

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma1dn_2


title: Sample_39

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_39


title: AS2_mC_liver_run2

value: female


title: RL1_rna_muscle

description: Total RNAseq from adult tissue


title: AS2_mC_liver_run1


title: Sample_37

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_37


title: PARK2-PD1 rep1 line DN PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into terminally differentiated neurons
TPM_DN.tsv
PARK2-PD1dn_1


title: Sample_36

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_36


title: Sample_35

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_35


title: Sample_34

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_34


title: norma2 rep3 line DN HD 1.1S

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma2dn_3


title: PARK2-PD1 rep3 line NP PDS14

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD3np_3

source_name: neural progenitors

value: neural progenitors

value: PARK2:heterozygous deletion of 2 exon


title: RL2_rna_liver

description: Total RNAseq from adult tissue

value: liver


title: Sample_42

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_42


title: Sample_32

description:
Adipose_normcounts.txt
Adipose_rawcounts.txt
Sample_32

value: 21 months


title: RL1_rna_liver

description: Total RNAseq from adult tissue


title: Sample_29

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_29

value: 22 months


title: norma2 rep1 line DN HD 1.1S

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma2dn_1


title: PARK2-PD1 rep1 line NP PDS14

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD3np_1


title: norma1 rep1 line DN RG2L

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma1dn_1


title: norma1 rep3 line DN RG2L

description:
iPSCs from healthy donors were differentiated into terminally differentiated neurons
TPM_DN.tsv
norma1dn_3


title: Sample_18

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_18

value: 20 months


title: DL3_rna_muscle

description: Total RNAseq from adult tissue

organism: Diplotaxodon limnothrissa


title: Sample_15

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_15

value: CNTR11CYCLES RF4 days


title: Sample_26

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_26


title: Sample_24

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_24

value: HFCD+FMD 11CYCLES RF4 days


title: RL3_rna_muscle

description: Total RNAseq from adult tissue


title: PARK2-PD1 rep3 line NP PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD2np_3

value: PARK2:homozygous deletion of 8 exon

value: Parkinson's disease


title: PARK2-PD1 rep2 line NP PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD2np_2


title: Sample_23

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_23


title: Sample_20

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_20


title: Sample_25

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_25


title: Sample_19

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_19


title: Sample_21

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_21


title: RL3_rna_liver

description: Total RNAseq from adult tissue

value: male

value: wild-caught


title: Sample_16

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_16

value: CNTR 11CYCLES RF4 days


title: DL2_rna_muscle

description: Total RNAseq from adult tissue


title: Sample_13

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_13


title: PARK2-PD1 rep2 line NP PDS14

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD3np_2


title: DL1_rna_muscle

description: Total RNAseq from adult tissue


title: Replicate 1 abundance not5delta 3418

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

description: Biological replicate 1 of 2.

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on mean fluorescence signal (background fluorescence substraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards E. coli tRNALys2, human tRNASer3, E. coli tRNATyr2, human tRNAHis1) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios.

organism: Saccharomyces cerevisiae

source_name: cultivated not5delta uncharged cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNALys2, E. coli tRNATyr2, human tRNASer3, human tRNAHis1) were added to 5 µg extracted total RNA prior to deacetylation.
2. For  abundance arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9); For tRNA charging arrays total RNA  was oxidized with periodate and thereafter treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation; tRNA standards were added prior the deacylation step.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 1h at RT in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol: Cells were cultivated as described in: Pansenko et al.  Co-translational assembly of proteasome subunits in NOT1-containing assemblysomes, Nature Structural & Molecular Biologyvolume 26, pages110–120 (2019).

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich) and for arrays to determine the charged fraction with acidic phenol (pH 4.5) according to manufacturer's protocol

tag: genotype/variation

value: not5D (isogenic except not5::KANMX4)

source_name: cultivated wild-type cells - uncharged tRNA


title: DL3_rna_liver

description: Total RNAseq from adult tissue


title: PARK2-PD1 rep1 line NP PDS13

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD2np_1


title: Sample_14

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_14

tag: treatment


title: Sample_17

description:
Heart_normcounts.txt
Heart_rawcounts.txt
Sample_17


title: Replicate 1 abundance not4delta 3417

description: Biological replicate 1 of 2.

source_name: cultivated not4delta uncharged cells

value: not4D (isogenic except not4::KANMX4)


title: Replicate 2 abundance not5delta 3418

description: Biological replicate 2 of 2.


