title: Healthy – wbl 9

city: Heraklion

first: George

last: Bertsias

address: Andrea Kalokerinou 13

department: Medical School

country: Greece

institute: University of Crete

description: Healthy – wbl 9

data_processing:
Raw fastQ files were pre-processed by assessing quality control (QC) with FASTQC. Low-quality 3’ read ends (minimum two-colour chemistry score of 20), N tails, and adapter remains were trimmed/clipped using cutadapt, allowing reads of at least 25 nucleotide length. Filtered reads were then mapped against the UCSC hg19 human reference transcriptome using STAR aligner by setting the “-- outFilterMultimapNmax” parameter to 5. Μapped reads were filtered in order to discard chimeric alignments, alignments with more than 2 mismatches, and keep only uniquely aligned reads (MAPQ = 255).
Counting on Ensembl genes and statistical analysis (differential expression analysis) was performed with metaseqR using DESeq2 for normalization and differential testing, and applying default settings for each assay (exon count summarization for RNA-seq and 3’ UTR summarization for Quant-seq). For paired-samples comparisons, ‘donor id’ was included in the DESeq2 model.
Assembly: hg19
Supplementary files format and content: count_matrix_SLEpatients_wholeblood20.txt: contains raw counts for each individual.
Supplementary files format and content: normalized_counts_silencing.txt: contains normalized gene expression counts for each donor across different conditions, using deseq2 normalization.
Supplementary files format and content: normalized_counts_SLEvsHealthy_monocytes.txt: includes normalized counts using deseq2 package.
Supplementary files format and content: metaseqr_all_out_untr_female_vs_untr_male.txt: includes normalized read counts for all analyzed genes for female and male SLE patients, extracting from metaseq.

source_name: peripheral blood

growth_protocol: RPMI-1640, GlutaMAX Supplement (Gibco) including 10% heat-inactivated FBS (Gibco), 100 IU/mL penicillin and 100 μg/mL streptomycin (Gibco)

extract_protocol:
RNA was isolated using the NucleoSpin RNA extraction kit (Macherey-Nagel). RNA was quantitated with the Nanodrop photometric method and quality control was performed with the Agilent Bioanalyzer RNA nano kit.
RNA libraries for RNA-seq were prepared with Illumina TruSeq RNA library prep kit following manufacturer 's protocol.

treatment_protocol: Cultured monocytes were stimulated with 10 ng/ml human macrophage colony-stimulating factor (M-CSF; Peprotech), 10ng/ml recombinant human TNF (Peprotech), 100 IU/ml IFN-α (PBL Science) overnight at 37oC/5% CO2, followed by 10ng/ml LPS (Sigma) challenge for 1-4 hours

value: peripheral blood

value: whole blood cells

value: male

value: untreated

tag: disease state

value: Healthy


title: Healthy – wbl 8

status: Public on Sep 01 2025

type: SRA

description: Healthy – wbl 8

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: Sex

tag: treatment


title: 279842_R_B18_all_tgct_T2

city: London

first: Rushad

last: Pavri

address: Guy's Campus, Great Maze Pond, SE1 9RT

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King’s College London

description: Library name: 279842_R_B18_all_tgct_T2

library_source: genomic

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Assembly: Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Supplementary files format and content: NCBI hg38
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

molecule: genomic DNA

source_name: Ramos

growth_protocol: see Methods

extract_protocol:
cells were harvested and genomic.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

treatment_protocol: see Methods

value: Ramos

tag: cell line

value: Burkitt's Lymphoma


title: Jurkat cell resting ChIP-seq H3K27me3 rep1

city: Guangzhou

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

country: China

institute: Guangzhou Women and Children's Medical Center

data_processing:
For data analysis, sequences with adaptors and low quality were trimmed for all 150-bp paired-end reads.
The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (v0.7.17).
All samples were processed separately, and unique mapped reads were retained.
Peaks were called using MACS2 (v2.1.1) with IgG as the control.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig

source_name: Jurkat cell

growth_protocol: Jurkat (Clone E6-1) cell line (ATCC, CRL-9855) was cultured in Iscove’s Modified Eagle’s Medium (IMDM; Thermo Fisher Scientific, 31980030) containing 10% FBS and Penicillin and Streptomycin. All cell lines were authenticated by Short Tandem Repeat (STR) and tested no mycoplasma contamination utilizing the Quantiative PCR mycoplasma detection kit (Sigma-Aldrich, MP0040A).

extract_protocol:
1 × 10^7 Jurkat cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 9 minutes at room temperature and subsequently quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice using ice-cold lysis buffer, which consisted of 20 mM Tris-HCl (pH 7.5) (Thermo Fisher Scientific, 15567027), 2 mM EDTA (Thermo Fisher Scientific, 15575020), 1% Triton X-100 (Sigma-Aldrich, T8787), 0.1% SDS (Thermo Fisher Scientific, 15525017), 0.1% sodium deoxycholate (Sigma-Aldrich, D6750), and 1× protease inhibitors (Thermo Fisher Scientific, 78425) for 15 minutes with slow rotation at 4°C. The nuclear lysates were sonicated to obtain DNA fragments ranging from 200 to 500 bp using a Biorupter system (Diagenode, B01060001) at high energy, with a working time of 30 seconds and a resting time of 30 seconds, for a total of 30 cycles, until the solutions became clear. After removing insoluble debris, the lysates were incubated separately with specific antibodies against Rabbit IgG (1:100, Cell Signaling Technology, 7074), CTCF (1:100, Abcam, ab128873), ZNF384 (1:100, Novus Biologicals, NBP3-30592), H3K27me3 (1:100, Cell Signaling Technology, 9733), Rpb1 NTD (1:100, Cell Signaling Technology, 14958), H3K4me1 (1:100, Cell Signaling Technology, 5326), H3K4me3 (1:100, Cell Signaling Technology, 9751), or H3K27ac (1:100, Abcam, ab4729), and then purified using protein A-agarose beads (Millipore, 16-157). The beads were washed four times with TE buffer (10 mM Tris-HCl pH 8.0 [Thermo Fisher Scientific, 15568025] and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% sodium deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction.
ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions and were sequenced on a HiSeq X Ten platform (Illumina).

treatment_protocol: Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

value: Jurkat cell

value: Cells derived from human T cells

tag: chip antibody

value: H3K27me3 antibody (CST, #9733)

value: resting


title: NASH_w2_3

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

description: Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50mg/kg). Livers were perfused for 5min with 40ml of perfusion medium SC-1 to remove the blood and for rapid destruction of intercellular junctions, followed by perfusion with 40ml of SC-2 medium containing 10mg collagenase for 5min to break up the supporting extracellular matrix. Each lobe was dissected off, and the tissue was disrupted inside of a beaker containing 50ml of SC-2 with 20mg collagenase (Roche) and 1ml DNase I (Sigma) followed by rotating incubation for 20min at 37°C. Cells were then filtered through a 100μm strainer and centrifuged at 50g for 2min at room temperature. Hepatocytes were washed once with 1X PBS and centrifuged again at 50g for 2min. Pellet was resuspend with 2ml of 1X PBS containing 0.04% BSA, filtered through a 70µm strainer and FACS sorted. 500,000 sorted cells were collected and lysed for RNA extraction.

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt with parameters -q 20,20 --minmum-length 40, -a AGATCGGAAGAG, -a "A{100}".
Trimmed sequence reads were mapped to the mouse genome GRCm39 using STAR v2.7.1a (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).

value: Liver

value: Hepatocyte

tag: strain

tag: diet

value: NASH-inducing diet

tag: time on_nash_diet

value: 2 weeks


title: Jurkat cell resting ChIP-seq H3K4me3 rep1

value: H3K4me3 antibody (CST, #9751)


title: Healthy – wbl 7

description: Healthy – wbl 7


title: 279873_R_B18_all_tgct_T2

description: Library name: 279873_R_B18_all_tgct_T2


title: Healthy – wbl 10

description: Healthy – wbl 10


title: NASH_w2_2


title: Healthy – wbl 6

description: Healthy – wbl 6


title: 279841_R_B18_all_tgct_T2

description: Library name: 279841_R_B18_all_tgct_T2


title: 279877_R_B18_all_aact_A3

description: Library name: 279877_R_B18_all_aact_A3


title: NASH_w2_1


title: Jurkat cell resting ChIP-seq H3K4me1 rep1

value: H3K4me1 antibody (CST, #5236)


title: Healthy – wbl 5

description: Healthy – wbl 5

value: peripheral blood

value: female


title: Jurkat cell resting ChIP-seq H3K27ac rep1

value: H3K27ac antibody (Abcam, #ab4729)


title: NASH_w1_4

value: 1 week


title: Jurkat cell resting ChIP-seq Input rep1


title: Jurkat cell stimulated Capture HiC replicate 2

data_processing:
The quality-controlled sequencing data were initially aligned to the human reference genome GRCh37/hg19 using the HiCUP(v0.7.4) software.
The identification of reliable chromatin interaction loops was performed using the CHiCAGO software,
Two biological replicates from both resting and stimulated Jurkat cells were subsequently analyzed with the input into the edgeR (v3.28.1) software to detect changes in loop strength.
Assembly: GRCh37/hg19
Supplementary files format and content: ibed files include chromatin interaction loops
Library strategy: Capture HiC

extract_protocol:
Jurkat cells were counted, and 2 × 10^7 cells were crosslinked with 1% formaldehyde (Sigma-Aldrich, F8775) in phosphate-buffered saline (PBS; Sigma-Aldrich, P4417) at room temperature for 8 minutes, and then quenched with 0.125 M glycine (Invitrogen, 15527013) on ice for 5 minutes. Next, the crosslinked cells were lysed in Hi-C lysis buffer (10 mM Tris-HCl pH 8.0 [Thermo Fisher Scientific, 15568025], 10 mM NaCl [Invitrogen, AM9760G], and 0.2% Igepal CA630 [Sigma-Aldrich, I3021]) with 50 μl of a protease inhibitor cocktail (MCE, HY-K0010). Nuclei were extracted and digested with the MboI restriction enzyme (NEB, R0147) for 2 hours. After digestion, the nuclei were resuspended in NEB buffer supplemented with DNA polymerase I, Large (Klenow) fragment (NEB, M0210) to fill in the restriction fragment overhangs with Biotin-14-dATP (Life Technologies, 19524-016) for 1 hour. Proximal ligation was performed with T4 DNA ligase (NEB, M0202) for 4 hours at 16°C, and the nuclei were harvested for DNA de-crosslinking and purification. The purified DNA was sheared using a Biorupter system (Diagenode, B01060001), and AMPure XP beads (Beckman Coulter, A63880) were used to select a size range of 300–600 bp products. The DNA was subjected to DNA biotin pull-down using Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) and prepared for Illumina sequencing. The library was subsequently amplified and purified. The RNA-targeted sequence capture probe library targeting the CD28-ICOS-CTLA4 locus was designed and ordered from Agilent (China). Interactions in the CD28-ICOS-CTLA4 locus were captured according to the manufacturer’s instructions. The captured DNA was eluted with Nuclease-Free Water (Thermo Fisher Scientific, AM9930). Sixty micrograms of DNA were used for PCR amplification.
the Capture HiC libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the kit’s instructions, and next-generation sequencing was performed on a HiSeq X Ten platform.

