title: human melanoma cell line SkMel28S_rep2

city: RENNES

first: Sebastien

last: CORRE

address: Faculté de médecine, 2 av du Pr Léon Bernard

department: IGDR

institute: CNRS UMR6290

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were aligned to the human genome release hg38 using HISAT2 V2.0.5, default parameter
Quantification of genes was then performed using CUFFDIFF v2.2.1, default parameter
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Melanoma

growth_protocol: Human melanoma cell lines (SK28, 501Mel, M229) were grown in humidified air (37°C, 5% CO2) in RPMI-1640 medium supplemented with 10% Fetal Bovine and 1% Penicillin-Streptomycin antibiotics.

extract_protocol:
Total RNA was extracted from melanoma cell lines using Nucleospin RNA kit following the recommandations of Macherey Nagel.
Libraries were generated from 500ng of total RNAs using Truseq RNA Library Prep Kit v2 (Illumina) following the recommandations. The concentration of library was first quantified by Qubit2.0, then diluted to 1 ng/ul,  and the insert size was checked by Agilent 2100 and was further quantified by qPCR (library concentration > 2 nM). If the library is qualified, it will be sequenced on an NovaSeq 6000 Illumina platform according to  effective concentration and data volume and using NovaSeq 6000 Reagent Kits.

treatment_protocol: Human melanoma cell lines (SK28, 501Mel, M229) have been treated with c-Src inbhibitors (Dasatinib, Selleckchem, S1021) or (Bosutinib, Selleckchem, S1014) at the dose of 1mM for 24h in culture medium, or with ITE (2-(1’H-indole-3’-carbonyl)-thiazole-4-carboxylic acid methyl ester) (5mM, MCE, HY-19317) for 24h.

value: Melanoma

value: BRAFi sensitive SkMel28

value: wild type

value: untreated


title: H3K4ME3 Hypoxia Sample 2

status: Public on Oct 18 2022

type: SRA

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

description:
H3K4ME3_H2
H3K4me3-Hypoxia_peaks.bed

library_source: genomic

data_processing:
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools.
The peaks were then called using chromstaR in differential mode.
Assembly: mm10
Supplementary files format and content: Tab-separated text file of peaks called by chromstaR.

molecule: genomic DNA

organism: Mus musculus

source_name: cell culture

growth_protocol: Bone-marrow MSCs were cultured in T25 flasks under humidified conditions in hypoxia (2% O2, 5% CO2, 37°C) or normoxia (21% O2, 5% CO2, 37°C). Cells were cultured in control α-MEM medium. On day 3 of cell culture the medium was changed,  on day 5 cells  were passaged, using Trypsin-EDTA. On day 12, FACS was used to isolated purified MSCs.

extract_protocol:
ChIP-seq was performed as described previously (Tessarz et al., 2014), using 105 MSCs per IP.
Following DNA purification libraries were prepared using Nextera PCR primers and the NEBNext High-Fidelity PCR Master Mix. Libraries were PCR amplified. DNA concentration of the libraries was measured with Qubit and library quality was assessed by running samples on the TapeStation.

tag: age

value: 3-5 months

tag: oxygen level

tag: cell type

value: Bone-marrow MSCs


title: 18lo_biorep3

city: Aurora

first: Victor

middle: A

last: Ruthig

state: CO

department: Pediatrics, Section of Developmental Biology

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
Supp_ScriptFull.txt
DND1seq__Supp_DND1seqFilters.RData
DND1seq_Supp_Dnd1Terseq_Unique.csv
DND1seq_Supp_GCList_Junique.csv
DND1seq_Supp_GCList_Lunique.csv
DND1seq_Supp_GCList_T_Iunique.csv
DND1seq_Supp_GCList_T_T1unique.csv
DND1seq_Supp_GO-0000077(DNAdamage).csv
DND1seq_Supp_GO-0003723(RNAbinding).csv
DND1seq_Supp_GO-0006119(OxidativePhosphorylation).csv
DND1seq_Supp_GO-0006412(Translation).csv
DND1seq_Supp_GO-0007010(CytoOrg).csv
DND1seq_Supp_GO-0007049(CellCycle).csv
DND1seq_Supp_GO-0016570(HistoneModification).csv
DND1seq_Supp_GO-0030198(ECMorg).csv
DND1seq_Supp_GO-0033182(HistUbi).csv
DND1seq_Supp_GO-0044391(RibosomalSubunit).csv
DND1seq_Supp_GO-0045786(NegCellCycle).csv
DND1seq_Supp_GO-0045787(PosCellCycle).csv
DND1seq_Supp_GO-0048193(Golgi).csv
DND1seq_Supp_GO-0051276(ChroOrg).csv
DND1seq_Supp_GO-0061621(CanonicalGlycolysis).csv
DND1seq_Supp_GO-0071103(DNAconCha).csv
DND1seq_Supp_GO-1902275(RchrOrg).csv
DND1seq_Supp_lohiGeneList.csv
DND1seq_Supp_RIPgeneList.csv
DND1seq_Supp_SomaList_Junique.csv
DND1seq_Supp_SomaList_Sunique.csv
DND1seq_Supp_SomaList_Tunique.csv
Proc_DND1seq_Filtering.xlsx
hiloRNAseq_Supp_DND1-GFP_hiloRNA-seq.RData
hiloRNAseq_Supp_MGIBatchReport_hilo.csv
Proc_hiloRNAseq_hiloRNAseqMaster.xlsx

library_source: transcriptomic

data_processing:
Basecalling performed on Illumina NovaSeq 6000 as 50bp paired-end reads
Reads mapped to the mm10 (GRCm38) mouse genome using Salmon (v1.3.0)
Mapped reads annotated using the Ensemble Mus musculus reference (version 79)
Differential gene expression analysis performed using DeSeq2 (v1.32.0)
Further annnotation and filtering was performed in RSQLite (v2.2.8)
Genome_build: GRCm38
Supplementary_files_format_and_content: intermediate and supporting files, including full pipeline script and Rdata environment, final output as excel file with TPM and differential expression values for each sample

molecule: total RNA

source_name: Male Germ Cells

extract_protocol:
Testes were collected from DND1(EGFP/EGFP) fetuses at E16.5 and E18.5, testes were disassociated, male germ cells were sorted as DND1-lo and DND1-hi using FACS for GFP, total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
Sample libraries were prepared with SMART-SeqRTM v4 UltraRTM Low Input RNA Kit (Takara Clontech Kit Cat# 63488).

tag: strain background

value: CD1 hybrid

tag: allele

tag: developmental stage


title: ada2, LIT, rep2 [ADA2-LIT-2]

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

data_processing:
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of C. neoformans H99 and annotation data were downloaded from the NCBI FTP server, derived from Broad Insitute.
The reads were aligned to the C. neoformans H99 genome sequence using Hisat2 v2.2.1 with the HISAT and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30” and “– dta -1” options and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with the “-Sb -@ 8” option for converting, and “-@ 20 –m 2000000000” option for sorting, and the other parameters were set as default.
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using the “-p 12” option, and also the “-B” option to run the Ballgown analysis. Assembled transcripts were merged to a single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase of exon per Million fragments mapped (FPKM). The FPKM and read count matrix were generated by the R package “isoformswitchanalyzerR” and analyzed by DESeq2. Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown
The volcano plot was illustrated by using R v4.1.0 and R package "EnhancedVolcano", with the cutoff (more than two-fold changes with p< 0.05). PCA plot was generated by R package "DeBrowser" and heatmap was also generated by following R package
KEGG pathway analysis was performed using the R package "Cluster profiler", after changing H99S gene locus ID to JEC21 orthologue locus ID.
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample

organism: Cryptococcus neoformans

growth_protocol: Cryptococcus neoformans strains were grown at 30°C for 16hr in a YPD medium and transferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8.

extract_protocol:
Then the cells were harvested by centrifugation and lyophilized. Total RNAs were prepared as described above and purified with RNeasy Mini Kit (QIAGEN). The concentration was measured by Quant-IT RiboGreen (Invitrogen).
The quality of the RNA was verified by the TapeStation RNA screentape (Agilent). Cultured samples were prepared independently three times, and the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by the Illumina platform.

treatment_protocol: Half of the cells were further incubated in an LIT liquid medium for 2hr

tag: cell line

value: Fungi

tag: genotype

value: ada2 knockout

tag: treatment

value: capsule-inducing condition


title: 18lo_biorep2


title: human melanoma cell line SkMel28S_rep1

country: France

organism: Homo sapiens

tag: tissue


title: ada2, LIT, rep1 [ADA2-LIT-1]


title: 18hi_biorep2


title: H3K27AC Hypoxia Sample 2

description:
H3K27AC_H2
H3K27ac-Hypoxia_peaks.bed


title: human melanoma cell line SkMel28S-AKR KO_rep2

value: AhR -/-


title: ada2, basal, rep3 [ADA2-Basal-3]

value: basal


title: H3K4ME3 Hypoxia Sample 1

description:
H3K4ME3_H1
H3K4me3-Hypoxia_peaks.bed


title: 18hi_biorep1


title: human melanoma cell line SkMel28S-AKR KO_rep1


title: human melanoma cell line SkMel28S-AKR KO and rescue with CA-AhR_rep2

value: AhR -/- rescue CA-AhR (constitutively active)


title: 16lo_biorep4


title: human melanoma cell line SkMel28S-AKR KO and rescue with CA-AhR_rep1


title: Input Hypoxia Sample 1

description:
Input_H1
none


title: H3K27AC Hypoxia Sample 1

description:
H3K27AC_H1
H3K27ac-Hypoxia_peaks.bed


title: 16hi_biorep4


title: MHC- DP TCR transcripts (file prefix: NDP_TCR_)

city: Boston

first: Jonathan

middle: S.