title: PARK2-PD1 rep3 line NP PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD1np_3

tag: genotype

value: PARK2:2 exon (del 202-203 AG), 1 intron (splicing mutation IVS1+1G/A)


title: DL2_rna_liver

description: Total RNAseq from adult tissue


title: Replicate 2 abundance not4delta 3417

description: Biological replicate 2 of 2.


title: norma3 rep3 line NP RFD 3.9 L

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma3np_3

value: normal

value: healthy


title: DL1_rna_liver

description: Total RNAseq from adult tissue


title: Replicate 2 charging not5delta 3418

description: Biological replicate 2 of 2.

source_name: cultivated not5delta charged cells


title: LA1-5s Normoxia R2

city: Vilnius

first: Giedrius

last: Vilkaitis

address: Sauletekio av. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

data_processing:
Select reads with length >= 80 nt
Select reads with 5' adapter and trim 3' adapter from the remaining reads
Align reads to a human genome (hg19 build), minimum mapping quality 30
Remove PCR duplicates (used an in house script)
Calculate coverage per CG (used an in house script)
Calculate weighted coverage and CG density (used an in house script)
Calculate h-density (used an in house script)
Genome_build: hg19
Supplementary_files_format_and_content: "h_density" bedGraph files contain hmTOP-seq h-density values for each CG

growth_protocol: 1:1 mixture of MEM medium with nonessential amino acids and Ham's F12 nutrient mixture; 15% FBS (SK-N-BE(2)), 15% heat-inactivated FBS (BE(2)-C and BE(2)-M17), 10% FBS (LA-N-1, LA1-5s and LA1-55n); 37°C; 5% CO2.

extract_protocol:
Standard DNA phenol-chloroform extraction
5hmC in sonicated  genomic DNA was glycosylated with 6-azide-glucose. After ligation of adapters as described previously (Stasevskij et al., 2017),  the alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety of the modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads and subsequently used in a DNA priming reaction from the tethed oligonucleotide. Primed DNA library was amplified, size-selected and subjected to Ion Proton sequencing.

treatment_protocol: Normoxia - 72 h in atmospheric O2 concentration; hypoxia - 72 h in 1% O2

value: normoxia


title: Replicate 1 charging WT 3415

description: Biological replicate 1 of 2.

source_name: cultivated wild-type cells - charged tRNA

value: MY3415 [BY4739 (Euroscarf) MATalpha his3 leu2 ura3 lys2]


title: LA1-5s Normoxia Control


title: norma3 rep2 line NP RFD 3.9 L

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma3np_2

value: neural progenitors


title: PARK2-PD1 rep2 line NP PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD1np_2


title: Replicate 1 charging not4delta 3417

description: Biological replicate 1 of 2.

source_name: cultivated not4delta charged cells


title: LA1-5s Normoxia R1


title: Replicate 2 charging not4delta 3417

description: Biological replicate 2 of 2.


title: Batch2 BR-Combination 0.08uM rep3

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

description:
BR-Combination 0.08uM rep3
Batch2

data_processing:
Quality check and adapter trimming of RNA-seq data were conducted using FastQC and TrimGalore (https://www.bioinformatics.babraham.ac.uk/), respectively.
The cleaned reads were mapped to human genome assembly GRCh38 (hg38) via the STAR aligner (v2.7.3a).
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) with human gene annotation GRCh38.84.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

growth_protocol: Human lung cancer A549 cell line (CCL-185) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in RPMI1640 (Gibco, Grand Island, NY, USA) containing 10% heat-inactivated fetal bovine serum (FBS, Gibco), 100 IU/mL penicillin/100 mg/mL streptomycin (P/S; Gibco).

extract_protocol:
Total RNA was isolated from tissue using Maxwell (Promega) based method.
One 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.   The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega). The library is circularized at 37 °C for 30 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 100 bp paired-end reads.

treatment_protocol: We obtained lyophilized powder of water extract of Bupleuri Radix (W-BR; 3-10-0054) and ethanol extract of Bupleuri Radix (E-BR; 3-10-0097) from Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM; Naju, Korea). Each powder was dissolved in 2% dimethyl sulfoxide (DMSO; Sigma, St Louis, MO, USA) to a final concentration of 10 mg/mL, filtered, and stored at -20°C until use.

value: Combination of seven compounds (Saikosaponin A,Saikosaponin B1,Saikosaponin B2,Saikosaponin B3,Saikosaponin B4,Saikosaponin C,Saikosaponin D)

tag: treatment dose


title: LA1-5s Hypoxia Control

value: hypoxia


title: Replicate 1 charging not5delta 3418

description: Biological replicate 1 of 2.