value: anti-CD3/CD28 stimulated


title: 279874_R_B18_all_aact_A3

description: Library name: 279874_R_B18_all_aact_A3

value: Ramos


title: Healthy – wbl 3

description: Healthy – wbl 3

value: whole blood cells

value: untreated

value: Healthy


title: Jurkat cell stimulated Capture HiC replicate 1

value: Jurkat cell

value: Cells derived from human T cells


title: NASH_w1_3

value: Liver


title: 279875_R_B18_all_aact_A3

description: Library name: 279875_R_B18_all_aact_A3

value: Burkitt's Lymphoma


title: Healthy – wbl 4

description: Healthy – wbl 4


title: NASH_w1_2

value: Hepatocyte

value: NASH-inducing diet


title: Healthy – wbl 2

description: Healthy – wbl 2


title: Jurkat cell Neg CRISPRa-seq replicate 1

data_processing:
Two replicates of both the sorted group (the top 10% of Jurkat cells expressing CD28) and the unsorted group were sequenced and underwent quality control using MAGeCK-VISPR.
We extracted the sgRNA sequences from the original 150-bp reads, and the abundance of guides was determined using the MAGeCK “count” module based on the extracted sgRNAs.
We utilized the non-targeting control guides to estimate the size factor for normalization and assessed significant enrichment at the enhancer level according to the MAGeCK-test algorithm.
Finally, significant hits were identified with a false discovery rate (FDR) of less than 0.05.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-separated values files
Library strategy: CRISPRa screening

extract_protocol:
We generated the Jurkat-dCas9-VP64 cell line that stably expressing the Lenti-dCas9-VP64-blast (Addgene, 61425) transgene, as described below. The lentiviral library was titered using the Lenti-PacTM HIV qRT-PCR Titration Kit (GeneCopoeia, LT005). Jurkat-dCas9-VP64 cells were infected with lentiviral gRNA library by resuspending the cells at a concentration of 2 × 10^6 cells per ml in fresh media containing the titered lentivirus and 2 µg/ml polybrene (Millipore, TR-1003). The cells were spin-infected for 1.5 hours at 1,200 × g and 4°C, followed by resuspension in fresh media at a concentration of 0.5 × 10^6 cells per ml. To limit the number of cells expressing multiple gRNAs, a low multiplicity of infection (MOI) of 0.25 was employed to ensure that only 10−20% of the cells were infected. After 24 hours, 1 µg/ml puromycin (ApeXbio, B7587) was added to select for effectively infected Jurkat-VP64 cells and to eliminate uninfected cells. The number of initially infected cells was at least 200 times the number of gRNAs in the library, and this ratio was maintained throughout the experiment. Seven days post-infection, cells were sorted based on CD28 expression. Briefly, the cells were resuspended in sterile sort buffer (PBS + 2% FBS) containing FITC anti-human CD28 antibody (Biolegend, 302906) at a 1:25 dilution. The cells were stained for 30 minutes on ice, washed twice with sort buffer, and passed through a 70-µm mesh (BD, 352350). The top 10% of Jurkat cells expressing CD28 were sorted according to their CD28 expression levels according to the previous study15. The total number of cells collected was at least 200 times the number of gRNAs in the library. Additionally, unsorted cells, also at least 200 times the number of gRNAs in the library, were collected at this time. Duplicate infections and sorts were performed for each library. The collected cells were centrifuged at 1,500 × g for 5 minutes, and the cell pellets were stored at -80°C until genomic DNA was extracted. Genomic DNA samples were extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102) for PCR amplification (Vazyme, N616).
The amplified products were subjected to library construction using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions, followed by next-generation sequencing on a HiSeq X Ten platform.

value: resting


title: NASH_w1_1


title: Jurkat cell resting Capture HiC replicate 2


title: 279853_R_B18_all_aact_A3

description: Library name: 279853_R_B18_all_aact_A3


title: Jurkat cell resting Capture HiC replicate 1


title: 279852_R_B18_all_aact_A3

description: Library name: 279852_R_B18_all_aact_A3


title: SLE Patient – wbl 10

description: SLE Patient – wbl 10

value: male


title: ND_5

value: normal diet

value: 0 weeks


title: 279876_R_B18_all_aact_A3

description: Library name: 279876_R_B18_all_aact_A3


title: Jurkat cell stimulated 4C-seq

data_processing:
For data analysis, quality control of the 4C-seq library was performed using FastQC.
Sequences containing adaptors and those of low quality were discarded for further analysis.
The Bioconductor package Basic4Cseq (v1.34) was employed to filter, analyze, and visualize the 4C-seq data.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-separated values files
Library strategy: 4C-seq

extract_protocol:
Jurkat cells were counted, and approximately 1 × 10^7 cells were utilized for each 4C experiment. The cells were cross-linked with 1.5% formaldehyde, quenched with 0.125 M glycine, and lysed using a cold lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× Protease Inhibitors. They were then digested with DpnII (NEB, R0543M) for 4 hours at 37°C while shaking at 1,000 x g for more than three cycles until the digestion efficiency exceeded 90%. Following digestion, the samples were ligated with T4 DNA ligase (NEB, M0202M) in a 7-mL reaction system after enzyme inactivation. Cross-links were reversed by adding Protein K (Thermo Fisher Scientific, AM2548) overnight at 65°C, followed by RNase A treatment for 45 minutes at 37°C. The ligation products were purified using Phenol/Chloroform/Isoamyl Alcohol (25:24:1) (Thermo Fisher Scientific, 15593-049). The purified DNA samples were then digested with CviQI (Thermo Fisher Scientific, ER0211) for the rs5837875-containing region (GRCh37/hg19 chr2: 204,646,121–204,648,210) and subsequently ligated with T4 DNA ligase overnight in a 14-mL reaction system. The ligation samples were purified again using Phenol/Chloroform/Isoamyl Alcohol (25:24:1) and further purified with the QIAquick PCR Purification Kit.
The purified products were amplified using VAHTS HiFi Amplification Mix (Vazyme, N616) with 12 × 200 ng of DNA. 4C-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3, following the kit’s instructions, and were sequenced on a HiSeq X Ten platform.

value: stimulated by anti-CD3 and anti-CD28


title: ND_4


title: 279839_R_B18_all_aact_A3

description: Library name: 279839_R_B18_all_aact_A3


title: ND_3


title: SLE Patient – wbl 8

description: SLE Patient – wbl 8

value: peripheral blood


title: Jurkat cell resting 4C-seq

value: resting (untreatment)


title: SLE Patient – wbl 9

description: SLE Patient – wbl 9


title: 242062_R_B18_agct2_9bp

description: Library name: 242062_R_B18_agct2_9bp

value: Ramos


title: SHALiPE-seq, HEK293T, TDP-43 kd, NAI, Rep2

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

data_processing:
The adapters were first removed using Cutadapt v1.15 and the reads shorter than 20nt or with quality score lower than 30 were filtered out.
The remaining reads were mapped to human or mouse transcriptome reference using Bowtie2 v2.3.3.1.
Next, the mapped reads with more than 3 mismatches or mismatch at the first base were removed, RT stops were counted and reactivity scores were calculated using StructureFold2 package.
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes SHAPE reactivity score of each transcript
Library strategy: SHALiPE-seq

extract_protocol:
Total RNAs were extracted and quantified using RNeasy Plus Mini Kit (Qiagen, 74136) and Nanodrop ND-1000 Spectrophotometer. Poly(A)-selected RNAs were enriched using Poly(A)Purist™ MAG Kit  (Thermo Fisher Scientific, AM1922).
Each library was prepared with 500 ng poly(A)-selected RNAs after 2 rounds of selection (Thermo Fisher Scientific, AM1922). The poly(A) RNAs were fragmented to around 300 nt length at 95°C for 1 min and purified using RNA clean and concentrator (Zymo research, R1016). The fragmented RNA was then subjected to a 5' dephosphorylation reaction at 37°C for 30 min by adding rSAP (NEB, M0371L) and PNK enzyme (NEB, M0201S) in 1× T4 PNK buffer (NEB, B0201S). Next, the 3’adapter was ligated to the dephosphorylated RNA using T4 RNA ligase 2 KQ (NEB, M0373L) at 25°C for 1 h. Excess adapters were digested and removed by adding RecJf (NEB, M0331) and 5’ deadenylase (NEB, M0331) for 30 min at 30°C followed by column purification (Zymo research, R1016). The following reverse transcription (RT) was performed in 1 X RT buffer (20 mM Tris, pH 7.5, 4 mM MgCl2, 1 mM DTT, 0.5 mM dNTPs, 150 mM LiCl) with SuperScript III enzyme (Thermo Scientific, 18080093) at 42°C for 40 min. RNA was digested by 2M NaOH and the reaction was neutralized with 1M Tris-HCl (pH 7.5) followed by column purification (Zymo research, R1016). The 5’adapter was ligated to the cDNA with Quick T4 DNA ligase (NEB, M2200L) and incubated in 37°C overnight. On second day, the ligated product was first purified by column (Zymo research, R1016), then USER II enzyme (NEB, M5509) was added to cleave the product followed by a second column purification (Zymo research, R1016). The purified product was used for PCR cycle test and amplification with different barcoded reverse primer. PCR products with 150–400 bp were cut and purified with 2% agarose gel and column (Zymo research, D4008).

treatment_protocol: Control and TDP-43 knockdown cells were harvested in 1X PBS buffer (Thermo Fisher Scientific, 10010049) and probed with NAI (100 mM in final) or 5% DMSO as negative control for 15 min at 37°C, 500 rpm. Then DTT (200 mM in final) was added immediately to quench each probing reaction. The cells were spinned down at 500 g for 3 min at room temperature for RNA extraction.