last: Duke-Cohan

state: MA

address: 450 Brookline Avenue JF517

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: sc-TCR repertoire

data_processing:
Library strategy: TCR-seq
For the thymocyte scRNA-Seq analysis, all raw sequencing reads were processed using the 10X Genomics CellRanger bioinformatics pipeline v3.0.2.
For the thymocyte scRNA-Seq analysis, all analysis was performed using the 10x Loupe browser v4.2 (for Gene expression) and the 10x Single-cell V(D)J browser v3.0.0 (for TCR clonotypic analysis).
For the Gene Expression analysis of the stromal support cells expressing MHC (OP9-DL4) or not expressing MHC (OP9-DL4-Tap2/B2m-KO), all initial processing  (Quality control: Error Rate Distribution, GC content distribution and data filtering), mapping to mouse reference genome, and normalized gene expression quantification, was performed by the sequencing facility at Novogene using standard procedures.
Genome_build: mm10

source_name: Thymocytes developing for 9 days in vitro from stem cells

growth_protocol: Wild-type hematopoietic stem cells isolated from fetal liver were cultured on stromal support cells expressing MHC (OP9-DL4) or not expressing MHC (OP9-DL4-Tap2/B2m-KO) for 9d

extract_protocol:
Following growth cells were separated by surface phenotype using FACS into DN3a, DN3b, DN4 and DP cells
Cell separation protocol: Isolated cells were washed, assessed for viability, and loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA libraries were generated using the Single Cell 5’ Reagent Kit (10X Genomics) per user guide together with the 5' V(D)J Kit (10X Genomics)for parallel determination of single cell TCR alpha and beta chains representation

tag: strain

value: hematopoietic stem cells


title: human melanoma cell line SkMel28R_rep2

value: BRAFi resistant SkMel28


title: 16lo_biorep3


title: 18lo_biorep1


title: WT, LIT, rep6 [WT_LIT_2hr_3]

value: WT


title: ada2, basal, rep1 [ADA2-Basal-1]


title: WT, LIT, rep5 [WT_LIT_2hr_2]


title: ada2, basal, rep2 [ADA2-Basal-2]


title: MHC- DN4 TCR transcripts (file prefix: NDN4_TCR_)

description: sc-TCR repertoire


title: MHC- DN3b TCR transcripts (file prefix: NDN3b_TCR_)

description: sc-TCR repertoire


title: WT, LIT, rep4 [WT_LIT_2hr_1]


title: WT, LIT, rep3 [WT-LIT-3]


title: human melanoma cell line SkMel28R-AKR KO_rep2


title: 16lo_biorep2


title: 16hi_biorep2


title: MHC- DN3a TCR transcripts (file prefix: NDN3a_TCR_)

description: sc-TCR repertoire


title: human melanoma cell line SkMel28R-AKR KO_rep1


title: WT, LIT, rep2 [WT-LIT-2]


title: MHC+ DP TCR transcripts (file prefix: PDP_TCR_)

description: sc-TCR repertoire


title: human melanoma cell line SkMel28R-ITE treated_rep2

value: ITE (2-(1’H-indole-3’-carbonyl)-thiazole-4-carboxylic acid methyl ester) (5mM) for 24h


title: Input Hypoxia Sample 2

description:
Input_H2
none


title: 16lo_biorep1


title: WT, LIT, rep1 [WT-LIT-1]


title: MHC+ DN4 TCR transcripts (file prefix: PDN4_TCR_)

description: sc-TCR repertoire


title: human melanoma cell line SkMel28R-ITE treated_rep1

value: Melanoma


title: 16hi_biorep1


title: human melanoma cell line SkMel28R_rep1


title: 16hi_biorep3


title: WT, basal, rep6 [WT_basal_3]


title: bud32(K54A), basal, rep3

data_processing:
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of Cryptococcus neoformans H99 and annotation data were downloaded from the NCBI ftp server
The reads were aligned to the Cryptococcus neoformans H99 genome sequence using Hisat2 v2.2.1 with the Hisat and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30”and “– dta -1”option and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with “-Sb -@ 8”option for converting, and “-@ 20 –m 2000000000” option for sorting and the other parameters set as default
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using “-p 12” option, and also “-B” option to run the Ballgown analysis.
Assembled transcripts were merged to single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase ofexon per Million fragments mapped (FPKM). The FPKM and readcount matrix was generated by R package “isoformswitchanalyzerR” and analyzed by DESeq2.
Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown. Volcano plot was illustrated by using R v4.1.0, with the cutoff (more than two-fold changes with p< 0.05).
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample

growth_protocol: C. neoformans strains grown overnight in YPD medium weretransferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.6.

extract_protocol:
The cells were then harvested by centrifugation and lyophilized. Total RNAs were isolated by Easy-BLUE (iNtRON), treated with DNase I (Qiagen), and puriﬁed with RNeasy MiniElute clean up kit (Qiagen) following the manufacturer’s instruction
Cultured samples were prepared independently three times for each strain, the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by Illumina platform.

value: K54A change of bud32


title: MHC+ DN3b TCR transcripts (file prefix: PDN3b_TCR_)

description: sc-TCR repertoire


title: human melanoma cell line SkMel28R-Das treated_rep1

value: wild type

value: Dasatinib (5mM) for 24h


title: human melanoma cell line SkMel28R-Das treated_rep2


title: WT, basal, rep5 [WT_basal_2]


title: bud32(K54A), basal, rep2


title: OP9-DL4 Class I knockout transcripts

description: RNA-Seq

data_processing:
For the thymocyte scRNA-Seq analysis, all raw sequencing reads were processed using the 10X Genomics CellRanger bioinformatics pipeline v3.0.2.
For the thymocyte scRNA-Seq analysis, all analysis was performed using the 10x Loupe browser v4.2 (for Gene expression) and the 10x Single-cell V(D)J browser v3.0.0 (for TCR clonotypic analysis).
For the Gene Expression analysis of the stromal support cells expressing MHC (OP9-DL4) or not expressing MHC (OP9-DL4-Tap2/B2m-KO), all initial processing  (Quality control: Error Rate Distribution, GC content distribution and data filtering), mapping to mouse reference genome, and normalized gene expression quantification, was performed by the sequencing facility at Novogene using standard procedures.
Genome_build: mm10

source_name: Bone marrow stromal cell line lacking all major MHC expression

extract_protocol:
Isolated cells were washed, assessed for viability, and 4x10e5/sample used for total RNA isolation using the Rneasy "Mini" protocol (Qiagen)
Total RNA processed for quality and library preparation by Novogene for 150PE sequencing

value: C57BL/6J female x C3H/HeJ male


title: MHC+ DN3a TCR transcripts (file prefix: PDN3a_TCR_)

description: sc-TCR repertoire


title: bud32(K54A), basal, rep1


title: gat201, LIT, rep2 [GAT201-LIT-2]

value: gat201 knockout


title: human melanoma cell line SkMel28R-AKR KO and rescue with CA-AhR_rep2

value: untreated


title: WT, basal, rep3 [WT-Basal-3]

value: Fungi


title: OP9-DL4  transcripts

description: RNA-Seq

source_name: Bone marrow stromal cell line


title: WT, basal, rep2 [WT-Basal-2]


title: kae1, basal, rep3

value: kae1 knockout


title: MHC- DP transcripts (file prefix: NDP_)

description: scRNA-Seq


title: WT, basal, rep1 [WT-Basal-1]


title: kae1, basal, rep2


title: MHC- DN4 transcripts (file prefix: NDN4_)

description: scRNA-Seq


title: kae1, basal, rep1


title: bud32, basal, rep3

value: bud32 knockout


title: WT, basal, rep4 [WT_basal_1]


title: human melanoma cell line SkMel28R-Bos treated_rep1

value: Bosutinib (1mM) for 24h


title: human melanoma cell line SkMel28R-Bos treated_rep2


title: NWR_PGCLCs_rep1

city: Osaka

first: Masafumi

last: Hayashi

address: 2-2 Yamada-oka, Suita

department: Department of Genome Biology

country: Japan

institute: Osaka University

data_processing:
Obtained reads were mapped to the CerSimSim1.0/cerSim1 genome using STAR. Mapped reads were counted and processed to TPM value by RSEM.
The gene ID were converted to human gene symbol using a rhinoceros-human-mouse correspondence table.
Genome_build: CerSimSim1.0/cerSim1
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

molecule: polyA RNA

organism: Ceratotherium simum cottoni

source_name: primordial germ cell like cells at day 4 of northern white rhinoceros induced by advanced RPMI 1640 with 10% KSR supplemented with LIF, SCF, EGF, Y-27632, IWR1, bpV, and forskolin

growth_protocol: Embryonic stem cells of southern white rhinoceros and induced pluripotent stem cells of northern white rhinoceros were maintained in hypoxic condition(5% O2 and 5% CO2) with DMEM/F12, 20% KSR, and 10 ng/ml of bFGF with or without 20ng/ml of activin A.

extract_protocol:
Total RNAs were extracted and purified using an RNeasy Micro Kit, and mRNAs were isolated with the NEBNext poly(A) mRNA magnetic isolation module (NEB).
Purified RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

value: primordial germ cell like cells

tag: parental line


title: human melanoma cell line-Mel501R-Ctrl(DMSO)

value: BRAFi resistant Mel501

value: DMSO (0,1%) for 24h


title: bud32, basal, rep2

value: basal


title: NWR_Preinduction_rep2

source_name: pre-induced cells of northern white rhinoceros

value: pre-induced cells

value: WT


title: human melanoma cell line SkMel28R-AKR KO and rescue with CA-AhR_rep1

value: Melanoma

value: BRAFi resistant SkMel28

value: AhR -/- rescue CA-AhR (constitutively active)


title: MHC- DN3a transcripts (file prefix: NDN3a_)

description: scRNA-Seq

value: hematopoietic stem cells


title: MHC+ DP transcripts (file prefix: PDP_)

description: scRNA-Seq


title: bud32, basal, rep1


title: human melanoma cell line-M229R-Ctrl(DMSO)

value: BRAFi resistant M229

value: wild type


title: NWR_iPSCs_rep2

source_name: induced pluripotent stm cells of northern white rhinoceros

value: embryonic stem cells


title: NWR_Preinduction_rep1


title: MHC+ DN4 transcripts (file prefix: PDN4_)

description: scRNA-Seq


title: human melanoma cell line-Mel501R-Bos treated


title: MHC+ DN3b transcripts (file prefix: PDN3b_)

description: scRNA-Seq


title: human melanoma cell line-M229R-Das treated

value: Dasatinib (5mM) for 24h


title: WT, basal, rep3

value: Fungi


title: NWR_iPSCs_rep1


title: WT, basal, rep2


title: human melanoma cell line-M229R-Bos treated


title: NWR_PGCLCs_rep2


title: MHC+ DN3a transcripts (file prefix: PDN3a_)

description: scRNA-Seq


title: MHC- DN3b transcripts (file prefix: NDN3b_)

description: scRNA-Seq


title: human melanoma cell line-Mel501R-Das treated


title: total RNAseq, swi6Chp1-like-CD, rep2

status: Public on Oct 17 2022

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
smallRNA-seq:Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Qiagen 3' adaptors were trimmed using cutadapt (v1.18) with the parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie (v1.2.2) with parameters -f -M 10000 -v 0 -S --best --strata. Bowtie sam output was converted to bam using samtools (v1.9). Bam files were converted to bed using bedtools bamtobed (v2.27.1), bed files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
RNA-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Fastq files were aligned using STAR (v2.7.3a) with the parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1 --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM --outSAMunmapped Within. STAR sam output was converted to bam using samtools (v1.9). Bam files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: mm10; Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV. Counts per million (CPM) table for the RNAseq samples as a text file.