title: Batch2 BR-Combination 2uM rep3

description:
BR-Combination 2uM rep3
Batch2


title: Batch2 BR-Combination 0.4uM rep3

description:
BR-Combination 0.4uM rep3
Batch2


title: Batch2 Saikosaponin D 0.2uM rep3

description:
Saikosaponin D 0.2uM rep3
Batch2

value: Saikosaponin D


title: LA1-5s Hypoxia R2


title: Replicate 2 charging WT 3415

description: Biological replicate 2 of 2.


title: PARK2-PD1 rep1 line NP PDL 1.5L

description:
iPSCs from Parkinson's disease patients were differentiated into uncommitted neural progenitors
TPM_NP.tsv
PARK2-PD1np_1


title: LA1-5s Hypoxia R1


title: norma2 rep3 line NP HD 1.1S

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma2np_3


title: Batch2 Saikosaponin D 1uM rep3

description:
Saikosaponin D 1uM rep3
Batch2


title: LA1-55n Normoxia Control


title: Batch2 Saikosaponin D 5uM rep3

description:
Saikosaponin D 5uM rep3
Batch2


title: LA1-55n Normoxia R2


title: norma2 rep2 line NP HD 1.1S

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma2np_2


title: LA1-55n Normoxia R1


title: LA1-55n Hypoxia Control


title: Batch2 BR-Combination 0.08uM rep2

description:
BR-Combination 0.08uM rep2
Batch2


title: norma1 rep2 line NP RG2L

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma1np_2


title: LA1-55n Hypoxia R2


title: norma3 rep1 line NP RFD 3.9 L

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma3np_1


title: LA1-55n Hypoxia R1


title: LA-N-1 Normoxia R2


title: Batch2 BR-Combination 2uM rep2

description:
BR-Combination 2uM rep2
Batch2


title: Batch2 Saikosaponin D 0.2uM rep2

description:
Saikosaponin D 0.2uM rep2
Batch2


title: LA-N-1 Normoxia Control


title: Batch2 BR-Combination 0.4uM rep2

description:
BR-Combination 0.4uM rep2
Batch2


title: norma1 rep1 line NP RG2L

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma1np_1


title: Batch2 Saikosaponin D 5uM rep2

description:
Saikosaponin D 5uM rep2
Batch2


title: LA-N-1 Hypoxia R2


title: BE(2)-C Normoxia Control


title: LA-N-1 Normoxia R1


title: BE(2)-C Hypoxia Control


title: LA-N-1 Hypoxia R1


title: Batch2 Saikosaponin D 1uM rep2

description:
Saikosaponin D 1uM rep2
Batch2


title: BE(2)-C Normoxia R2


title: BE(2)-C Hypoxia R2


title: norma2 rep1 line NP HD 1.1S

description:
iPSCs from healthy donors were differentiated into uncommitted neural progenitors
TPM_NP.tsv
norma2np_1


title: BE(2)-C Normoxia R1


title: Batch2 BR-Combination 0.4uM rep1

description:
BR-Combination 0.4uM rep1
Batch2


title: BE(2)-M17 Normoxia R2


title: Batch2 BR-Combination 0.08uM rep1

description:
BR-Combination 0.08uM rep1
Batch2


title: Batch2 BR-Combination 2uM rep1

description:
BR-Combination 2uM rep1
Batch2


title: BE(2)-M17 Hypoxia Control


title: BE(2)-C Hypoxia R1


title: LA-N-1 Hypoxia Control


title: BE(2)-M17 Normoxia R1


title: Batch2 Saikosaponin D 0.2uM rep1

description:
Saikosaponin D 0.2uM rep1
Batch2


title: BE(2)-M17 Hypoxia R2


title: BE(2)-M17 Hypoxia R1


title: Batch2 Saikosaponin D 1uM rep1

description:
Saikosaponin D 1uM rep1
Batch2


title: SK-N-BE(2) Normoxia R2


title: SK-N-BE(2) Normoxia Control


title: Batch2 Saikosaponin D 5uM rep1

description:
Saikosaponin D 5uM rep1
Batch2


title: BE(2)-M17 Normoxia Control


title: SK-N-BE(2) Normoxia R1


title: SK-N-BE(2) Hypoxia Control


title: Batch2 Saikosaponin C 0.4uM rep3

description:
Saikosaponin C 0.4uM rep3
Batch2

value: Saikosaponin C


title: E14_HiMeDIP

city: London

first: Miguel

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Library strategy: HiChIP
Reads were aligned using PAtChER (https://github.com/MBrancoLab/PAtChER), with -d 20000 for human data and -d 10000 for mouse data.
Read pairing information was removed using PAtChER's unpair tool.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation.
Normalised bigWig tracks were generated by dividing the HiChIP tracks by the corresponding Hi-C tracks, using bigwigCompare (deeptools) with --pseudocount 0.01 --skipZeroOverZero.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: BigWig tracks