tag: genotype

value: TDP-43 knockdown

value: NAI


title: SLE Patient – wbl 7

description: SLE Patient – wbl 7

value: whole blood cells

value: untreated

value: Healthy


title: 242061_R_B18_agct2_9bp

description: Library name: 242061_R_B18_agct2_9bp


title: ND_1

value: Liver


title: SLE Patient – wbl 5

description: SLE Patient – wbl 5

value: female

value: SLE


title: Healthy – wbl 1

description: Healthy – wbl 1


title: 242031_R_B18_agct2_9bp

description: Library name: 242031_R_B18_agct2_9bp

value: Burkitt's Lymphoma


title: SLE Patient – wbl 6

description: SLE Patient – wbl 6


title: 242032_R_B18_agct2_9bp

description: Library name: 242032_R_B18_agct2_9bp


title: SHALiPE-seq, HEK293T, Ctrl, NAI, Rep1

value: WT


title: SHALiPE-seq, HEK293T, Ctrl, NAI, Rep2


title: SLE Patient – wbl 4

description: SLE Patient – wbl 4


title: 227364_R_B18_agct2_9bp

description: Library name: 227364_R_B18_agct2_9bp


title: SHALiPE-seq, HEK293T, TDP-43 kd, NAI, Rep1


title: SHALiPE-seq, HEK293T, TDP-43 kd, DMSO, Rep2

value: DMSO


title: RNA-Seq_SRCAP_degron_0h_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

data_processing:
Raw reads with spike-in were firstly trimmed by Cutadapt software and then mapped to mm10 and dm6 genome using STAR software.
PCR duplicates, reads that were not primarily mapped were discarded for further analysis.
Bam files were converted to bw format by deepTools software normalized by the reads mapped to dm6 genome.
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i/mLIF medium, which composed of DMEM containing 1 mM L-glutamine, 1× nucleosides (Sigma, ES-008), 1× nonessential amino acids (Milipore, TMS-001-C), 1× sodium pyruvate (Gibco, 11360070), 1× penicillin/ streptomycin (Gibco, 15140-122), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107), and also supplemented with 15% fetal bovine serum (FBS) (VivaCell, 04-001-1A), incubated at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
Extracted total RNA using Trizol reagent following the instruction
Cells were lysed directly in Trizol reagent and extracted RNA according to the manufacturer’s instruction, after examination the concentration and integrity of the total RNA, samples were delivered for poly(A) RNA library generation

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 24h, then cells were harvested for next assays.

value: mouse embryonic stem cells

value: SRCAP degron 0h


title: SLE Patient – wbl 3

description: SLE Patient – wbl 3


title: RNA-Seq_SRCAP_degron_24h_rep2

value: SRCAP degron 24h


title: 279840_R_B18_all_aact_A3

description: Library name: 279840_R_B18_all_aact_A3


title: 227363_R_B18_agct2_9bp

description: Library name: 227363_R_B18_agct2_9bp


title: SHALiPE-seq, HEK293T, TDP-43 kd, DMSO, Rep1


title: SLE Patient – wbl 2

description: SLE Patient – wbl 2

value: peripheral blood


title: RNA-Seq_SRCAP_degron_0h_rep1


title: SHALiPE-seq, HEK293T, Ctrl, DMSO, Rep2


title: ND_2

value: Hepatocyte

value: normal diet

value: 0 weeks


title: 227358_R_B18_agct2_9bp

description: Library name: 227358_R_B18_agct2_9bp

value: Ramos


title: SLE Patient – wbl 1

description: SLE Patient – wbl 1

value: whole blood cells


title: RNA-Seq_P400_degron_24h_rep2

value: P400 degron 24h


title: SHALiPE-seq, HEK293T, Ctrl, DMSO, Rep1


title: 227357_R_B18_agct2_9bp

description: Library name: 227357_R_B18_agct2_9bp


title: RNA-Seq_P400_degron_24h_rep1


title: RNA-Seq_SRCAP_degron_24h_rep1


title: LuCaP35CR_docetaxel_resistant_21

city: Boston

first: Steven

middle: P

last: Balk

state: MA

address: 3 Blackfan Circle

department: Hematology/Oncology

country: USA

institute: Harvard Medical School

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters.
cufflinks v2.2.1 was used to generate FPKM values.
Assembly: hg19
Supplementary files format and content: Comma-separated values file includes FPKM values for each sample.
Supplementary files format and content: Comma-separated values file includes differential gene expressions (log2(Fold Change) and statistical values).

source_name: Prostate

growth_protocol: Mice with LuCaP35CR or LuCaP70CR xenograft tumors. Mice with LNCaP FOXJ1_OE and LNCaP EV xenografts.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.
Transcriptome library construction with polyA selection (with Novogene for LuCaP70CR and FOXJ1 libraries; with GENWIZ for LuCaP35CR).

treatment_protocol: Mice with LuCaP35CR or LuCaP70CR xenograft tumors were treated with either vehicle or docetaxel (DTX) at 30 mg/kg by i.p. injection every 21 days starting at day 0 as indicated. Docetaxel and vehicle treated xenografts were harvested when they reached ~1500 mm3. The treated tumors were harvested 2 weeks after their final dose of docetaxel. Mice bearing LNCaP FOXJ1_OE and LNCaP EV xenografts were treated with docetaxel (DTX, 30 mg/kg). The first dose was administered when tumors reached ~250 mm3 (Day 9), and a second dose was given on Day 30. Mice for both groups were  sacrificed 5 days after the second dose, and the tumors were harvested for RNA sequencing.

value: Prostate

value: LuCaP35CR xenograft

value: prostate cancer

value: docetaxel at 30 mg/kg by i.p. injection every 21 days


title: Seca.rep2

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

description: 3' RNA

data_processing:
"Hisat2" were used for mapping with the parameters 'hisat2 -p 16 --no-softclip --no-discordant'.
Getting the mapped 'bam' files, bedtools v2.28.0  was used to gather mapping position information and saved as a bed file, by parameters 'bedtools bamtobed '.
PAS coverages were culculated from the bed file by using 'bedtools coverage'.
Genome_build: Human: hg38
Supplementary_files_format_and_content: csv file

source_name: MCF7 cell line

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium DMEM, Gibco supplemented with 10% fetal bovine serum FBS, Gibco at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cultured cells were washed once with PBS before adding TRIzol Vazyme, Cat no. R401-01. Total RNA extracted according to the manufacturer’s instructions. RNA was eluted in 20 μl RNase-free water.
To build 3’ end mRNA library, QuantSeq 3’mRNA-Seq Library Prep Kit REV for Illumina Lexogen was used with total RNA of an RNA integrity number RIN above 9.0. In details, 3’ end regions of each sample 500 ng total RNA as input were reverse-transcribed using an anchored oligo-dT primer, and their second strand synthesis was initiated by random priming. PCR amplification was then performed to obtain an Illumina compatible sequencing library. All libraries were sequenced in paired-end 2 × 151 nt format on an Illumina HiSeq X Ten machine.

value: Seca

tag: compound name

value: Secaubryenol

tag: treatment concentration


title: RNA-Seq_P400_degron_0h_rep2

value: P400 degron 0h


title: LuCaP35CR_docetaxel_resistant_19

value: WT


title: LuCaP35CR_docetaxel_resistant_18


title: RNA-Seq_P400_degron_0h_rep1

value: mouse embryonic stem cells


title: 242018_R_B18_agct2_6bp

description: Library name: 242018_R_B18_agct2_6bp

value: Burkitt's Lymphoma


title: RNA-Seq_INO80_degron_24h_rep2

value: INO80 degron 24h


title: con.3

description: 3' RNA

value: DMSO

value: control (DMSO)


title: LuCaP35CR_docetaxel_resistant_20


title: LuCaP35CR_docetaxel_resistant_17


title: con.4

description: 3' RNA


title: RNA-Seq_INO80_degron_24h_rep1


title: Seca.rep1

description: 3' RNA


title: CA.2

description: 3' RNA

value: CA

value: Coronalolic acid


title: LuCaP35CR_docetaxel_resistant_7


title: 227360_R_B18_agct2_6bp

description: Library name: 227360_R_B18_agct2_6bp

value: Ramos


title: 242017_R_B18_agct2_6bp

description: Library name: 242017_R_B18_agct2_6bp


title: 227359_R_B18_agct2_6bp

description: Library name: 227359_R_B18_agct2_6bp


title: RNA-Seq_INO80_degron_0h_rep2

value: INO80 degron 0h


title: LuCaP35CR_docetaxel_sensitive_4

value: Prostate

value: vehicle at 30 mg/kg by i.p. injection every 21 days


title: RNA-Seq_INO80_degron_0h_rep1


title: CA.1

description: 3' RNA


title: 11GJ.2

description: 3' RNA

value: Gardenia Jasminoide 9

value: 75 uM


title: Cut&Tag_SRCAP_SRCAP_degron_1h_rep2

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software. Reads with spike-in were mapped to both mm10 and hg19 genome.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method. Bam files with spike-in were normalized by the reads mapped to hg19 genome.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0) for ChIP-Seq, and gel extraction using DNA extract kit for Cut&Tag
ChIP-seq, briefly, the pretreated cells were harvested by trypsinization following 1% formaldehyde (final concentration, wt/vol) crosslinked and stored at -80 °C for downstream experiments. For chromatin immunoprecipitation, 20 million crosslinked cells (5% HEK293T cell were added as spikein) were lysed gently for chromatin isolation with ice-cold NP-40 lysis buffer and glycerol / urea buffer, finally centrifugated at 12,000 rpm for 1 min at 4 °C, the pellet of chromatin were resuspended in 1 ml sonication buffer, 1000 U MNase (NEB, M0247) and 5 mM CaCl2 were added and incubated for 15 min at 37 °C with 750 rpm shaking. After quenched by 20 μl 0.5 M EDTA and 40 μl 0.5 M EGTA in ice bath, the chromatin was sonicated using Qsonica Q800R3 DNA Shearing Sonicator for 15 min with 60% AMPL. Soluble chromatin was isolated by centrifugation at 1,2000 rpm for 10 min at 4 °C, 20 μl supernatant were sampled as input, the rest supernatant was transferred into 2 new DNase free tube for immunoprecipitation. 1 μl GFP abs (ABcam, ab290), 1 μg RPB1 NTD abs (CST, 14958S), and equal isotype IgG control for each ChIP reaction, respectively. After incubation overnight at 4 °C with low-speed rotation, 30 μl Protein G magnetic beads were added into the mixture to capture for 4 h, then washed beads once with sonication buffer, twice with high-salt wash buffer, twice with LiCl wash buffer and finally three times with TE buffer. For ChIP-seq, beads were eluted and then decrosslinked with 4 μl proteinase K (Sigma, 20 mg/ml) at 65 °C overnight, DNA was purified through the Tris saturated equilibrium phenol (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), and the ChIP library was prepared following the instruction of VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608-01); Cut&Tag was performed according to the manufacture of Hyperactive Universal Cut&Tag Assay Kit for Illumina (Vazyme, TD903-01), with 5% spikein 293T cells
ChIP-Seq, Cut&Tag