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 30 degrees celsius.

extract_protocol:
Total RNA was extracted with the MasterPure RNA Purification Kit from epicenter (MPY03100).
Total RNA libraries were prepared with TruSeq Stranded Total RNA kit (Illumina, 20020599) according to manufacturer’s instructions.

value: h90 ade6-M210 leu1-32 ura4-DS/E mat3M::GFP-NatR swi6::swi6E80V-V82E-S116E-D120N-S122F


title: total RNAseq, clr4wt, rep3

value: h90 ade6-M216 leu1-32 ura4-DS/E


title: total RNAseq, swi6Chp1-like-CD, rep1


title: sgScramble treated astrocytes 2

type: RNA

city: Philadelphia

first: Guang-Xian

last: Zhang

state: PA

address: 900 walnut street

institute: Thomas Jefferson University

description: Primary astrocytes isolated from brain of p2-3 pups

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring software. RMA normalization was performed on the cel files generated from the samples.

label: biotin

source_name: brain

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Astrocytes were isolated from brain of p2-3 pups.

extract_protocol: Cells were isolated and RNAs were extracted by using Qiagen RNeasy Plus Kits. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: Primary astrocytes were infected with lentivirus carrying sgSirt1 or sgScramble, and selected with puromycin for 3 days, after which cells were treated with cocktail (C1q, IL-1α, TNF-α) for 24 hours.

value: astrocytes

tag: transduced with

value: sgScramble


title: sgSirt1 treated astrocytes 2


title: H3K9me2 ChIPseq, swi6Chp1-like-CD, rep1

extract_protocol:
ChIP was performed as described in Kuzdere et al. (2021). ChIP DNA was purified using AMPure XP beads.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.


title: Input ChIPseq, clr4wt, rep2


title: Input ChIPseq, swi6Chp1-like-CD, rep2


title: sgScramble treated astrocytes 1


title: H3K9me3 ChIPseq, swi6Chp1-like-CD, rep1


title: H3K9me3 ChIPseq, clr4wt, rep1


title: H3K9me2 ChIPseq, swi6Chp1-like-CD, rep2


title: sgSirt1 treated astrocytes 1


title: Input Swi6 ChIPseq, swi6Chp1-like-CD, rep2


title: H3K9me2 ChIPseq, clr4wt, rep2


title: H3K9me3 ChIPseq, swi6Chp1-like-CD, rep2


title: Input ChIPseq, clr4wt, rep1


title: total RNAseq, clr4wt, rep1


title: H3K9me3 ChIPseq, clr4wt, rep2


title: Input Swi6 ChIPseq, swi6Chp1-like-CD, rep1


title: Input Swi6 ChIPseq, clr4wt, rep1


title: H3K9me2 ChIPseq, clr4wt, rep1


title: WT, basal, rep1


title: total RNAseq, swi6Chp1-like-CD, rep3


title: Input Swi6 ChIPseq, clr4wt, rep2


title: ChIPseq_clr4wt_H3K9me3_1h_SpikeIn

value: h-/h- ade6-M210/ade6-M216 pat1::NatR/pat1::NatR pat1-as(L95A)::HygR/pat1-as(L95A)::HygR lys1::MatPc-Bleo


title: ChIPseq_clr4wt_Input_1h_SpikeIn


title: ChIPseq_clr4wt_H3K9me2_1h_SpikeIn


title: total RNAseq, clr4wt, rep2


title: Input ChIPseq, swi6Chp1-like-CD, rep1


title: ChIPseq_clr4wt_Input_Mitosis_as_SpikeIn


title: ChIPseq_clr4wt_H3K9me3_Mitosis_as_SpikeIn


title: ChIPseq_clr4wt_H3K9me2_Mitosis_as_SpikeIn


title: Input ChIPseq, clr4wt, Meiosis 7h, rep1, me2, me3

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 25°C or 30°C, depending on the strain. For more details see Methods section in Kuzdere et al. (2021)

extract_protocol:
ChIP was performed as described in Kuzdere et al. (2021). In brief, exponentially growing or synchronized fission yeast cells were fixed with formaldehyde and lysed by beat-beating. Chromatin was sheared by sonication and the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.


title: Input ChIPseq, clr4wt, Meiosis 6h, rep1, me2, me3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 2h, rep1


title: Input ChIPseq, clr4wt, Meiosis 2h, rep1, me2, me3


title: Input ChIPseq, clr4wt, Meiosis 3h, rep1, me2, me3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 1h


title: H3 ChIPseq, clr4wt, Mitosis (as.)


title: H3K9me3 ChIPseq, clr4wt, Mitosis (as.)


title: H3 ChIPseq, clr4wt, Meiosis 1h


title: Input ChIPseq, clr4wt, Meiosis 4h, rep1, me2, me3


title: Input ChIPseq, clr4wt, Meiosis 1h, rep1, me2, me3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 0h, rep1


title: H3K9me2 ChIPseq, clr4wt, Mitosis (as.)


title: total RNAseq, clr4wt, Meiosis 7h

value: h-/h- ade6-M210/ade6-M216 pat1::NatR/pat1::NatR pat1-as(L95A)::HygR/pat1-as(L95A)::HygR cen2(D107)::KanR-ura4+-lacO his7+::lacI-GFP lys1::MatPc-Bleo


title: Input ChIPseq, clr4wt, Meiosis 8h, rep1, me2, me3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 1h, rep1


title: H3K9me3 ChIPseq, clr4wt, Meiosis 1h


title: total RNAseq, clr4wt, Meiosis 5h


title: total RNAseq, clr4wt, Meiosis 4h


title: total RNAseq, clr4wt, Meiosis 3h


title: total RNAseq, clr4wt, Meiosis 2h


title: total RNAseq, clr4wt, Meiosis 1h


title: total RNAseq, clr4wt, Meiosis 0h


title: total RNAseq, clr4wt, Meiosis 6h


title: Input ChIPseq, clr4wt, Meiosis 0h, rep1, me2, me3


title: Input ChIPseq, clr4wt, Meiosis 5h, rep1, me2, me3


title: total RNAseq, clr4wt, Mitosis (as.)


title: total RNAseq, clr4wt, Meiosis 8h


title: LNCaP WT cells- RNAseq_GCN2iB_24hr_1

city: Indianapolis

first: Kirk

middle: Alan

last: Staschke

state: IN

address: 635 Barnhill Drive, MS4063

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Barcodes and sequencing adapters were trimmed using TrimGalore
Reads were aligned to Human reference genome GRCh38 (ENSEMBL) using HISAT2 aligner
Mapped reads were assigned to annotated genomic features of GRCh38 using featureCounts
Differential expression analysis was carried out using DESeq2 package
Genome_build: GRCh38 ENSEMBL
Supplementary_files_format_and_content: comma-separated values (csv) file shows the number of reads mapping to each gene (unnormalized counts) for all the samples

source_name: Human Prostate cancer cell line

growth_protocol: WT LNCaP cells were grown in phenol red free RPMI1640 complete media supplemented with 10% FBS and 1x Penicilin/Streptomycin

extract_protocol:
For mRNA seq, RNA was extracted with RNA easy plus kit (Qiagen) according to manufacturer's protocol.
Total RNA was submitted to Genewiz (South Plainfield, NJ) where they performed polyA selection followed by library preparation and sequencing.

treatment_protocol: WT LNCaP cells were plated and subjected to DMSO or GCN2iB treatment for 6 hours or 24hours in replicates of four

value: LNCaP

value: Human Lymph Node Carcinoma of the prostate


title: LNCaP WT cells- RNAseq_GCN2iB_6hr_1


title: LNCaP WT cells- RNAseq_GCN2iB_6hr_2


title: LNCaP WT cells- RNAseq_GCN2iB_24hr_2


title: LNCaP WT cells- RNAseq_GCN2iB_6hr_4


title: LNCaP WT cells- RNAseq_DMSO_3

value: DMSO


title: LNCaP WT cells- RNAseq_DMSO_1


title: LNCaP WT cells- RNAseq_DMSO_2


title: LNCaP WT cells- CHARGEseq_GCN2iB_EAA_8hr_4

description: tRNA

data_processing:
Barcodes and sequencing adapters were trimmed using cutadapt
Reads were aligned to custom human tRNA reference file constructed from gtRNAdb GRCh38 (UCSC) using Bowtie2 aligner
Charging status of the aligned tRNA was determined as outlined in the methods
Differential tRNA charging was calculated as mentioned in the methods
Genome_build: Custom human tRNA reference file constructed from gtRNAdb GRCh38 (UCSC)
Supplementary_files_format_and_content: comma-separated values (csv) file shows the read counts for total, uncharged and charged tRNAs (unnormalized counts) for all the samples

extract_protocol:
For CHARGE seq, total RNA was extracted with TRIzol (Life Technologies) according to manufacturer's protocol followed by tRNA extraction as mentioned in the methods
tRNA library was made in the lab as described in the methods and library was submitted to Genewiz (South Plainfield, NJ) where they performed sequencing

treatment_protocol: WT LNCaP cells were plated and subjected to DMSO or GCN2iB or GCN2iB plus EAA treatment for 8 hours in replicates of four


title: LNCaP WT cells- CHARGEseq_GCN2iB_EAA_8hr_2

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_EAA_8hr_1

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_8hr_4

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_8hr_1

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_8hr_2

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_8hr_3

description: tRNA


title: LNCaP WT cells- CHARGEseq_DMSO_2

description: tRNA


title: LNCaP WT cells- CHARGEseq_DMSO_1

description: tRNA


title: LNCaP WT cells- CHARGEseq_DMSO_3

description: tRNA


title: LNCaP WT cells- CHARGEseq_GCN2iB_EAA_8hr_3

description: tRNA


title: LNCaP WT cells- CHARGEseq_DMSO_4

description: tRNA


title: Liver Fli1/Erg KO, rep2

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
nfcore atacseq pipeline version 1.21
Adapters were trimmed with Trim Galore! (v0.6.4)
Alignment with BWA (v0.7.17-r1188)
Duplicates marked Picard (v2.23.1)
Samtools (v1.10) BEDtools (v2.29.2) and Pysam (v0.15.3) to remove duplicates, blacklisted regions, multmapped reads, and poor quality reads
MACS2 (v2.2.7.1) was used to call peaks with parameters --broad --broad-cutoff 0.1 -g mm --keep-dup all --nomodel -f BAMPE
Assembly: Ensembl 90 GRCm38
Supplementary files format and content: MACS2 broadPeak file output for each sample

source_name: Liver in vivo ECs

growth_protocol: cells were isolated from mouse liver

extract_protocol:
Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels.
Sorted endothelial cells were processed for ATAC-seq using the Zymo DNA Clean & Concentrator-5 kit and using NEBNext X2 MasterMix (New England Biolabs).