source_name: E14 ES cells

growth_protocol: E14 ESCs were grown in DMEM GlutaMAX supplemented with 15% FBS, non-essential amino acids, 50μM 2-mercaptoethanol, antibiotic-antimycotic and 1,000 U/ml LIF. MCF7 and 2102Ep cells were grown in DMEM GlutaMAX supplemented with 10% FBS, penicillin-streptomycin and non-essential amino acids.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. After heat denaturation, methylated DNA was immunoprecipitated using an anti-5mC antibody (Active Motif 61479). Immunoprecipitated DNA was purified, followed by isolation of ligated fragments using streptavidin beads, and library amplification.
Libraries were prepared using the NEBNext ultra II DNA library prep kit.

value: E14 ES cells

tag: antibody

value: anti-5-methylcytosine (Active Motif 61479)


title: SK-N-BE(2) Hypoxia R2


title: SK-N-BE(2) Hypoxia R1


title: MZ1_rna_liver

description: Total RNAseq from adult tissue

organism: Maylandia zebra

value: liver

value: male


title: Batch2 Saikosaponin C 2uM rep3

description:
Saikosaponin C 2uM rep3
Batch2


title: MZ3_rna_muscle

description: Total RNAseq from adult tissue

value: skeletal muscle

value: wild-caught


title: GR-Input

city: Nanjing

first: shao

middle: yi

last: xue

address: LongMian street

institute: Nanjing Medical University

description: total RNA

data_processing:
Quality control: The library preparations were sequenced on an Illumina Novaseq or Hiseq platform with a paired-end read length of 150 bp according to the standard protocols. The sequencing was carried out with Min6 cells independent biological replicates.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
Peak calling: After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
Peak annotation: In the peak calling result, each peak was corresponding on gene, in which the peak was located in its exon. These genes were supposed as peak related genes, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software (version 3.0) to test the statistical enrichment of peak related genes in KEGG pathways.Besides, the distribution of peak on different function regions, such as 5’ UTR, CDS, 3’UTR was performed.
Different peak analysis: Differential peak calling was performed using exomePeak R package (version 2.16.0) with parameters of P-value less than 0.05 and fold_change more than 1. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Genome_build: mm10
Supplementary_files_format_and_content: differ peak text files and BigWig files(can be observed by IGV or uploaded to browsers such as UCSC for observation )

source_name: Mouse insulinoma cells

growth_protocol: The Min6 cells were cultured in DMEM medium containing 25mM D- glucose, 15％ FBS, 10mM HEPES, 1mM sodium pyruvate, 100 U/mL penicillin, 100 ug/mL streptomycin and 50μmol/L beta- mercaptoethanol, and incubated in a cell incubator at 37℃ with 95% air and 5% CO2.

extract_protocol:
RNA in cells was extracted by Trizol, m6A on mRNA was specifically identified by m6A antibody, and methylated RNA fragments were enriched by RNA immunoprecipitation method
The mRNA m6A was sequenced by MeRIP-seq at Novogene (Beijing, China). Briefly, a total of 300 µg RNAs were extracted from the Min6 cells. The integrity and concentration of extracted RNAs were detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare), respectively. Fragmented mRNA (~100 nt) was incubated for 2 hr at 4℃ with anti-m6A polyclonal antibody (Synaptic Systems) in the immunoprecipitation experiment. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit for Illumina (New England Biolabs). The library preparations were sequenced on an Illumina Novaseq or Hiseq platform with a paired-end read length of 150 bp according to the standard protocols.

treatment_protocol: Before transfection, the cell state was observed, and a proper amount of cells were inoculated into 10cm dishes, and the cell density was controlled at 50%~70%. After 16-24 hours, Lipofectamine 2000(Invitrogen) was used for transfection, and 10ug plasmid and 12 ul Lipofectamine 2000 were added to each 10cm dish. 24 hours after transfection, RNAs were extracted by trizol reagent.