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 1h, then cells were harvested for next assays.

value: P400 degron 1h


title: 242048_R_B18_agct2_6bp

description: Library name: 242048_R_B18_agct2_6bp


title: LuCaP35CR_docetaxel_sensitive_3

value: LuCaP35CR xenograft

value: prostate cancer


title: 242047_R_B18_agct2_6bp

description: Library name: 242047_R_B18_agct2_6bp


title: 227353_R_B18_agct2_6bp

description: Library name: 227353_R_B18_agct2_6bp


title: LuCaP35CR_docetaxel_sensitive_2

value: WT


title: Cut&Tag_SRCAP_SRCAP_degron_1h_rep1

value: mouse embryonic stem cells


title: 242050_R_B18_agct2_3bp

description: Library name: 242050_R_B18_agct2_3bp

value: Burkitt's Lymphoma


title: Cut&Tag_SRCAP_SRCAP_degron_0h_rep2

value: P400 degron 0h


title: Cut&Tag_SRCAP_SRCAP_degron_0h_rep1


title: 11GJ.1

description: 3' RNA


title: 8GJ.1

description: 3' RNA

value: Gardenia Jasminoide 8

value: 50 uM


title: 8GJ.2

description: 3' RNA


title: 242020_R_B18_agct2_3bp

description: Library name: 242020_R_B18_agct2_3bp


title: LuCaP35CR_docetaxel_sensitive_1


title: AML4_24hr_Combo_3_S36

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
The paired-end reads were mapped to the human genome (hg19) using STAR (v2.5.1b) with default parameters.
Assembly: hg19
Supplementary files format and content: tsv, raw read counts

source_name: Primary Patient AML

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin. Primary AML patient samples were cultured in StemSpan SFEMII supplemented with 100 ng/mL human SCF, 10 ng/mL human IL3, 20 ng/mL human IL6, 20 ng/mL human TPO, and 100 ng/mL human FLT3 L.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen, Germany) or TRIzol LS (ThermoFisher, USA).
RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. The quality and concertation of the libraries were examined by Bioanalyzer High Sensitivity DNA Chip (Agilent). The multiplexed RNA-Seq libraries were paired-end sequenced for 150 bp on the Illumina HiSeq 4000 platform.

treatment_protocol:
Cells were lentivirally infected with indicated sgRNA for gene knockout
Cells were treated with DMSO, 500nM FICZ, 100nM JQ1, or in combination for 24hrs. Primary AML patient samples were treated with DMSO, 1µM FICZ, 200nM JQ1 or in combination for 24 hours.

value: Primary Patient AML

value: Acute myeloid leukemia cells

value: COMBO

tag: time


title: 242049_R_B18_agct2_3bp

description: Library name: 242049_R_B18_agct2_3bp

value: Ramos


title: 7GJ.2

description: 3' RNA

value: Gardenia Jasminoide 7

value: 30 uM


title: AML4_24hr_Combo_2_S35


title: Cut&Tag_P400_P400_degron_1h_rep2


title: 227354_R_B18_agct2_6bp

description: Library name: 227354_R_B18_agct2_6bp


title: 7GJ.1

description: 3' RNA


title: 242019_R_B18_agct2_3bp

description: Library name: 242019_R_B18_agct2_3bp


title: Cut&Tag_P400_P400_degron_0h_rep2


title: Cut&Tag_P400_P400_degron_1h_rep1


title: AML4_24hr_JQ1_3_S33


title: AML4_24hr_Combo_1_S34


title: 6GJ.2

description: 3' RNA

value: Gardenia Jasminoide 6


title: 227362_R_B18_agct2_3bp

description: Library name: 227362_R_B18_agct2_3bp


title: Cut&Tag_P400_P400_degron_0h_rep1


title: 227361_R_B18_agct2_3bp

description: Library name: 227361_R_B18_agct2_3bp


title: AML4_24hr_JQ1_2_S32


title: 227356_R_B18_agct2_3bp

description: Library name: 227356_R_B18_agct2_3bp


title: AML4_24hr_JQ1_1_S31


title: 5GJ.2

description: 3' RNA

value: Gardenia Jasminoide 5


title: Cut&Tag_INTS5_SRCAP_degron_1h_rep2

value: SRCAP degron 1h


title: 227355_R_B18_agct2_3bp

description: Library name: 227355_R_B18_agct2_3bp


title: 5GJ.1

description: 3' RNA


title: Cut&Tag_INTS5_SRCAP_degron_1h_rep1


title: Cut&Tag_INTS5_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: control-rep1

description: 3' RNA

value: DMSO

value: control (DMSO)


title: 279868_R_B18_agct1_6bpstop

description: Library name: 279868_R_B18_agct1_6bpstop


title: 279869_R_B18_agct1_6bpstop

description: Library name: 279869_R_B18_agct1_6bpstop


title: Cut&Tag_INTS5_SRCAP_degron_0h_rep1

value: mouse embryonic stem cells


title: 4GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 4

value: 75 uM


title: AML4_24hr_FICZ_1_S28

value: FICZ


title: AML4_24hr_DMSO_3_S27


title: Cut&Tag_INTS5_P400_degron_1h_rep2

value: P400 degron 1h


title: 279849_R_B18_agct1_6bpstop

description: Library name: 279849_R_B18_agct1_6bpstop

value: Burkitt's Lymphoma


title: 6GJ.1

description: 3' RNA


title: Cut&Tag_INTS5_P400_degron_1h_rep1


title: 4GJ-rep2

description: 3' RNA


title: 242046_R_B18_agct1_6bpstop

description: Library name: 242046_R_B18_agct1_6bpstop


title: Cut&Tag_INTS5_P400_degron_0h_rep2

value: P400 degron 0h


title: AML4_24hr_DMSO_1_S25

value: Primary Patient AML

value: Acute myeloid leukemia cells


title: 242045_R_B18_agct1_6bpstop

description: Library name: 242045_R_B18_agct1_6bpstop

value: Ramos


title: AML4_24hr_DMSO_2_S26


title: Cut&Tag_INTS5_P400_degron_0h_rep1


title: AML3_24hr_Combo_3_S24

value: COMBO


title: 3GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 3

value: 30 uM


title: AML4_24hr_FICZ_2_S29


title: AML4_24hr_FICZ_3_S30


title: control-rep2

description: 3' RNA


title: 3GJ-rep2

description: 3' RNA


title: 242015_R_B18_agct1_6bpstop

description: Library name: 242015_R_B18_agct1_6bpstop


title: Cut&Tag_INTS5_INO80_degron_1h_rep2

value: INO80 degron 1h


title: 279867_R_B18_agct1_3bpstop

description: Library name: 279867_R_B18_agct1_3bpstop


title: 3GJ-rep1

description: 3' RNA


title: AML3_24hr_Combo_1_S22


title: 242016_R_B18_agct1_6bpstop

description: Library name: 242016_R_B18_agct1_6bpstop


title: Cut&Tag_INTS5_INO80_degron_1h_rep1


title: 2GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 2

value: 50 uM


title: 279836_R_B18_agct1_6bpstop

description: Library name: 279836_R_B18_agct1_6bpstop


title: AML3_24hr_JQ1_3_S21


title: 4GJ-rep1

description: 3' RNA


title: AML3_24hr_Combo_2_S23


title: 2GJ-rep2

description: 3' RNA


title: Cut&Tag_INTS5_INO80_degron_0h_rep1

value: INO80 degron 0h


title: 279848_R_B18_agct1_3bpstop

description: Library name: 279848_R_B18_agct1_3bpstop


title: 279866_R_B18_agct1_3bpstop

description: Library name: 279866_R_B18_agct1_3bpstop


title: AML3_24hr_JQ1_2_S20


title: Cut&Tag_INO80_INO80_degron_1h_rep2

value: mouse embryonic stem cells


title: AML3_24hr_JQ1_1_S19


title: 279835_R_B18_agct1_3bpstop

description: Library name: 279835_R_B18_agct1_3bpstop


title: Cut&Tag_INO80_INO80_degron_1h_rep1


title: AML3_24hr_FICZ_3_S18


title: 1GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 1


title: 242044_R_B18_agct1_3bpstop

description: Library name: 242044_R_B18_agct1_3bpstop


title: 1GJ-rep2

description: 3' RNA


title: Cut&Tag_INO80_INO80_degron_0h_rep2


title: AML3_24hr_FICZ_1_S16


title: 1GJ-rep1

description: 3' RNA


title: Cut&Tag_INO80_INO80_degron_0h_rep1


title: AML3_24hr_FICZ_2_S17


title: 242043_R_B18_agct1_3bpstop

description: Library name: 242043_R_B18_agct1_3bpstop


title: 14GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 11


title: Cut&Tag_INTS5_INO80_degron_0h_rep2


title: AML3_24hr_DMSO_3_S15

value: DMSO


title: 242013_R_B18_agct1_3bpstop

description: Library name: 242013_R_B18_agct1_3bpstop


title: 14GJ-rep2

description: 3' RNA


title: 14GJ-rep1

description: 3' RNA


title: 2GJ-rep1

description: 3' RNA


title: Microbiota of Saliva from subject HIV5 [GN9]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN9