treatment_protocol: mice were treated with tamoxifen to induce gene deletion

value: Erg and Fli1 double knockout

value: Liver

value: Liver in vivo ECs


title: Liver Fli1/Erg KO, rep3


title: Liver Fli1/Erg KO, rep1


title: Liver Control, rep3

value: WT Control


title: Liver Control, rep1


title: LNCaP WT cells- RNAseq_GCN2iB_6hr_3


title: LNCaP WT cells- RNAseq_GCN2iB_24hr_3


title: LNCaP WT cells- RNAseq_GCN2iB_24hr_4


title: Liver D7 KO, rep5

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt

source_name: Liver in vivo D7

growth_protocol: cells were isolated from mouse liver at day 7 post tamoxifen induction

extract_protocol:
Mice were intravital injected with VE-cadherin antibody. Tissues were dissociated by Collagenase Dispase digestion and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.


title: Liver Control, rep2


title: Liver D7 Control, rep2

value: Wild Type


title: Liver D7 KO, rep1


title: Liver D7 KO, rep2


title: Liver D7 Control, rep4


title: Liver D7 Control, rep3


title: Liver D7 KO, rep4


title: Liver D7 Control, rep1


title: Liver D7 KO, rep3


title: LNCaP WT cells- RNAseq_DMSO_4


title: dKO Il1b + Tnfa, rep 1

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt (raw gene counts)

source_name: Liver in vitro ECs

growth_protocol: cells were isolated from mouse liver and cultured in vitro in EC media

extract_protocol:
Cells were labeled in culture with VE-cadherin antibody. Cells were harvested with acutase and stained for CD45 and CD31. Endothelial cells were sorted as live (Dapi negative), CD45 negative, CD31 positive, VE-cadherin positive cels. Sorted endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with 4-OHT to induce gene deletion and with or without IL1B and TNFA to incude inflammatory response

value: dKO

value: Il1b + Tnfa

value: Liver in vitro ECs


title: Fli1/Erg Brain, rep 3

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: counts.txt (raw gene count matrix)

source_name: Brain ECs in vitro

growth_protocol: Cells were isolated from mouse brain and cultured in vitro in EC media.

extract_protocol:
Cells were harvested with acutase, washed, and sorted for RNA-seq.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 4-OHT to induce gene deletion.

value: brain

value: cultured brain ECs


title: WT Il1b + Tnfa, rep 2

value: WT


title: dKO Control, rep 1

value: Control


title: WT Control, rep 2


title: WT Il1b + Tnfa, rep 1


title: dKO Il1b + Tnfa, rep 2


title: WT Control, rep 1


title: Fli1/Erg Brain, rep 2


title: Fli1/Erg Brain, rep 1


title: Control Brain, rep 2

value: Wild Type Control


title: Melb-a, iBRD9, 48 hours, replicate3

city: TOLEDO

first: Ivana

middle: L.

last: de la Serna

state: OH

address: 3000 Arlington Ave

department: Cell and Cancer Biology

institute: UNIV OF TOLEDO College of Medicine and Life Sciences

data_processing:
Raw data was converted to by CASAVA version 1.8.2
Sequence reads were trimmed for adapters, low quality, to achieve a Q score of over 50% of read is less than or equal to 5.
Mapping was to GRCm39 using ophat2 version 2.1.1 and bowtie2 version 2.4.5.
Read count and normalization was done using Gene Expression Analysis and CLC Genomic Workbench version 12.

source_name: skin

growth_protocol: Melb-a melanoblasts were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 40pM fibroplast growth factor, and 10ng/ml stem cell factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was prepared from vehicle (DMSO) or i-BRD9 treated Melb-a melanoblasts by TRIzol extraction (Invitrogen, Carlsbad, CA, USA) followed by the RNeasy kit (Qiagen, Hilden, Germany).
mRNA was purified using polyT oligo-attached magnetic beads and used to construct a library with the NEBNext Ultra RNA Library Kit. This was accomplished using by using Random hexamers and M-MuLV Reverse Transcriptase to generate the first cDNA strand. Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H.Double stranded cNDA was purified using AMPure XP beads. Fragments of 150-200 bp in lenght were purified using AMPure XP systme (Beckman Coulter)

treatment_protocol: When cells were 70% confluent, they were switched to DMEM supplemented with 10% fetal bovine serum (FBS), 2nM alpha melanocyte stimulating hormone (NDP-alpha MSH) and 200nM phorbol-myristate-acetate in the presence of vehicle (DMSO) or 10 microMolar iBRD9 for 48 hours

value: skin

value: Melb-a

value: Melanocyte

value: differentiation, iBRD9


title: Control Brain, rep 1


title: Control Brain, rep 3


title: Melb-a, iBRD9, 48 hours, replicate 2


title: Melb-a, DMSO, 48 hours, replicate 3

value: differentiation, Vehicle


title: Melb-a, iBRD9, 48 hours, replicate 1


title: Melb-a, DMSO 48 hours,  replicate2


title: Melb-a, DMSO, 48 hours,  replicate 1


title: ATACseq_Chd8cKO_2

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-Seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: format:fpkm_matrix ; Contain the estimated expression values produced by Cufflinks.
ATAC-Seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated by MACS14

source_name: mouse E14.5 NPCs

extract_protocol: ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 50,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.

treatment_protocol: ATAC-seq: For GFP+ NPC sorting, single cell suspension was prepared from E14.5 control and Chd8 cKO mouse cortices with papain dissociation, and cells were resuspended in PBS with 2 mM EDTA and 0.5% BSA for sorting.

tag: sample type

value: Chd8 cKO

tag: genotype/variation

value: Chd8 c/c, Emx1-cre, ccGFP

value: FACS sorted GFP+ NPCs


title: ATACseq_Control_1

value: Emx1-cre, ccGFP


title: ATACseq_Chd8cKO_1

source_name: mouse E14.6 NPCs


title: Ti-treated,  shoot, 03 days L2

city: Irapuato

first: Luis

middle: Herrera

last: Estrella

state: Guanajuato

address: Libr. Norte carr. León Km 9.6

department: UGA/Langebio

country: Mexico

institute: Centro de Investigacion y de Estudios avanzados del IPN

description: Ti-treated,  shoot, 03 days

data_processing:
FastQC v0.11.9 to check quality of sequencing reads
TrimGalore v0.6.6 and cutaddapt to remove adapters and low-quality sequences.
Reads abundance was quantified using the pseudo alignment program kallisto v0.44.0, using the A. thaliana genome Araport11
To integrate the transcript-level abundance estimates from kallisto into the edgeR pipeline we used the R package tximport v1.20.0
Assembly: Araport11
Supplementary files format and content: Root_norm.txt is a tab-delimited text files include normalized CPMs values for each Root tissue Sample
Supplementary files format and content: Shoot_norm.txt is a tab-delimited text files include normalized CPMs values for each Shoot tissue Sample

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: Arabidopsis seeds were surface sterilized and then kept in water in the dark at 4oC for two days for stratification. Arabidopsis seeds were sown onto 1% agar-0.1X MS medium plates. Seedlings were grown in a Percival chamber at 22 oC and a 16h light/8h dark photoperiod with a PAR intensity of ≈135 µmol·m-2·s-1. After five days, 160 seedlings were transfered to its respective treatment.

extract_protocol:
Root and shoot tissue from the 160 seedlings per treatment were collected separately and pooled in a single replicate, then flash-frozen in liquid nitrogen and homogenized to isolate total RNA using TRIzol
mRNA-seq libraries were generated using the TruSeq Illumina protocol

treatment_protocol: Ti 2mM were added to the MS agar media

value: Shoot

value: Ti 2mM


title: Control,  shoot, 03 days K2

description: Control,  shoot, 03 days


title: Ti-treated,  shoot, 03 days L3

description: Ti-treated,  shoot, 03 days


title: Ti-treated,  shoot, 03 days L1

description: Ti-treated,  shoot, 03 days


title: ATACseq_Control_2


title: dKO Control, rep 2

value: dKO

value: Liver

value: Liver in vitro ECs


title: Control,  shoot, 03 days K1

description: Control,  shoot, 03 days


title: Ti-treated,  root, 03 days H3

description: Ti-treated,  root, 03 days

source_name: Root

value: Root


title: Control,  root, 03 days G1

description: Control,  root, 03 days

value: Control


title: Control,  root, 03 days G2

description: Control,  root, 03 days


title: Ti-treated,  shoot, 10 days F3

description: Ti-treated,  shoot, 10 days


title: Ti-treated,  shoot, 10 days F2

description: Ti-treated,  shoot, 10 days


title: Ti-treated,  root, 03 days H2

description: Ti-treated,  root, 03 days


title: Control,  root, 03 days G3

description: Control,  root, 03 days


title: Ti-treated,  root, 03 days H1

description: Ti-treated,  root, 03 days


title: Control,  shoot, 10 days E2

description: Control,  shoot, 10 days


title: Ti-treated,  root, 10 days B3

description: Ti-treated,  root, 10 days


title: Control,  shoot, 10 days E3

description: Control,  shoot, 10 days


title: Ti-treated,  root, 10 days B2

description: Ti-treated,  root, 10 days


title: Ti-treated,  root, 10 days B1

description: Ti-treated,  root, 10 days


title: Control,  shoot, 10 days E1

description: Control,  shoot, 10 days


title: Control,  root, 10 days A2

description: Control,  root, 10 days


title: Control,  root, 10 days A3

description: Control,  root, 10 days


title: Control,  shoot, 03 days K3

description: Control,  shoot, 03 days


title: Control,  root, 10 days A1

description: Control,  root, 10 days


title: ft10-ga-3h-2

city: Singapore

first: Sally

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
STAR ver 2.7.7a, for genome mapping
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Raw read counts, one sample per tab in the compiled .xlsx file

source_name: Rosette leaf

growth_protocol: 30-day old ft-10 Arabidopsis plants grown in soil at 22 ˚C with long day (16h/8h day/night) conditions and light intensity ~100 µmol m-2 s-1.