value: Mouse insulinoma cells

value: transfected GR expression vector


title: MZ1_rna_muscle

description: Total RNAseq from adult tissue


title: MZ2_rna_muscle

description: Total RNAseq from adult tissue


title: MZ3_rna_liver

description: Total RNAseq from adult tissue


title: Batch2 Saikosaponin B4 0.4uM rep3

description:
Saikosaponin B4 0.4uM rep3
Batch2

value: Saikosaponin B4


title: MZ2_rna_liver

description: Total RNAseq from adult tissue


title: E14_HiC

data_processing:
Reads were aligned using PAtChER (https://github.com/MBrancoLab/PAtChER), with -d 20000 for human data and -d 10000 for mouse data.
Read pairing information was removed using PAtChER's unpair tool.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: BigWig tracks

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. To match the HiChIP protocol, DNA was heat denatured, followed by purification, isolation of ligated fragments using streptavidin beads, and library amplification.
Libraries were prepared using the NEBNext ultra II DNA library prep kit.


title: AC2_mC_liver_run2

description:
WGBS from adult tissue
AC_l_n2_50bpmean_SNPcorr.bw

organism: Astatotilapia calliptera


title: Batch2 Saikosaponin C 2uM rep2

description:
Saikosaponin C 2uM rep2
Batch2


title: Batch2 Saikosaponin B4 10uM rep3

description:
Saikosaponin B4 10uM rep3
Batch2


title: Batch2 Saikosaponin C 0.4uM rep2

description:
Saikosaponin C 0.4uM rep2
Batch2


title: Batch2 Saikosaponin C 10uM rep3

description:
Saikosaponin C 10uM rep3
Batch2


title: AC2_mC_liver_run1


title: Ctrl-Input

description: total RNA

value: transfected control vector


title: Batch2 Saikosaponin B4 0.4uM rep2

description:
Saikosaponin B4 0.4uM rep2
Batch2


title: Batch2 Saikosaponin B4 2uM rep3

description:
Saikosaponin B4 2uM rep3
Batch2


title: Ctrl-m6A-IP

description: m6A-IP RNA


title: AC1_mC_liver_run2


title: AC1_mC_liver_run1


title: Min6-NC

data_processing:
Differential expression analysis of two conditions/groups (twobiologicalreplicatespercondition) was performed using the DESeq2 R package(1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.There sulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.Genes with an adjusted P-value<0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary_files_format_and_content: raw gene counts for every gene and every sample and Matrix table for GRvsNC Differential genes and enrichment analysis

growth_protocol: The Min6 cells were cultured in DMEM medium containing 25mM D- glucose, 15％ FBS, 10mM HEPES, 1mM sodium pyruvate, 100 U/mL penicillin, 100 ug/mL streptomycin and 50umol/L beta-mercaptoethanol, and incubated in a cell incubator at 37℃ with 95% air and 5% CO2.

extract_protocol:
Total RNA was extracted by Trizol and used for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before transfection, the cell state was observed, and a proper amount of cells were inoculated into 3.5cm dishes, and the cell density was controlled at 50%~70%. After 16-24 hours, Lipofectamine 2000(Invitrogen) was used for transfection, and 4ug plasmid and 4.8 ul Lipofectamine 2000 were added to each 3.5cm dish.


title: Min6-GR


title: PG3_rna_muscle

description: Total RNAseq from adult tissue

organism: Petrotilapia genalutea


title: Batch2 Saikosaponin B4 2uM rep2

description:
Saikosaponin B4 2uM rep2
Batch2


title: GR-m6A-IP

description: m6A-IP RNA


title: iMEFB_washout_rep2

city: Paris

first: Daniel

last: Holoch

address: 26 rue d'Ulm

institute: Institut Curie, Centre de Recherche

data_processing:
Adapter trimming (Trim Galore! 0.4.4 wrapper with default settings)
Discard reads aligning to complete mouse rRNA sequence (Bowtie 2.2.9)
Alignment to mouse genome (Tophat 2.1.1 & Bowtie 2.2.9)
Gene counts (FeatureCounts 1.5.1)
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.txt files contain gene counts
Supplementary_files_format_and_content: read_counts.txt files contain wild-type and mutant read counts for targeted experiments

source_name: Immortalized mouse embryonic fibroblast line B

extract_protocol:
Total or nascent RNA was extracted using Trizol reageant following manufacturer's instructions
Truseq Stranded mRNA

value: c-myc-immortalized mouse embryonic fibroblasts

tag: genotype/treatment

value: wild-type after washout of  2 uM UNC1999 + 4 uM A395

tag: fraction

value: total RNA