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming: qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check: qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
ASV generation: qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 275 --p-trunc-len-r 168 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
taxonomic assignment: qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
further analyses: R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

source_name: Saliva

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
paired-end (2x300) amplicon sequencing; Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Saliva

tag: patient id

tag: treatment time

tag: treatment condition

value: HIV

tag: terapy response

tag: caries

value: yes

tag: oral infections

value: no

tag: abitudinal mouthwash

tag: smoker


title: AML3_24hr_DMSO_2_S14

tag: cell line

value: Primary Patient AML

tag: cell type

value: Acute myeloid leukemia cells

tag: treatment


title: AML3_24hr_DMSO_1_S13


title: 12GJ-rep3

description: 3' RNA

value: Gardenia Jasminoide 10

value: 75 uM


title: Cut&Tag_H2AZ_SRCAP_degron_1h_rep2

value: SRCAP degron 1h


title: Microbiota of Saliva from subject HIV4 [GN8]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN8

tag: tissue

value: Treatment


title: Microbiota of Saliva from subject HIV4 [GN7]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN7


title: Cut&Tag_H2AZ_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: Cut&Tag_H2AZ_SRCAP_degron_0h_rep1


title: Cut&Tag_H2AZ_INO80_degron_1h_rep2

value: INO80 degron 1h


title: AML2_24hr_Combo_2_S11

value: COMBO


title: Microbiota of Saliva from subject HIV3 [GN6]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN6

value: Responding


title: 12GJ-rep2

description: 3' RNA


title: Cut&Tag_H2AZ_INO80_degron_1h_rep1

value: mouse embryonic stem cells


title: 12GJ-rep1

description: 3' RNA


title: 242014_R_B18_agct1_3bpstop

description: Library name: 242014_R_B18_agct1_3bpstop

value: Ramos

value: Burkitt's Lymphoma


title: Cut&Tag_H2AZ_INO80_degron_0h_rep2

value: INO80 degron 0h


title: Cut&Tag_H2AZ_SRCAP_degron_1h_rep1


title: Microbiota of Saliva from subject HIV2 [GN4]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN4

value: Saliva


title: kidney, KlothoKl/Kl, female, replicate 3

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

description: Library name: CFdk105_S23_R1_001

data_processing:
Partek Flow
sequence reads were trimmed based on quality score Phred <20 (default)
trimmed sequence reads were aligned with StarAligner 2.78a and mapped to mm39
read counts and TPM normalization were done using Partek Flow
Assembly: mm39
Supplementary files format and content: txt file includes TPM normalization for each sample

source_name: kidney

growth_protocol: Animals are congenic

extract_protocol:
miRNeasy Mini Kit (Qiagen Inc.)
New England Biolabs Ultra Directional RNA Library Prep Kit.
cDNA libraries purified with AmpureXP beads, quantified on the Agilent Bioanalyzer,  Qubit Fluorometric Quantification

treatment_protocol: kidneys flash frozen after perfusion and dissection

value: kidney

tag: strain

value: C57Bl/6J mouse

tag: Sex

value: female

tag: disease state

value: renal disease

tag: developmental stage

value: 48 days

value: Kl/Kl


title: kidney, KlothoKl/Kl, female, replicate 4

description: Library name: CFdk143_S24_R1_001

value: 52 days

tag: genotype


title: AML2_24hr_JQ1_3_S9

value: Primary Patient AML

value: Acute myeloid leukemia cells

tag: time


title: Cut&Tag_H2AZ_INO80_degron_0h_rep1


title: AML2_24hr_JQ1_2_S8


title: kidney, KlothoKl/Kl, female, replicate 2

description: Library name: CFK20_S22_R1_001

value: 47 days


title: AML2_24hr_Combo_3_S12

value: COMBO


title: kidney, KlothoKl/Kl, female, replicate 1

description: Library name: CFK22_S21_R1_001


title: Microbiota of Saliva from subject HIV12 [GN24]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN24

tag: patient id

tag: treatment time

value: Treatment

value: yes

value: no


title: AML2_24hr_JQ1_1_S7


title: ChIP-Seq_SRCAP_degron_input

value: mouse embryonic stem cells

value: SRCAP degron 0h


title: Microbiota of Saliva from subject HIV2 [GN3]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN3

value: Saliva

tag: treatment condition

value: HIV

tag: terapy response


title: ChIP-Seq_RPB1_SRCAP_degron_1h_rep2

value: SRCAP degron 1h


title: AML2_24hr_FICZ_3_S6

value: FICZ


title: kidney, KlothoCtrl, female, replicate 4

description: Library name: CFdk107_S20_R1_001

value: kidney

value: C57Bl/6J mouse

value: female

value: healthy renal function

value: +/Kl


title: AML2_24hr_FICZ_2_S5

value: Primary Patient AML

value: Acute myeloid leukemia cells


title: Microbiota of Saliva from subject HIV12 [GN23]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN23

tag: caries

tag: oral infections


title: ChIP-Seq_RPB1_SRCAP_degron_1h_rep1


title: Microbiota of Saliva from subject HIV11 [GN22]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN22

value: Responding

tag: abitudinal mouthwash

tag: smoker


title: kidney, KlothoCtrl, female, replicate 3

description: Library name: CFdk160_S19_R1_001

value: 57 days


title: ChIP-Seq_RPB1_SRCAP_degron_0h_rep2

tag: cell line

tag: cell type


title: Microbiota of Saliva from subject HIV11 [GN21]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN21

tag: tissue

value: yes


title: AML2_24hr_Combo_1_S10

tag: treatment

value: COMBO


title: ChIP-Seq_RPB1_SRCAP_degron_0h_rep1

value: mouse embryonic stem cells


title: Microbiota of Saliva from subject HIV3 [GN5]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN5

value: no


title: kidney, KlothoCtrl, female, replicate 2

description: Library name: CFK21_S18_R1_001

tag: strain

tag: Sex

value: 47 days


title: Microbiota of Saliva from subject HIV10 [GN20]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN20

value: Saliva

value: Treatment


title: kidney, KlothoCtrl, female, replicate 1

description: Library name: CFK19_S17_R1_001

tag: disease state

tag: developmental stage


title: AML2_24hr_DMSO_3_S3

value: DMSO

tag: time


title: Microbiota of Saliva from subject HIV1 [GN2]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN2

tag: patient id


title: ChIP-Seq_RPB1_P400_degron_1h_rep2

value: P400 degron 1h


title: ChIP-Seq_RPB1_P400_degron_1h_rep1


title: kidney, KlothoKl/Kl, male, replicate 4

description: Library name: CFdk183_S24_R1_001

value: kidney

value: C57Bl/6J mouse

value: male

value: renal disease

value: 59 days

tag: genotype

value: Kl/Kl


title: AML2_24hr_DMSO_2_S2

value: Primary Patient AML

value: Acute myeloid leukemia cells


title: AML2_24hr_DMSO_1_S1


title: Microbiota of Saliva from subject HIV10 [GN19]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN19

tag: treatment time

tag: treatment condition

value: HIV

value: yes


title: kidney, KlothoKl/Kl, male, replicate 3

description: Library name: CFdk23_S23_R1_001

value: 46 days


title: kidney, KlothoKl/Kl, male, replicate 2

description: Library name: CFK9_S22_R1_001

value: 49 days


title: ChIP-Seq_RPB1_P400_degron_0h_rep2

value: mouse embryonic stem cells

value: P400 degron 0h


title: K562_OE_COMBO_Rep2

description:
K562_salmon.merged.gene_counts.tsv
OEFJ2

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen, Germany).
RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. The quality and concertation of the libraries were examined by Bioanalyzer High Sensitivity DNA Chip (Agilent). The multiplexed RNA-Seq libraries were paired-end sequenced for 150 bp on the Illumina HiSeq 4000 platform.

treatment_protocol:
Cells were lentivirally infected with indicated sgRNA for gene knockout
Cells were treated with DMSO, 500nM FICZ, 100nM JQ1, or in combination for 24hrs.

value: Chronic myeloid leukemia cells

value: AHR overexpression

tag: agent

value: COMBO


title: ChIP-Seq_RPB1_P400_degron_0h_rep1


title: K562_OE_COMBO_Rep1

description:
K562_salmon.merged.gene_counts.tsv
OEFJ1


title: Microbiota of Saliva from subject HIV9 [GN18]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN18

value: Saliva

value: Treatment

tag: terapy response

tag: caries

value: no

tag: oral infections


title: AML2_24hr_FICZ_1_S4

tag: cell line

value: FICZ


title: Microbiota of Saliva from subject HIV8 [GN16]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN16

tag: abitudinal mouthwash

tag: smoker


title: ChIP-Seq_RPB1_INO80_degron_1h_rep2

tag: cell type

tag: treatment

value: INO80 degron 1h


title: K562_OE_JQ1_Rep2

description:
K562_salmon.merged.gene_counts.tsv
OEDJ2


title: kidney, KlothoKl/Kl, male, replicate 1

description: Library name: CFK44_S21_R1_001

tag: tissue

value: kidney

tag: strain

value: C57Bl/6J mouse

tag: Sex

value: male

value: renal disease

value: 47 days

value: Kl/Kl


title: ChIP-Seq_RPB1_INO80_degron_1h_rep1


title: K562_OE_JQ1_Rep1

description:
K562_salmon.merged.gene_counts.tsv
OEDJ1

tag: time


title: Microbiota of Saliva from subject HIV8 [GN15]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN15

tag: patient id

value: HIV

value: yes


title: kidney, KlothoCtrl, male, replicate 3

description: Library name: CFdk25_S19_R1_001

tag: disease state

value: healthy renal function

tag: developmental stage

value: 46 days

tag: genotype


title: ChIP-Seq_RPB1_INO80_degron_0h_rep2

value: mouse embryonic stem cells

value: INO80 degron 0h


title: Microbiota of Saliva from subject HIV7 [GN14]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN14

value: Saliva

tag: treatment time

tag: treatment condition


title: ChIP-Seq_RPB1_INO80_degron_0h_rep1


title: K562_OE_FICZ_Rep2

description:
K562_salmon.merged.gene_counts.tsv
OEDF2

value: Chronic myeloid leukemia cells

value: AHR overexpression

tag: agent


title: Microbiota of Saliva from subject HIV7 [GN13]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN13

tag: terapy response

tag: caries

tag: oral infections

value: no


title: kidney, KlothoCtrl, male, replicate 1

description: Library name: CFK45_S17_R1_001

value: +/Kl


title: ChIP-Seq_P400_degron_input

tag: cell line

value: P400 degron 0h


title: Wt_Unstarved 3

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description: Library name: WT_3

data_processing:
BCL raw data was converted to FASTQ data and demultiplexed by bcl2fastq Conversion Software (Illumina)
After checking the quality of the samples (FastQC, v.0.11.7), the files were mapped to the mouse genome (Genome build GRCm38) downloaded from Ensembl using the STAR aligner (v. 2.7.4a).
The mapped bam files were then quantified on a gene level based on the Ensembl annotations, using the HTseq tool in Python.
Using the DESeq2 package (R 4.0.3, DESeq version 1.30.1), the count data was normalized by the size factor to estimate the effective library size. A filtering step of removing genes with low reads in all conditions was used (total of all Wt or Gcn ko counts < 1) .
The analysis of two different conditions against each other resulted in a list of differentially expressed genes for each comparison. Genes with an adjusted p-value of ≤ 0.05 were then considered to be differentially expressed for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: GeneCounts_Normalized_fullDataset.txt
Supplementary files format and content: GeneCounts_raw_fullDataset.txt

growth_protocol: ES cells were grown on 0.1% gelatin-coated dishes in DMEM high glucose GlutaMAX containing 15% fetal bovine serum, 1% penicillin-streptomycin, Œ≤-mercaptoethanol and 10 ng/ml recombinant murine leukemia inhibitory factor. Cells were incubated at 37¬∞C in 5% CO2.