extract_protocol:
Microneedles were first removed from plant samples, then leaves were frozen in liquid nitrogen. RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instruction. DNase digestion was carried out during the RNA extraction procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Silk microneedles loaded with 15 mM GA3 (3h, 24h, 168h), or empty (24h) silk microneedle injection onto Arabidopsis rosette leaves

value: Rosette leaf

value: GA3-loaded silk microneedle injection

tag: time

value: 3 hours


title: ft10-mock-24h-3

value: Mock silk microneedle injection

value: 24 hours


title: ft10-ga-24h-2


title: ft10-ga-168h-2

value: 168 hours


title: ft10-ga-168h-1


title: ft10-ga-3h-3


title: ft10-mock-24h-2


title: ft10-ga-0h-2

value: 0 hours


title: Ti-treated,  shoot, 10 days F1

description: Ti-treated,  shoot, 10 days


title: ft10-ga-3h-1


title: ft10-ga-0h-3


title: ft10-ga-0h-1


title: ft10-mock-24h-1


title: ft10-ga-24h-3


title: Donor Control 4

description:
CTRL
9_S17_R1_001

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCh38
Supplementary files format and content: raw gene count matrix

source_name: Donor MSCs

growth_protocol: Cells were isolated from human bone marrow and cultured in vitro as described in the manuscript.

extract_protocol:
Cells were harvested from culture using accutase, stained with CD31 and VE-cadherin antibodies, labeled with Dapi, and sorted. Sorted cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with lentivectors for ERG/FLI1 overexpression or with empty cassetes.

value: in vivo MSCs

tag: condition

value: Donor MSC Control


title: Donor Control 2

description:
CTRL
3_S11_R1_001


title: ft10-ga-24h-1


title: HTR8_48 h_siRNA against Prdx2_replicate 2

city: Shanghai

first: Fan

last: Wu

address: 910 Hengshan Rd

country: China

institute: International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine

description:
siPrdx2-2
Gene expression after 48 h of transfection with siRNA against Prdx2

hyb_protocol: Cy3-labeled cRNA was hybridized to SurePrint G3 Human Gene Expression v3 8x60K Microarray (Agilent-072363) for 17 hours using Gene Expression Hybridizeation Kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version 14.8, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: HTR8  transfected with siRNA against Prdx2 for 48 h

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP using the LowInput QuickAmp Labeling Kit One-Color (Agilent technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: The HTR8 cells were cultured in Dulbecco’s modified Eagle’s medium/F12 containing 10% fetal bovine serum (Gibco, Grand Island, NY, USA) at 37 °C in a 5% CO2 atmosphere.

extract_protocol: RNA was extracted from cells using the TRIzol reagent (Life Technologies, Grand Island, NY, USA). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific, Waltham, MA, USA) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: siRNA targeting the human Prdx2 gene was designed: 5′-GCCAGATCACTGTTAATGA-3′. The siPrdx2 or negative control siRNA were transfected into HTR8 cells at a final concentration of 100 nmol/L using the Oligofectamine reagent (Invitrogen, Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. Cells were cultured for 48 h after transfection before they were harvested.


title: Donor VE-ced+ FE 3

description:
FE Overexpression
4_S12_R1_001

value: Donor MSC FE Overexpression


title: Donor VE-ced+ FE 2

description:
FE Overexpression
1_S9_R1_001


title: Donor VE-ced+ FE 4

description:
FE Overexpression
7_S15_R1_001


title: Donor Control 1

description:
CTRL
12_S20_R1_001


title: Donor VE-ced+ FE 1

description:
FE Overexpression
10_S18_R1_001


title: HTR8_48 h_siRNA against Prdx2_replicate 3

description:
siPrdx2-3
Gene expression after 48 h of transfection with siRNA against Prdx2

value: transfected with siRNA against Prdx2 for 48 h


title: Cardiac pericytes (PC) treated  with sunitinib and thalidomide, rep1

city: palo alto

first: Chun

last: Liu

state: CA

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

data_processing:
Adapter sequences were trimmed and low quality bases were filter out.
Processed reads were aligned to referrence genome (hg19) with TopHat and Cufflinks.
Assembly: hg19
Supplementary files format and content: The csv file includes raw counts for each Sample.

source_name: iPSC-differentiated cardiac pericytes

growth_protocol: iPSC-derived cardiac pericytes were maintained in ScienCell Pericyte Medium (#1201).

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using library construction NEBNext kit following the standard protocols.

treatment_protocol: Before drug treatment, cells were serum starved for 48 hours in basal medium+0.5% FBS. Suntinib was added at 5 µM and Thalidomide was added at 1  µM for 48 hours in  0.5%FBS basal medium. Cells were then collected for RNA extraction and sequencing.

value: iPSC-differentiated cardiac pericytes

value: WT

value: sunitinib and thalidomide


title: Cardiac pericytes (PC) treated  with DMSO, rep2

value: DMSO


title: Cardiac pericytes (PC) treated  with sunitinib, rep1

value: sunitinib


title: HTR8_48 h_negative control siRNA_replicate 3

description:
NC-3
Gene expression after 48 h of transfection with negative control siRNA

source_name: HTR8  transfected with negative control siRNA for 48 h


title: si-NC-1

city: Shijiazhuang

first: Lie

address: Jiankang Road No.12

institute: The Fourth Affiliated Hospital of Hebei Medical University

description: Differential gene expression of si-NC transfected KYSE150 cells compared with transfected si-circMAN1A2 cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: KYSE150 cells were cultured in DMEM (Seven, China) complete medium containing 10% fetal bovine serum(Gibco, USA) and 1% penicillin double antibody(Gibco, USA) .

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: KYSE150 cells were transiently transfected by  si-NC or si-circMANA2 with HiPerfect transfection reagent (Qiagen, Valencia, CA).

value: si-NC


title: Cardiac pericytes (PC) treated  with DMSO, rep1


title: Cardiac pericytes (PC) treated  with sunitinib and thalidomide, rep2


title: HTR8_48 h_siRNA against Prdx2_replicate 1

description:
siPrdx2-1
Gene expression after 48 h of transfection with siRNA against Prdx2


title: HTR8_48 h_negative control siRNA_replicate 1

description:
NC-1
Gene expression after 48 h of transfection with negative control siRNA

value: transfected with negative control siRNA for 48 h


title: si-NC-3


title: si-circMAN1A2-3

description: Differential gene expression of circ-MAN1A2 transfected KYSE150 cells compared with transfected si-NC cells


title: HTR8_48 h_negative control siRNA_replicate 2

description:
NC-2
Gene expression after 48 h of transfection with negative control siRNA


title: AMC-161-ESC_R

city: Amsterdam

first: Mark

last: Dings

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
Samples were sequenced on an Illumina HiSeq4000 with single 50bp reads at 100x106 reads per sample.
Data went through quality control using FastQC.
Genome_build: Reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1, and annotated with Gencode v32.
Supplementary_files_format_and_content: For gene set enrichment, count files were converted into DESeq2_vst values using DESeq2 in R. Differential gene expression between pretreatment biopsies and posttreatment resection material was determined by using the limma R package. Gene set enrichment analysis was performed on using all Hallmark gene sets19 using the subcamera function of CMScaller (ref20), and fGSEA (ref21).

source_name: Esophageal patient post treatment resection

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA universal kit (Qiagen, Hilden, Germany). NanoDrop (Thermo Fisher, Waltham, MA) was used to measure RNA concentration. Biopsies were sent for RNA sequencing in case tumor purity was ≥ 30% and RNA concentration was above 20 ng/µL.
Library preparation was performed using Total RNA library prep RiboErase (Roche, Basel, Switzerland).

value: resection

value: chemoradiated


title: si-NC-2


title: AMC-161-ESC

source_name: Esophageal patient pre treatment biopsy

value: biopsy

value: untreated


title: Donor Control 3

description:
CTRL
6_S14_R1_001


title: AMC-076-ESC_R


title: AMC-070-EAC_R


title: AMC-076-ESC


title: si-circMAN1A2-2


title: si-circMAN1A2-1


title: AMC-050-EAC


title: AMC-050-EAC_R


title: AMC-070-EAC


title: AMC-045-EAC_R


title: AMC-045-EAC


title: Cardiac pericytes (PC) treated  with sunitinib, rep2


title: PCM100_dup

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Fastq files were QC'd using fastQC
QC'd fastq files were aligned to the GRCh38 human reference genome using the Rsubread align function
Gene counts were quantified using featureCounts in R
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene count information for each sample

extract_protocol:
RNA was extracted from thawed Tempus tubes using Norgen Preserved Blood RNA kits according to manufacturer's instructions, including DNase treatment. RNA integrity was assessed using the Bioanalyser Nano Assay with all samples having RNA integrity number (RIN) 7-10. 1000 nanograms of the isolated total RNA was globin reduced from 29 of the 58 samples using the GLOBINclear™ - Human Kit.
200ng of RNA was converted to double-stranded cDNA (ds-cDNA). The ds-cDNA were subjected to heat denatured and circularised by the splint oligo sequence to generate the single stranded circle DNA followed by rolling circle replication to create DNA nanoball (DNB) using the MGIeasy RNA Library Prep. Samples were sequenced using the MGI DNBSEQ-G400RS, at two 100-base paired-end reads.

value: Whole blood

value: Diagnosis


title: AMC-043-ESC_R


title: PCM100


title: AMC-043-ESC


title: PCM098_dup


title: SY5YtetCASZ1b_Tet-Rep3

city: Bethesda

first: Zhihui

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample.

source_name: SH-SY5Y cells

growth_protocol: The CASZ1b stably transfected SH-SY5Y cells (SY5YtetCASZ1b) in which CASZ1b expression is tetracycline (Tet) inducible. The cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was isolated from SY5YtetCASZ1b cells that treated with or without Tet for 48 hr

value: Neuroblastoma


title: SY5YtetCASZ1b_Tet-Rep2


title: PCM099_dup

value: Treatment


title: PCM098


title: PCM097_dup


title: PCM097


title: SY5YtetCASZ1b_Ctrl-Rep2


title: SY5YtetCASZ1b_Ctrl-Rep1


title: SY5YtetCASZ1b_Ctrl-Rep3


title: SY5YtetCASZ1b_Tet-Rep1


title: PCM096_dup


title: PCM096


title: PCM095


title: PCM094_dup


title: PCM095_dup


title: PCM093


title: PCM092_dup


title: PCM093_dup


title: PCM090_dup


title: PCM091


title: PCM091_dup


title: PCM092


title: PCM090


title: PCM099


title: PCM089


title: PCM089_dup


title: PCM088_dup


title: PCM087


title: PCM087_dup


title: PCM088


title: PCM085_dup


title: PCM085


title: PCM086_dup


title: PCM086


title: PCM084_dup


title: PCM083_dup


title: PCM081_dup


title: PCM084


title: PCM094


title: PCM081


title: PCM080_dup


title: PCM083


title: PCM079_dup


title: PCM080


title: PCM079


title: PCM077_dup


title: PCM078


title: PCM078_dup


title: PCM076_dup


title: PCM076


title: PCM075


title: PCM075_dup


title: PCM077


title: PCM074


title: PCM074_dup


title: PCM071_dup


title: PCM071


title: PCM073


title: PCM035_dup

value: TB endpoint


title: 2D cultured EVs_biol rep 1

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

institute: Tsinghua University

description: EV small RNA

data_processing:
The raw data of smallRNA will be evaluated first. 1) Remove tags with lower sequencing quality; 2) Remove tags with 5' adaptor contamination; 3) Remove tags without 3' adapter sequence; 4) Remove tags without inserted fragments; 5) Remove tags containing polyA; 6) Remove tags smaller than 15nt; 7) Make statistics of the length distribution of small RNA fragments. The filtered data is called clean tags and is still stored in FASTQ format
We used Bowtie2 to align clean reads to the reference set and other small RNA databases, except that Rfam was aligned using cmsearch. The default alignment parameters are as follows: Bowtie2: -q -L 16 --phred64 -p 6; cmsearch: --cpu 6 --noali
The expression of miRNA is calculated by the following formula: expression = C*1000000/T
Assembly: GRCh38.p13
Supplementary files format and content: xls files include read count values for each Sample

source_name: Mesenchymal stem cells

extract_protocol:
Total RNA was extracted using the miRNeasy Serum/Plasma kit (cat. no. 77064; Qiagen, Inc.) according to the manufacturer's protocol. Extracted EV RNA was used to prepare miRNA next-generation sequencing (NGS) libraries with the QIAseq miRNA Library kit (cat. no. 331505; Qiagen, Inc.).
1) 3' end adaptor ligation: Ligate the 5-adenylated and 3-blocked adaptor to the 3' end of the small RNA fragment. 2) Add Unique molecular identifiers (UMI) labeled Primer. 3) 5' end adaptor ligation. 4) First strand synthesis with Unique molecular identifiers (UMI) labeled Primer. 5) Second strand synthesis. 6) Fragment selection. 7) Library quantitative and pooling cyclization. 8) Library QC. 9) Sequencing on DNBSEQ.

value: Mesenchymal stem cells

value: Cell culture medium ultracentrifugation


title: Gelatin high density beads derived Evs

description: EV small RNA


title: 2D cultured EVs_biol rep 2

description: EV small RNA


title: Matrigel bulk gel derived EVs

description: EV small RNA


title: Matrigel low density beads derived EVs

description: EV small RNA


title: Matrigel high density beads derived EVs_biol rep 1

description: EV small RNA


title: PCM035


title: Post cecal ligation and puncture 12 hours aD KO mouse lung neutrophils, 2

city: Boston

first: Koichi

last: Yuki

address: 300 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
CLC genomic benchwork
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner v.2.5.2b
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was purified using Qiagen RNeasy Plus Mini Kit
Illumina Nextera XT library was used for sequencing library preparation

treatment_protocol: Cecal ligation and puncture surgery was perfomed in 8-12 week old male mice.

value: Lung

value: Primary cells

value: Neutrophils

value: aD KO

value: Cecal ligation and pucture, 12 hours


title: Naïve aD KO mouse lung neutrophils, 1

value: No treatment


title: Post cecal ligation and puncture 12 hours aD KO mouse blood neutrophils, 2

source_name: Blood

value: Blood


title: Post cecal ligation and puncture 12 hours aD KO mouse blood neutrophils, 1


title: Post cecal ligation and puncture 12 hours aD KO mouse lung neutrophils, 1


title: PCM073_dup


title: Naïve aD KO mouse blood neutrophils, 1


title: Post cecal ligation and puncture 12 hours WT mouse lung neutrophils, 2

value: WT


title: Post cecal ligation and puncture 12 hours WT mouse lung neutrophils, 1


title: Naïve aD KO mouse blood neutrophils, 2


title: Post cecal ligation and puncture 12 hours WT mouse blood neutrophils, 1


title: Matrigel high density beads derived EVs_biol rep 2

description: EV small RNA


title: Naïve WT mouse blood neutrophils, 2


title: Naïve WT mouse lung neutrophils, 2


title: Post cecal ligation and puncture 12 hours WT mouse blood neutrophils, 2


title: Naïve WT mouse blood neutrophils, 1


title: Naïve WT mouse lung neutrophils, 1


title: Naïve aD KO mouse lung neutrophils, 2


title: Swi6 ChIPseq, swi6∆, rep2

data_processing:
smallRNA-seq:Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Qiagen 3' adaptors were trimmed using cutadapt (v1.18) with the parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie (v1.2.2) with parameters -f -M 10000 -v 0 -S --best --strata. Bowtie sam output was converted to bam using samtools (v1.9). Bam files were converted to bed using bedtools bamtobed (v2.27.1), bed files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
RNA-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Fastq files were aligned using STAR (v2.7.3a) with the parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1 --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM --outSAMunmapped Within. STAR sam output was converted to bam using samtools (v1.9). Bam files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: mm10; Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV. Counts per million (CPM) table for the RNAseq samples as a text file.

source_name: S. pombe cell culture

extract_protocol:
ChIP was performed as described in Kuzdere et al. (2021). In brief, exponentially growing or synchronized fission yeast cells were fixed with formaldehyde and lysed by beat-beating. Chromatin was sheared by sonication and the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.

value: h90 ade6-M210 leu1-32 ura4-DS/E mat3M::GFP-NatR swi6{delta}::ura3+


title: Swi6 ChIPseq, swi6∆, rep1


title: Swi6 ChIPseq, swi6Chp1-like-CD, rep2

value: h90 ade6-M210 leu1-32 ura4-DS/E mat3M::GFP-NatR swi6::swi6E80V-V82E-S116E-D120N-S122F


title: Swi6 ChIPseq, clr4F449Y, swi6Chp1-like-CD, rep2

value: h90 ade6-M210 leu1-32 ura4-DS/E mat3M::GFP-NatR swi6::swi6E80V-V82E-S116E-D120N-S122F clr4::clr4F449Y


title: Swi6 ChIPseq, clr4F449Y, rep2

value: h90 ade6-M216 leu1-32 ura4-DS/E clr4::clr4F449Y


title: Swi6 ChIPseq, swi6Chp1-like-CD, rep1


title: Swi6 ChIPseq, clr4F449Y, swi6Chp1-like-CD, rep1


title: G9R

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from cisplatin-resistant TGCT-PDC cells

hyb_protocol: Approximately 5.5 micro g of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45 degrees centigrade for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (TAC 4.0.2) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: Cisplatin-resistant TGCT-PGC cells

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: NEC8 cells were maintained in conventional two-dimentional culture with Dulbecco's modified Eagle's medium (DMEM). TCGT-PDC cells were maintained in three-dimentional spheroid culture with StemPro® hESC SFM medium. Cisplatin-resistant cells were cultured in the same media as the corresponding parental cells except the addition of cisplatin.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: No treatment was performed.

tag: tumor/cell type

value: Patient-derived cell of testicular germ cell tumor

tag: cell line background

value: TGCT-PDC

tag: phenotype

value: Cisplatin-resistant


title: Swi6 ChIPseq, clr4F449Y, rep1

city: Basel

first: Fabio

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research


title: 1-3C_H

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

description: total RNA isolated from sucrose density gradient fractions

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read and adapter/quality trimming of the sequencing reads.
The Tuxedo suite was used to align the reads to the rat Rnor_6.0 genome assembly (TopHat) and to assemble and quantify the expression of transcriptomes (Cufflinks, Cuffmerge and Cuffnorm).
Assembly: Rnor_6.0
Supplementary files format and content: Gene expression values in FPKM tracking format (ref: https://cole-trapnell-lab.github.io/cufflinks/file_formats/) are provided for each sample.

organism: Rattus norvegicus

source_name: liver, control diet, 2 wk

growth_protocol: Obesity-prone Sprague Dawley rats (op-SD), initial body weight 160–190 g, were fed either a control diet (CD; TD 08485), or a Western diet (WD; TD 88137) ad libitum for 2 wks.