extract_protocol:
RNA isolation was performed using the Direct-zol RNA Miniprep Plus kit from Zymo Research.
mRNA sequencing libraries were prepared with 1 ¬µg of total RNA of each sample using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: ES cells were seeded the day before then starved for 3h using SILAC medium supplemented with penicillin-streptomycin, GlutaMAX, glucose, 5% dialyzed FBS, Œ≤-mercaptoethanol, LIF, L-Lys and with or without L-Arg or L-Leu. The same medium containing all amino acids was used for the control treatment (unstarved). 3 replicates were used per condition.

tag: cell type

value: E14 ES cells

value: wild type


title: ChIP-Seq_INO80_degron_input

tag: treatment


title: Microbiota of Saliva from subject HIV6 [GN11]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN11

tag: tissue

tag: abitudinal mouthwash

tag: smoker


title: Wt_Unstarved 2

description: Library name: WT_2


title: Microbiota of Saliva from subject HIV9 [GN17]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN17


title: K562_EV_COMBO_Rep2

description:
K562_salmon.merged.gene_counts.tsv
EVFJ2

value: Wildtype

value: COMBO

tag: time


title: K562_OE_DMSO_Rep1

description:
K562_salmon.merged.gene_counts.tsv
OEDD1

value: DMSO


title: ChAR-Seq_SRCAP_degron_1h_rep2

data_processing:
Raw reads with spike-in were firstly trimmed by Cutadapt software and then mapped to mm10 and dm6 genome using Bowtie2 software
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software normalized by the reads mapped to dm6 genome.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: nuclear RNA

extract_protocol:
Extracted twice using Trizol reagent following the instruction
The chromatin RNAs were isolated and examined, the pretreated cells without crosslink were used to chromatin isolation as described above, then the native chromatin were extracted twice using Trizol reagent to obtain the chromatin associated RNA. After checked the quantity and quality and poly(A) RNA depletion, the ChAR-seq RNA library were generated using the no coding RNA library method with random primers and sequencing analyzed using Nova PE150 platform.
ChAR-Seq

value: SRCAP degron 1h


title: Microbiota of Saliva from subject HIV5 [GN10]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN10

tag: patient id

value: Treatment

value: Responding

value: yes


title: Threonin-starved 3

description: Library name: T_3


title: Microbiota of Saliva from subject HIV1 [GN1]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN1

value: HIV


title: Wt_Unstarved 1

description: Library name: WT_1


title: ChAR-Seq_SRCAP_degron_1h_rep1

value: mouse embryonic stem cells


title: K562_EV_JQ1_Rep2

description:
K562_salmon.merged.gene_counts.tsv
EVDJ2


title: kidney, KlothoCtrl, male, replicate 4

description: Library name: CFdk33_S20_R1_001

value: kidney

tag: strain

value: C57Bl/6J mouse

tag: Sex

value: male

tag: disease state

value: healthy renal function

value: 48 days


title: Threonin-starved 2

description: Library name: T_2

tag: genotype


title: K562_EV_COMBO_Rep1

description:
K562_salmon.merged.gene_counts.tsv
EVFJ1

value: Chronic myeloid leukemia cells


title: Microbiota of Saliva from subject Healthy_2 [GM99]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM99

value: Saliva

tag: treatment time

tag: treatment condition

value: Healthy

value: Unknown


title: kidney, KlothoCtrl, male, replicate 2

description: Library name: CFK46_S18_R1_001

tag: developmental stage

value: 47 days

value: +/Kl


title: K562_OE_FICZ_Rep1

description:
K562_salmon.merged.gene_counts.tsv
OEDF1

value: AHR overexpression

tag: agent

value: FICZ


title: ChAR-Seq_SRCAP_degron_0h_rep1

value: SRCAP degron 0h


title: K562_EV_JQ1_Rep1

description:
K562_salmon.merged.gene_counts.tsv
EVDJ1

value: Wildtype


title: Microbiota of Saliva from subject Healthy_15 [GM98]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM98

tag: terapy response

tag: caries

tag: oral infections


title: Microbiota of Saliva from subject HIV6 [GN12]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GN12

value: Treatment

value: Responding

value: no


title: Threonin-starved 1

description: Library name: T_1

tag: cell line

tag: cell type

value: E14 ES cells

value: wild type


title: K562_OE_DMSO_Rep2

description:
K562_salmon.merged.gene_counts.tsv
OEDD2

value: DMSO


title: ChAR-Seq_SRCAP_degron_0h_rep2

value: mouse embryonic stem cells

tag: treatment


title: ChAR-Seq_P400_degron_1h_rep2

value: P400 degron 1h


title: K562_EV_FICZ_Rep2

description:
K562_salmon.merged.gene_counts.tsv
EVDF2

value: Chronic myeloid leukemia cells


title: Microbiota of Saliva from subject Healthy_14 [GM97]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM97

tag: tissue

value: Saliva

value: Healthy

tag: abitudinal mouthwash

tag: smoker


title: Cystein-starved 3

description: Library name: C_3


title: Microbiota of Saliva from subject Healthy_13 [GM96]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM96

tag: patient id

value: Unknown


title: Cystein-starved 2

description: Library name: C_2


title: K562_EV_FICZ_Rep1

description:
K562_salmon.merged.gene_counts.tsv
EVDF1

tag: time


title: ChAR-Seq_P400_degron_0h_rep2

value: P400 degron 0h


title: K562_EV_DMSO_Rep2

description:
K562_salmon.merged.gene_counts.tsv
EVDD2


title: Microbiota of Saliva from subject Healthy_12 [GM95]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM95


title: ChAR-Seq_P400_degron_0h_rep1


title: K562_EV_DMSO_Rep1

description:
K562_salmon.merged.gene_counts.tsv
EVDD1


title: Cystein-starved 1

description: Library name: C_1


title: Microbiota of Saliva from subject Healthy_11 [GM94]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM94


title: 24hr Rv0009 treated RAW264.7_RNASeq_Set3

city: Kolkata

first: Joyoti

last: Basu

address: A.P.C. Road

department: Chemistry

country: India

institute: Bose Institute

description: Library name: 4C_24hr Rv0009 treated_RNASeq

data_processing:
Mouse GRCm39 reference genome and annotation files have been downloaded from Gencode.
Quality control for Fastq files was conducted using FastQC v0.11.7 and adapter trimming was done with Cutadapt v1.16 using Illumina Universal Adapter.
Reads were aligned to the Mouse reference genome using Hisat2 v2.1.0. followed by sorting via Samtools v1.19 9.
Gene counts were generated using FeatureCounts and differential analysis was performed using DESeq2.
Genes with a ≥ or ≤ 2-fold change, p ≤ 0.05, and FDR ≤ 0.05 were filtered across Untreated vs Rv0009 treated 4 hour, Rv0009 treated 8 hour and Rv0009 treated 24 hour comparisons.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Dulbecco's modified Eagle's medium (DMEM) with 10% Fetal Bovine Serum, 5mM L-glutamine, 2mM sodium pyruvate. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following  manufacturer’s protocol. Illumina NextSeq500 platforms with 2 x 150 bp v2 chemistry was used for sequencing.

treatment_protocol: Mouse macrophages (RAW264.7) were treated with purified Rv0009 (2.5 µg/ml) in DMEM medium supplemented with 10% FBS, 5mM L-glutamine, 2mM sodium pyruvate for 4 hour, 8 hour and 24 hour or left untreated (Biological Triplicate).

value: macrophage

tag: treament

value: recombinant Rv0009 protein

value: 24 hr


title: Microbiota of Saliva from subject Healthy_10 [GM93]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM93


title: U937_COMBO_Rep2

description:
U937_salmon.merged.gene_counts.tsv
R8_FJ_2

value: Acute myeloid leukemia cells

tag: genotype

value: Wildtype

value: COMBO


title: 8hr Rv0009 treated RAW264.7_RNASeq_Set3

description: Library name: 3C_8hr Rv0009 treated_RNASeq

value: 8 hr


title: ChAR-Seq_INO80_degron_1h_rep2

value: INO80 degron 1h


title: Microbiota of Saliva from subject Healthy_9 [GM92]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM92

tag: treatment time


title: ChAR-Seq_INO80_degron_1h_rep1


title: ChAR-Seq_INO80_degron_0h_rep2

value: INO80 degron 0h


title: U937_COMBO_Rep1

description:
U937_salmon.merged.gene_counts.tsv
R7_FJ_1


title: 4hr Rv0009 treated RAW264.7_RNASeq_Set3

description: Library name: 2C_4hr Rv0009 treated_RNASeq

value: 4 hr


title: ChAR-Seq_INO80_degron_0h_rep1

value: mouse embryonic stem cells


title: ChAR-Seq_P400_degron_1h_rep1

value: P400 degron 1h


title: U937_JQ1_Rep2

description:
U937_salmon.merged.gene_counts.tsv
R6_J_2


title: U937_JQ1_Rep1

description:
U937_salmon.merged.gene_counts.tsv
R5_J_1


title: Untreated RAW264.7_RNASeq_Set3

description: Library name: 1C_Untreated_RNASeq

value: untreated

value: 0 hr


title: Microbiota of Saliva from subject Healthy_1 [GM90]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM90

value: Saliva

tag: treatment condition

value: Healthy


title: Microbiota of Saliva from subject Healthy_8 [GM91]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM91

value: Unknown


title: 24hr Rv0009 treated RAW264.7_RNASeq_Set2

description: Library name: 4B_24hr Rv0009 treated_RNASeq

value: macrophage


title: Microbiota of Saliva from subject Healthy_6 [FL12]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
FL12


title: 8hr Rv0009 treated RAW264.7_RNASeq_Set2

description: Library name: 3B_8hr Rv0009 treated_RNASeq

value: recombinant Rv0009 protein


title: ATAC-Seq_SRCAP_degron_1h_rep2

data_processing:
Raw reads were firstly trimmed by Cutadapt software and then mapped to mm10 and genome by Bowtie2 software.
PCR duplicated, multiple mapped and discordant reads were discarded for further analysis.
Bam files were converted to bw format by deepTools software using RPGC as the normalization method.
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i/mLIF medium, which composed of DMEM containing 1 mM L-glutamine, 1× nucleosides (Sigma, ES-008), 1× nonessential amino acids (Milipore, TMS-001-C), 1× sodium pyruvate (Gibco, 11360070), 1× penicillin/ streptomycin (Gibco, 15140-122), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107), and also supplemented with 15% fetal bovine serum (FBS) (VivaCell, 04-001-1A), incubated at 37 °C with 5% CO2 in a humidified incubator

extract_protocol:
Extracted DNA according to the DNA extraction kit’s instruction
After the INO80, P400 and SRCAP degradation, ATAC-seq were performed as depicted before and following the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). 50000 viable cells were collected for penetrated with 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin in 50 μl cold RSB buffer, then fragmentated and tagged using the Tn5 transposase according to the kit manufacture for 30 min at 37°C in a thermomixer with 1000 rpm mixing. Reaction was stopped by addition 250 μl (5 volumes) of DNA binding buffer, and extracted DNA according to the DNA extraction kit’s instruction. The eluted DNA were amplified 8 cycles for library generation using the Illumina primers, and 200-500 bp fragments were selected for sequencing analysis.

treatment_protocol: For target protein degradation, the degron cells were firstly induced with 1 μg/ml Dox in the 2i medium to express the OsTir1 for 12 h, then 500 μM auxin were added to induced the degradation for 1h, then cells were harvested for next assays

value: SRCAP degron 1h


title: U937_FICZ_Rep1

description:
U937_salmon.merged.gene_counts.tsv
R3_F_1

value: Acute myeloid leukemia cells

value: FICZ


title: U937_FICZ_Rep2

description:
U937_salmon.merged.gene_counts.tsv
R4_F_2

value: Wildtype


title: ATAC-Seq_SRCAP_degron_1h_rep1


title: 4hr Rv0009 treated RAW264.7_RNASeq_Set2

description: Library name: 2B_4hr Rv0009 treated_RNASeq


title: ATAC-Seq_SRCAP_degron_0h_rep2

value: SRCAP degron 0h


title: U937_DMSO_Rep2

description:
U937_salmon.merged.gene_counts.tsv
R2_D_2

value: DMSO


title: Microbiota of Saliva from subject Healthy_5 [FL10]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
FL10


title: Untreated RAW264.7_RNASeq_Set2

description: Library name: 1B_Untreated_RNASeq


title: ATAC-Seq_SRCAP_degron_0h_rep1


title: U937_DMSO_Rep1

description:
U937_salmon.merged.gene_counts.tsv
R1_D_1


title: Microbiota of Saliva from subject Healthy_7 [FL4]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
FL4


title: ATAC-Seq_P400_degron_1h_rep2


title: cut_222_48h_3

city: Guiyang

first: Zhao

last: Yanchi

state: Guizhou

address: No. 9 Beijing Road

institute: Guizhou Medical University

data_processing:
Hisat software was used to compare the sequencing data with the zebrafish referenced genome. To evaluate the expression level of all mRNAs, we first realized sample reads through StringTie, and then calculated the FPKM (fragments per kilobase of transcript per million mapped reads) using stringtie and edgeR software. Finally, the differentially expressed genes (DEGs) were screened by the R software package according to the following criteria: log2 (fold-change) > 1 or <−1 and at p < 0.05. These DEGs were used for further analysis of functions and signaling pathways using Gene Ontology (GO; http://geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Danio rerio

source_name: whole organism

extract_protocol:
Total RNA was extracted using Invitrogen TRizol reagent (California, USA), and generation of the Illumina RNA sequence library and paired end sequencing (300±50 bp) were performed on an Illumina NovaSeq 6000 using aliquots (5 mg) of qualified total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: whole organism

value: WT

value: 48 hours after cut the caudal fin with 222mM glucose


title: Microbiota of Saliva from subject Healthy_4 [FL2]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
FL2


title: ATAC-Seq_P400_degron_1h_rep1

value: mouse embryonic stem cells

value: P400 degron 1h


title: cut_222_48h_2


title: 8hr Rv0009 treated RAW264.7_RNASeq_Set1

description: Library name: 3A_8hr Rv0009 treated_RNASeq

value: 8 hr


title: ATAC-Seq_P400_degron_0h_rep2

value: P400 degron 0h


title: cut_222_48h_1


title: Microbiota of Saliva from subject Healthy_3 [GM100]

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv
GM100

value: Saliva

value: Healthy


title: 4hr Rv0009 treated RAW264.7_RNASeq_Set1

description: Library name: 2A_4hr Rv0009 treated_RNASeq

value: macrophage

value: 4 hr


title: Untreated RAW264.7_RNASeq_Set1

description: Library name: 1A_Untreated_RNASeq

value: untreated

value: 0 hr


title: ATAC-Seq_P400_degron_0h_rep1


title: cut_222_24h_3

value: 24 hours after cut the caudal fin with 222mM glucose


title: RNA from stupicke seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep3

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
After adapter trimming and quality control, high quality reads were mapped on the tomato reference transcriptome based on SL4.0 genome version and ITAG4.0 annotation (Hosmani et al., 2019),using quasi-mapping alignment and quantification methods of Salmon algorithm v.1.2 (Patro et al., 2017). For gene expression analysis, raw RNA-Seq counts were first normalized as Transcripts Per Kilobase Million (TPM).
Assembly: tomato reference transcriptome based on SL4.0 genome version and ITAG4.0 annotation (Hosmani et al., 2019)
Supplementary files format and content: tab-delimited text (counts and TPM)

organism: Solanum lycopersicum

source_name: primed seeds

growth_protocol: Seed osmopriming solutions were prepared as following: 28.5 g of polyethylene glycol (PEG) 8000 were added to 100 ml of MilliQ sterile water to generate a solution with osmotic potential of -1 MPa at RT. Elicitor treatment used: 2 mM of MeJA (Sigma-Aldrich, St. Louis, USA) and water for control seeds. Two ml of seed priming solution (1 MPa ± elicitors) were then added into 30 mm Ø sterile glass Petri dishes containing 30 dry mature seeds on sterile Whatman filter paper to imbibe in dark at 20°C for 48h. Three biological replicates of 30 seeds each were used for each treatment. Seeds were then abundantly washed under tap water to remove the priming solution, blot-dried, and placed into a desiccator at 43% RH for 48h to re-dry them.

extract_protocol:
RNA samples were extracted from the same seed lot used to produce exudates following the seed priming treatment with or without elicitors using the NucleoSpin RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany) with lysis buffer containing 1% of polyvinylpyrrolidone (PVP-40) followed by incubation at room temperature for 10 minutes. RNA quantity and quality was measured using a NanoDrop ND‐1000 (NanoDrop Technologies, Wilmington, DE, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.
All samples showing 260/280 and 260/230 absorbance ratio >1.8, RNA Integrity Number, RIN>7 and 28S/18S>1.7 were sent to Beijing Genomics Institute (https:// www.bgi.com) (Hong Kong, China) for library preparation and sequencing on BGISEQ-500 platform, generating a minimum of 20M reads of 100 bp per sample (20M PE100).
PolyA enrichement library done by BGI

treatment_protocol: Elicitor treatment used: 2 mM of MeJA (Sigma-Aldrich, St Louis, USA) and water for control seeds

value: primed seeds

tag: replicates

value: Biol rep 3

value: mature seed (re-dried 48h after seed priming)

value: Stupicke

tag: elicitation

value: MeJA 48h


title: cut_222_24h_1

value: whole organism

value: WT


title: MtbH37Rv infected (20hrs) RAW264.7_H3K27ac_ChIPSeq

description: Library name: 20hrs Mtb Infected_H3K27ac_ChIPSeq

data_processing:
The raw reads were further processed by Cutadapt for removal of adapters.
ChIP-Seq reads were aligned with Ensembl GRCm39 genome using Bowtie2 alignment tool.
Peaks were called using HOMER.
After peak calling, we identified the peaks which are present in infected samples but not in uninfected sample using bedtools intersect.
Assembly: GRCm39
Supplementary files format and content: tab delimited text files include peak for each sample

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes. After quenching and cell lysis, Chromatin was sonicated using a Diagenode bioruptor NGS 600 (Diagenode).
Illumina HiSeq single-end sequencing with 75 x 1 chemistry sequencing platform technology was used.

treatment_protocol: Mouse macrophages (RAW264.7) were infected with M. tuberculosis (H37Rv) at an MOI 10 for 4 hours followed by washing and incubating cells in Dulbecco's modified Eagle's medium (DMEM) with 10% Fetal Bovine Serum, 5mM L-glutamine, 2mM sodium pyruvate and gentamycin (10 microgram/ml) for 2 hours.


title: MtbH37Rv infected (6hrs) RAW264.7_H3K27ac_ChIPSeq

description: Library name: 6hrs Mtb Infected_H3K27ac_ChIPSeq


title: 24hr Rv0009 treated RAW264.7_RNASeq_Set1

description: Library name: 4A_24hr Rv0009 treated_RNASeq

value: recombinant Rv0009 protein

value: 24 hr


title: RNA from stupicke seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep2

value: Biol rep 2


title: Uninfected RAW264.7_H3K27ac_ChIPSeq

description: Library name: Uninfected_H3K27ac_ChIPSeq


title: ATAC-Seq_INO80_degron_0h_rep2

value: mouse embryonic stem cells

value: INO80 degron 0h


title: RNA from stupicke seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep1

value: Biol rep 1


title: Infected leaves_3dpi_rep2

type: RNA

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

institute: INRA

hyb_protocol: Hybridization by NimbleGen Company

scan_protocol: Scanning by NimbleGen Company

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism:
Brassica napus
Plenodomus lingam

source_name: infected oilseed rape leaves_3 dpi

label_protocol: Labelling by NimbleGen Company

growth_protocol: Oilseed rape leaves were infected with Leptosphaeria maculans (isolate v23.1.3 ) spores and harvested 3 days post inoculation.

extract_protocol: RNA extraction was carried out using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs).