extract_protocol:
A sample (~1 g) of the left lobe of the liver was removed, and immediately homogenized in 7 volumes of ice-cold homogenization buffer [50 mM HEPES, pH 7.4, 75 mM KCl, 5 mM MgCl2, 250 mM sucrose, 10% Triton X-100, 13% sodium deoxycholate, 100 μg/mL cycloheximide, 2 mM dithiothreitol, and 5 µL/mL RNaseOUT (Invitrogen, no. 1077019)], using a Dounce homogenizer. The homogenate was transferred to a 50 mL conical tube and centrifuged at 4°C for 10 min at 3,000 x g.  Supernatants were then subjected to sucrose density gradient centrifugation at 4°C using a Beckman SW32T rotor at a centrifugal force of 198,200 x g for 3-h and 50 min.  Sucrose gradients (20-47% w/v) were made using the “flash/freeze” technique (42-44).  After centrifugation, gradients were separated into two fractions using a Density Gradient Fractionation System (ISCO Teledyne) while absorption at 254 nm was continuously recorded. The first fraction corresponded to the portion of the gradient containing mRNAs associated with three or fewer ribosomes (referred to hereafter as the light fraction), and the second fraction corresponded to the portion of the gradient containing mRNAs associated with four or more ribosomes (referred to as the heavy fraction). RNA was extracted from each fraction using 3x volume of TRIzol LS (Invitrogen, California; no. 15596026), followed by an overnight incubation with an equal volume of isopropanol at -20°C, per the manufacturer’s instructions. Heavy fractions were diluted with an equal volume of ribonuclease-free water before RNA extraction, to increase extraction efficiency.
20 µg of RNA from the livers of three rats/condition, i.e., rats fed either the CD or WD, or the light and heavy fractions from sucrose density gradients from three rats/condition, were combined prior RNAseq analysis.  RNA quality was assessed using an Agilent 2100 Bioanalyzer in the Penn State College of Medicine Genome Sciences Core (RRID:SCR021123).  Library preparation from each RNA fraction was performed using a KAPA RNA HyperPrep Kit with RiboErase (Roche Molecular Systems; no. KK8560) according to the manufacturer’s instructions. Briefly, first-strand DNA was synthesized using random primers and the RNA:cDNA hybrid was converted to double-stranded cDNA and dAMP was added to the 3’-ends.  Adapters were then ligated to the 3’-dAMP library fragments using the KAPA Single-Indexed Adapter kit (KAPA Biosystems; no. KR1317).  The resulting libraries were amplified, and the quality was assessed by electrophoresis followed by RNAseq analysis using an Illumina Novaseq

value: liver

value: obesity-prone Sprague Dawley

value: Control diet


title: 4-6W_L

source_name: liver, Western diet, 2 wk

value: Western diet


title: 4-6W_H


title: N8P

description: Gene expression data from parental NEC8 cells

source_name: Parental NEC8 cells

value: Conventional cell line of testicular germ cell tumor

value: parental


title: N8R

description: Gene expression data from cisplatin-resistant NEC8 cells

source_name: Cisplatin-resistant NEC8 cells


title: G9P

description: Gene expression data from parental TGCT-PDC cells

source_name: Parental TGCT-PDC cells


title: 1-3C_L


title: Swi6 ChIPseq, clr4wt, rep2

value: h90 ade6-M216 leu1-32 ura4-DS/E


title: H3 ChIPseq, clr4wt, Meiosis 7h, rep2

value: h-/h- ade6-M210/ade6-M216 pat1::NatR/pat1::NatR pat1-as(L95A)::HygR/pat1-as(L95A)::HygR lys1::MatPc-Bleo


title: H3 ChIPseq, clr4wt, Meiosis 8h, rep2


title: Swi6 ChIPseq, clr4wt, rep1


title: H3 ChIPseq, clr4wt, Meiosis 6h, rep2


title: 4-6W_T

description: total RNA


title: 1-3C_T

description: total RNA

source_name: liver, Control diet, 2 wk


title: H3 ChIPseq, clr4wt, Meiosis 5h, rep2


title: H3 ChIPseq, clr4wt, Meiosis 3h, rep2


title: H3 ChIPseq, clr4wt, Meiosis 2h, rep2


title: H3 ChIPseq, clr4wt, Meiosis 0h, rep2


title: Lymph Node 4 Protein

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

description: 5 different treatment groups including Control, Poly:IC, LPS, CpG, R848; multiplexed with B0301 anti-mouse Hashtag 1~5 Antibody

library_source: other

data_processing:
Data Preparation:  Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.1 (Team, 2014). Seurat package v4.0 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 1,500 and 4,300) and cells with too many mtRNA (average around 7.5%), resulting in a total of 43,412 cells. At the same time, sample demultiplexing and identification of cell treatment was accomplished in R using Seurat “HTODemux” function based on the filtered feature-barcode matrix generated by CellRanger. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were introduced into a combined Seurat object via “FindIntegrationAnchors” and “IntegrateData” functions (Stuart et al, 2019). Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
Differentially Expressed Genes: DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
Cell type Identification: To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. 11 distinct cell types were identified, including monocytes, DCs, cycling myeloid cells, macrophages, mast cells, T cells, B cells, NK cells, pDCs, cycling lymphocytes, fibroblasts (not shown). Monocytes, DCs, and cycling myeloid cells were isolated and re-clustered for the purpose of investigating their regulatory role during immune responses. “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Again, “FindAllMarkers” function was then applied and the top DEGs were examined to annotate the clusters. Migratory DC1, migratory DC2, resident DC1, resident DC2, and inflammatory DC2 were eventually identified and included in the final scRNA-seq layout.
Assembly: mm10
Supplementary files format and content: Integrated SeuratObject in rds format containing all 4 samples and different assays of expression/detection matrixes (for both mRNA and protein); The meta data in txt format for every cells, including the sample source, cell types, and UMAP coordinates (for both overall UMAP and reclustered AMs UMAP)

molecule: protein

source_name: Lung Draining Lymph Node

extract_protocol:
Five groups of mice (n=4) were immunized as described before without TLR adjuvant or with individual different TLR adjuvants: Poly:IC, LPS, CpG, R848 in 40 μl sterile PBS 24 hours before harvest. The LLNs were harvested and single cell suspensions were prepared. Cells were stained with flow cytometry antibodies and different TotalSeq A antibodies (BioLegend) according to the different TLR adjuvant treatment. After the staining, single cells suspensions were washed 3 times by resuspension in 4.5 ml HBSS plus 0.5% BSA, followed by centrifugation at 300g for 5 min at 4°C. After the final wash, cells from different treatment groups were resuspended and mixed. Myeloid cells were sorted as shown in Supplementary Figure 1A with the exclusion of Ly6G neutrophils. Sorted cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 2.5 × 105 cells/ml.
Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >35%. Single cells were then processed using the Chromium Next GEM Single Cell 3’ Platform (10X Genomics). Approximately 60,000 cells were loaded on each channel with an average recovery rate of 27,000 cells. Libraries were sequenced on NextSeq2000 (Illumina) with an average sequencing depth of 40,000 reads/cell.

value: Lung Draining Lymph Node


title: Lymph Node 4 mRNA

library_source: transcriptomic single cell


title: Input ChIPseq, clr4wt, Meiosis 7h, rep2, H3

last: Mohn


title: Input ChIPseq, clr4wt, Meiosis 6h, rep2, H3


title: Lymph Node 3 mRNA


title: Input ChIPseq, clr4wt, Meiosis 5h, rep2, H3


title: Input ChIPseq, clr4wt, Meiosis 3h, rep2, H3


title: H3 ChIPseq, clr4wt, Meiosis 4h, rep2


title: Input ChIPseq, clr4wt, Meiosis 4h, rep2, H3


title: H3 ChIPseq, clr4wt, Meiosis 1h, rep2


title: Lymph Node 2 mRNA


title: Input ChIPseq, clr4wt, Meiosis 8h, rep2, H3


title: Input ChIPseq, clr4wt, Meiosis 1h, rep2, H3


title: Input ChIPseq, clr4wt, Meiosis 2h, rep2, H3


title: Lymph Node 2 Protein


title: Lymph Node 1 mRNA


title: H3 ChIPseq, clr4wt, Meiosis 7h, rep1


title: Input ChIPseq, clr4wt, Meiosis 0h, rep2, H3


title: Lymph Node 1 Protein


title: H3 ChIPseq, clr4wt, Meiosis 8h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 6h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 4h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 1h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 0h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 2h, rep1


title: H3 ChIPseq, clr4wt, Meiosis 3h, rep1


title: Input ChIPseq, clr4wt, Meiosis 8h, rep1, H3


title: Input ChIPseq, clr4wt, Meiosis 6h, rep1, H3


title: Input ChIPseq, clr4wt, Meiosis 7h, rep1, H3


title: Lymph Node 3 Protein


title: H3 ChIPseq, clr4wt, Meiosis 5h, rep1


title: Input ChIPseq, clr4wt, Meiosis 5h, rep1, H3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 8h, rep2


title: Input ChIPseq, clr4wt, Meiosis 3h, rep1, H3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 7h, rep2


title: Input ChIPseq, clr4wt, Meiosis 0h, rep1, H3


title: Input ChIPseq, clr4wt, Meiosis 1h, rep1, H3


title: Input ChIPseq, clr4wt, Meiosis 2h, rep1, H3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 5h, rep2


title: H3K9me3 ChIPseq, clr4wt, Meiosis 4h, rep2


title: P19-Phox2b-Rep2

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

data_processing:
mapping STAR_2.4.2a (filter parameters outFilterMultimapNmax 5, outFilterMismatchNmax 10, outFilterMismatchNoverLmax 0.1, alignIntronMin 20, alignIntronMax 500000, chimSegmentMin 10, quantMode GeneCounts)
Read count extraction was performed using a custom R script to UCSC_knownGene.gff annotation)
Assembly: mm9
Supplementary files format and content: Raw read counts for each sample that served as input for DESeq2

source_name: P19 cells

growth_protocol: P19 murine embryonic teracarcinoma cells were obtained from ATTC (CRL-1825TM) and differentiated into neurons using 1 μM retinoic acid (Sigma) as follows: P19 cell suspension cultures were incubated for 4 days in neuronal differentiation media (94%DMEM, 5% FBS, 1% Pep/Strep and 1 μM retinoic acid) to allow for the formation of embryoid bodies. The embryoid bodies were treated with trypsin on the fourth day of differentiation and plated as a monolayer on laminin (10mg/ml) coated dishes for terminal neuronal differentiation. Cytosine β-D-arabinoside (AraC, 12μM; Sigma) was added to the differentiation media on the sixth day to eliminate proliferative cells and enrich for postmitotic neurons. Neurons were collected for chromatin and RNA extraction on the seventh day of differentiation.

extract_protocol:
Total RNA from P19 cells was extracted using Trizol-based protocols. RNA samples were DNase treated using the DNA-free DNA Removal Kit (Thermo Fisher Scientific; MA, USA) and analyzed on Agilent (California, USA) Bioanalyzer 2100 using the Agilent RNA 6000 Nano Kit.
The library was constructed from extracted RNA using Illumina TrueSeq Stranded mRNA Kit (TruSeq Stranded mRNA LT Sample Prep Kit) according to manfacturer's instructions

value: P19 cells

tag: cell type

value: embryonic carcinoma cell line (RA-induced)

value: Phox2b-WT transduced

value: RA induced neural differentiation


title: P19-Phox2b-Lbx1FS-Rep3

value: Lbx1-KO + Phox2b-WT and Lbx1FS-Flag transduced


title: P19-Phox2b-Rep3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 1h, rep2

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 25°C or 30°C, depending on the strain. For more details see Methods section in Kuzdere et al. (2021)


title: H3K9me3 ChIPseq, clr4wt, Meiosis 2h, rep2


title: P19-Phox2b-Rep1


title: H3K9me3 ChIPseq, clr4wt, Meiosis 6h, rep2


title: P19-Phox2b-Lbx1FS-Rep1


title: H3K9me2 ChIPseq, clr4wt, Meiosis 8h, rep2


title: H3K9me3 ChIPseq, clr4wt, Meiosis 0h, rep2


title: P19-Phox2b-Lbx1WT-Rep3

value: Lbx1-KO + Phox2b-WT and Lbx1WT-Flag transduced


title: H3K9me2 ChIPseq, clr4wt, Meiosis 7h, rep2


title: H3K9me3 ChIPseq, clr4wt, Meiosis 3h, rep2


title: P19-Phox2b-Lbx1FS-Rep2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 4h, rep2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 3h, rep2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 5h, rep2


title: P19-Phox2b-Lbx1WT-Rep2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 6h, rep2


title: Input ChIPseq, clr4wt, Meiosis 4h, rep1, H3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 2h, rep2


title: P19-Phox2b-Lbx1WT-Rep1


title: H3K9me2 ChIPseq, clr4wt, Meiosis 0h, rep2


title: Input ChIPseq, clr4wt, Meiosis 8h, rep2_me2_me3


title: P19-Wt-Rep2

value: normal P19 cells


title: Input ChIPseq, clr4wt, Meiosis 3h, rep2_me2_me3


title: P19-Wt-Rep1


title: P19-Wt-Rep3


title: Input ChIPseq, clr4wt, Meiosis 1h, rep2_me2_me3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 5h, rep1


title: Input ChIPseq, clr4wt, Meiosis 2h, rep2_me2_me3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 7h, rep1


title: H3K9me3 ChIPseq, clr4wt, Meiosis 8h, rep1


title: Input ChIPseq, clr4wt, Meiosis 6h, rep2_me2_me3


title: H3K9me3 ChIPseq, clr4wt, Meiosis 4h, rep1


title: Donor_6_Treg_HDAC7_ctrl

city: Toulouse

first: Pierre-Paul

last: Axisa

address: 2 avenue Hubert Curien

department: CRCT

institute: INSERM

data_processing:
Sequence reads were aligned to the human genome using STAR
Gene quantitation was performed with RSEM
Gene counts were then used as input for differential expression analysis with DESeq2, using a local fit and normal log fold change shrinkage. Batch and treatment were included as covariates in the model.
Genes with base mean < 10 were filtered out and genes with FDR < 0.1 were considered differentially expressed.
Assembly: GRCh38 release 88
Supplementary files format and content: rsem count matrix generatedby tximport

source_name: blood

growth_protocol: Sorted human Tregs were stimulated with plate bound anti-CD3 (UCHT1) and soluble anti-CD28 (both 1ug/ml) in the presence of IL-2 (20U/ml) for 7 days. After the first day, they were infected with lentiviral pseudoparticles containing WT or R166H mutated constructs.

extract_protocol:
cDNA libraries were generated with the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech).
Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina)
Libraries were sequenced with a 2 × 100 bp paired-end protocol HiSeq 2000 Sequencing System (Illumina)

value: blood

value: human primary regulatory T cells

value: HDAC7 R166H lentivirus


title: H3K9me3 ChIPseq, clr4wt, Meiosis 2h, rep1


title: GSC_CM_H3K27

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50.
Cleaned reads were mapped to the reference genome of hg38 using SOAP2 (https://github.com/BGI-flexlab/SOAPnuke), whose parameters was -v 2 -s 3 .
We used MACS2 (https://github.com/macs3-project/MACS) to identify peaks (open chromatin regions), in which '--bw 200 -g XXX -s 50 -p 1e-5 -m 10 30 --broad -B --trackline' was used. The significant regions were picked up if |M| >= 1 and P-value <=10-5.
Also, the gene element annotation of peak or different enrichment peak from different samples was carried out by bedtools (https://bedtools.readthedocs.io/en/latest/) intersect mode with overlap 50%.
Assembly: hg38
Supplementary files format and content: wig

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: U87 cells/GSC  were treated with bulk control/0.5mM 8-cpt-cAMP/1nM MS275 or a combination for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

value: GSC

tag: group

value: CM

tag: chip antibody


title: Input ChIPseq, clr4wt, Meiosis 0h, rep2_me2_me3


title: Donor_5_Treg_HDAC7_R166H

value: HDAC7 WT lentivirus


title: H3K9me3 ChIPseq, clr4wt, Meiosis 6h, rep1


title: Donor_5_Treg_HDAC7_ctrl


title: Input ChIPseq, clr4wt, Meiosis 4h, rep2_me2_me3


title: H3K9me2 ChIPseq, clr4wt, Meiosis 1h, rep2


title: Donor_5_Treg_HDAC7_WT

value: ctl

value: control lentivirus


title: Donor_6_Treg_HDAC7_R166H


title: GSC_CM_H3K14

tag: cell line


title: Input ChIPseq, clr4wt, Meiosis 7h, rep2_me2_me3

tag: genotype

value: h-/h- ade6-M210/ade6-M216 pat1::NatR/pat1::NatR pat1-as(L95A)::HygR/pat1-as(L95A)::HygR lys1::MatPc-Bleo


title: Input ChIPseq, clr4wt, Meiosis 5h, rep2_me2_me3


title: Donor_4_Treg_HDAC7_ctrl

tag: treatment


title: H3K9me3 ChIPseq, clr4wt, Meiosis 1h, rep1


title: GSC_CM_H3K9


title: Donor_6_Treg_HDAC7_WT

tag: tissue


title: H3K9me2 ChIPseq, clr4wt, Meiosis 8h, rep1

tag: strain


title: GSC_V_H3K27

value: V


title: Donor_4_Treg_HDAC7_R166H


title: Donor_4_Treg_HDAC7_WT


title: GSC_V_H3K9


title: H3K9me2 ChIPseq, clr4wt, Meiosis 5h, rep1


title: H3K9me2 ChIPseq, clr4wt, Meiosis 6h, rep1


title: Donor_3_Treg_HDAC7_R166H


title: Donor_3_Treg_HDAC7_WT


title: Donor_2_Treg_HDAC7_ctrl


title: U87_C_H3K14_2

value: C


title: U87_M_H3K14_2

value: M


title: U87_V_H3K14_2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 3h, rep1


title: H3K9me2 ChIPseq, clr4wt, Meiosis 4h, rep1


title: HA1

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

description: 10x Genomics

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was GRh38-1.2.0.
Assembly: GRh38-1.2.0
Supplementary files format and content: matrix files

source_name: Testis

extract_protocol:
Testicular cells were isolated from human testicular tissues by enzymatic digestion according to a previously described method. In brief, testicular tissues were enzymatically digested with 4 mg/ml collagenase type IV, 2.5 mg/ml hyaluronidase, and 1 mg/ml trypsin at 37°C for 20 min. Given the risk of damaging certain types of big cells (such as Sertoli cells), cut-up of the tissue was avoided during this process. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (Miltenyi Biotec) to remove dead cells. The cells were re-suspended in 0.05% BSA/PBS buffer before 10× Genomics library preparation.
RNA-seq library preparation and sequencing were performed in the same way as in our previous study. Briefly, single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libraries were sequenced on an Illumina NovaSeq 6000. The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was GRh38-1.2.0.

value: Testis

tag: disease

value: prostate cancer


title: U87_CM_H3K9_2


title: H3K9me3 ChIPseq, clr4wt, Meiosis 0h, rep1


title: Donor_2_Treg_HDAC7_WT


title: LOH1

description: 10x Genomics


title: U87_CM_H3K14_2


title: H3K9me2 ChIPseq, clr4wt, Meiosis 7h, rep1


title: Donor_1_Treg_HDAC7_R166H


title: Donor_3_Treg_HDAC7_ctrl


title: Donor_1_Treg_HDAC7_WT


title: Donor3_Treg_HDAC7_KD

growth_protocol: Sorted human Tregs (CD4+CD25hiCD127lo/neg) were stimulated with plate-bound anti-CD3 (UCHT1, 1 μg/ml) and soluble anti-CD28 (1 μg/ml).

treatment_protocol: After for 24 h, they were transduced with lentiviral particles by spinfection in the presence of Polybrene (5 μg/ml) in plates coated with Retronectin (50 μg/ml) (Takara/Clontech) and anti-CD3 (1–2 μg/ml). Five days after transduction, cells were sorted on the basis of expression of GFP.

value: HDAC7 KD shRNA


title: U87_M_H3K9_2


title: Donor_2_Treg_HDAC7_R166H


title: U87_C_H3K9_2


title: Y1

description: 10x Genomics


title: LOH2

description: 10x Genomics


title: HA2

description: 10x Genomics


title: U87_V_H3K9_2


title: Donor3_Treg_HDAC7_WT

value: HDAC7 scrambled control shRNA


title: U87_CM_H3K27


title: U87_V_H3K27


title: Peripheral blood sample from patient 1,2, and 3 after treatment

first: Feiye

address: No.13, Shiguagang Road, Haizhu District, Guangzhou

institute: Department of Oncology, Southern Medical University Hospital of Integrative Medicine

description:
SampleTag01 = Patient1_after-treatment
SampleTag02 = Patient2_after-treatment
SampleTag03 = Patient3_after-treatment
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided.

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers.
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Peripheral blood samples from patients before and after treatment were extracted and single cell whole transcriptome sequencing libraries were constructed using the BD platform Rhapsody reverse transcription kit and the BD Rhapsody whole transcriptome amplification kit.
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol.

tag: diagnosis

value: Hepatocellular carcinoma

tag: patient number

value: sintilimab and sorafenib

value: PBMC