tag: strain/isolate background

value: derived from infected Brassica napus leaves

tag: time point

value: 3 days post infection


title: MtbH37Rv infected (20hrs) RAW264.7_H3K4me3_ChIPSeq

description: Library name: 20hrs Mtb Infected_H3K4me3_ChIPSeq

value: macrophage


title: cut_222_3h_2

value: 3 hours after cut the caudal fin with 222mM glucose


title: RNA from stupicke seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep3

value: primed seeds

value: water


title: Infected leaves_3dpi_rep3


title: ATAC-Seq_INO80_degron_0h_rep1


title: Infected leaves_3dpi_rep1


title: MtbH37Rv infected (6hrs) RAW264.7_H3K4me3_ChIPSeq

description: Library name: 6hrs Mtb Infected_H3K4me3_ChIPSeq


title: KO_H3K4Me3

city: Wuhan

first: Chen

last: zhang

state: Hubei

address: Jiefang road 1037

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Raw paired-end sequenced reads were first cut for adaptor sequences and trimmed using trim_galore (v0.6.6).
Cleaned fastq data were mapped to the mm10 reference genome using Bowtie 2 (v2.4.2).
Samtools (v1.11) was used to convert and sort the SAM files into BAM format.
DeepTools was used to normalize the signals from sorted BAM files via bamCoverage.
Data were visualized using Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigWig file for each sample

source_name: CD4+ T cells

extract_protocol:
Briefly, 10^5 T cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C. After that, the cells were incubated with 1 μg rabbit anti-mouse H3K4me3 (Cell Signaling Technology, 9751, USA) antibody at 4 °C overnight. Goat anti-rabbit IgG was added and incubated for 1 h at 25 °C the next day. Then, the cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, the cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 hour. Tagmentation was then stopped by the addition of proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, the cells were plated on a magnet, and unbound liquid was removed. The beads were gently rinsed twice with 80% ethanol, and DNA was eluted with double-distilled water.
Libraries were constructed using the ‘TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina’ and the ‘TD202 TruePrep Index Kit V2 for Illumina’ from Vazyme Biotech.

tag: chip antibody

value: CD4+ T cells

value: Mthfd2 KO


title: cut_222_3h_1


title: cut_222_24h_2

value: 24 hours after cut the caudal fin with 222mM glucose


title: cut_130_48h_3

value: whole organism

value: 48 hours after cut the caudal fin with 130mM glucose


title: RNA from stupicke seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep2

value: mature seed (re-dried 48h after seed priming)

value: Stupicke


title: Uninfected RAW264.7_H3K4me3_ChIPSeq

description: Library name: Uninfected_H3K4me3_ChIPSeq

tag: cell line


title: WT_H3K4Me3

tag: cell type

value: WT


title: ATAC-Seq_INO80_degron_1h_rep2

value: mouse embryonic stem cells

tag: treatment

value: INO80 degron 1h


title: RNA from stupicke seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep1

tag: tissue

value: Biol rep 1


title: KO_Rep2

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v2.0.1) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v2.0.1) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.30.1) package of the R (version 4.0.4) software
Assembly: mm10
Supplementary files format and content: Comma-Separated Row counts for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 10 million cells were added with Trizol and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on NovaSeq 6000 platform .

value: spleen

value: TEaMthfd2 KO

value: cocultured with APCs sorted from the spleens of 8-week-old F1 (BALB/c x C57BL/6) mice.

value: 3 day


title: Control scRNA-seq

city: NEW HAVEN

first: Rongmo

last: Zhang

state: CT

address: 300 George street

institute: Yale

description: Library name: Control

library_source: transcriptomic single cell

data_processing:
10,000 cells were loaded for scRNA library preparation using the Chromium Single Cell Platform (10× Genomics) per manufacturer’s instruction. Briefly, cells were partitioned into Gel Beads in Emulsion in the Chromium system (Chromium Single Cell 3’ Library & Gel Bead Kit v4) at Yale Center for Genome Analysis, followed by cell lysis and barcoded reverse transcription of RNA, cDNA amplification and shearing, and 5’ adaptor and sample index attachment. Final scRNAseq libraries were sequenced on an Illumina NextSeq 500 using HiSeq paired-end, with read length of 150 base pairs. R package Seurat v4.4 was used for data processing, including cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction. To visualize the data, FeaturePlot, Vlnplot, DotPlot, chordDiagram and Heatmap were performed.
Assembly: MM9
Supplementary files format and content: aorta-Pdk4KO.rds can be loased to R-seruat, contains information on barcodes-features and matrix

source_name: aorta

growth_protocol: Mice, WT or Pdk4 smooth muscle cell specific Pdk4 KO under ApoE null background, were treated with High fat diet for 4 month. Fresh aorta were digested as described below.

extract_protocol:
The mice were euthanized with isoflurane, followed by immediate perfusion with 20 mL cold phosphate-buffered saline (PBS). Isolated fresh aortae were opened longitudinally and cut into 3 mm fragments, followed by cold digestion for 3 h at 4°C. Digesting cocktail is composed of .5 mg/mL collagenase A (10103578001, Roche), 0.5 mg/mL elastase (LS002294, Worthington Biochemical), 10 mg/mL Bacillus licheniformis protease (P5380, Sigma-Aldrich), 10 mg/mL Dispase II (D4693, Sigma-Aldrich),  125 U/mL DNase I (DN25, Sigma-Aldrich)  and 0.2% BSA in DMEM. Digested aortae were spined at 350 g for 5 min at 4°C, washed twice with 1% BSA in PBS, and stained with viability dye on ice for 20 min (1:2000, Thermo Fisher, 65-0865-14). Suspended cells were sorted for viable cells using flow cytometry, and collected in 0.04% BSA-PBS.
following Nextera XT Library Prep Kit

value: aorta

value: whole tissue

value: ApoE


title: cut_130_48h_2


title: ATAC-Seq_INO80_degron_1h_rep1


title: Pdk4 KO scRNA-seq

description: Library name: Pdk4 KO


title: KO_Rep1

value: CD4+ T cells


title: cut_222_3h_3

value: 3 hours after cut the caudal fin with 222mM glucose


title: cut_130_48h_1

value: whole organism


title: Pdk4 KO

description:
Library name: Pdk4 KO
10um Fresh frozen tissue section

data_processing:
Curio platform (https://platform.dnanexus.com/communities/curio_portal/login), section Seeker Tild ID: A0076_068. Running with cuiro seeker runner 2.0.
Assembly: GRCm38
Supplementary files format and content: aorta-Pdk4KO.rds can be loaded to R-seruat, contains all the spatial information. The section contains both Pdk4 KO and WT aortae. Pdk4 KO located to the left bottom corner, while WT located at the right bottom corner.
Library strategy: Spatial Transcriptomics

growth_protocol: Mice, WT or Pdk4 smooth muscle cell specific Pdk4 KO, were treated with High fat diet for 4 month. Fresh ascending aorta embedded in OCT were frozen on dry ice right after dissection. Samples were processed within 4 days of sections.

extract_protocol:
After dissection and PBS perfusion, 2 mm fresh ascending aortic segments were embedded in optimal cutting temperature (OCT) compound, and frozen immediately on dry ice. Aortic sections in 10 µm thickness were obtained with Leica cryostat. Sections were mounted on cryoCube slide (Curio Bioscience)
following Nextera XT Library Prep Kit

value: both WT (right) & KO (left) located in the same section


title: RNA from criollo seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep2

value: primed seeds

value: Biol rep 2

value: mature seed (re-dried 48h after seed priming)

value: Criollo

value: MeJA 48h


title: WT_Rep2

value: TEaWT


title: cut_130_24h_3

value: WT

value: 24 hours after cut the caudal fin with 130mM glucose


title: RNA from criollo seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep1

value: Biol rep 1


title: dmso-72h-n-3

city: Utrecht

first: Amir

last: Giladi

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Bulk RNA-seq libraries were generated via the SORT-seq method (REF), and sequenced on a NextSeq500 Illumina machine. Resulting bulk RNA-seq data was mapped to the mouse genome (mm38) using STAR (version 2.7.8a). umi_tools (version 1.1.1) was used to collapse PCR-amplified reads into distinct transcripts. Samples with less than 500,000 transcripts were determined as low quality and discarded from further analysis, resulting in median depth of 960,086 transcripts per sample.
Assembly: mm38
Supplementary files format and content: Tab-delimited text file containing number of unique transcripts (UMI) per gene per sample.

source_name: duodenum-derived organoids

growth_protocol: All organoids were obtained from the duodenum of male or virgin female mice older than 8 weeks as described previously52. Organoids were embedded in BME and cultured with ENR media including Advanced DMEM/F-12 (Life Technologies) supplemented with; murine recombinant epidermal growth factor (50 ng/ml; Life Technologies), murine recombinant Noggin (100 ng/ml; PeproTech), human recombinant R-Spondin 1 (500 ng/ml; Peprotech), n-acetylcysteine (1 mM; Sigma-Aldrich), N2 supplement (1×; Life Technologies) and B27 supplement (1×; Life Technologies), GlutaMAX (2 mM; Life Technologies), Hepes (10 mM; Life Technologies), and penicillin-streptomycin (100 U/ml; 100 μg/ml; Life Technologies). For passaging, organoids were removed from BME and mechanically dissociated into single-crypt domains, and then transferred to fresh BME. Passage was performed every 1-2 weeks with a 1:5 split ratio. Conditions were kept stable in the incubator with 5% CO2 and 20% O2 at 37°C.

extract_protocol:
Organoids (20-50 organoids per sample) were harvested from the microfluidic chip. Total RNA was isolated using TRIzol Reagent (Invitrogen, #15596018).
Bulk RNA sequencing was performed according to the Sort-seq method (Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas, Cell Syst 3, 385-394 e383, doi:10.1016/j.cels.2016.09.002) 2016

treatment_protocol: Microfluidics experiments were performed as described previously38,53. In short, a mold for microfluidic chips was made using a 3D printer (Atum3D) (chip design available upon request). PDMS (SYLGARD #01673921/ #01673921, 1:8 ratio) was poured in the mold to create the microfluidic chip. The chip and a glass slide (Marienfeld, No 1.5H, high precision, 70x70 mm) were bonded using plasma treatment (Diener electronic, Femto). Chip and Tubing were UV cleaned and the microfluidic chip (in PBS with Pen/strep) was degassed together with the conditioned and DAPT media for 4 hours. The concentration of the DAPT media depended on the pulse timing (90min: 1.38µM, 130min: 2µM, 170min; 2.6µM, 2µM; for 170 min we tested two different concentrations to find one that did not change oscillation amplitude or absolute intensity (Fig. 4 and Extended Data Fig. 12). Organoids were passaged 3-4 days before performing a live-imaged microfluidic experiment for 20-24h. For the RNA bulk sequencing and immunofluorescence microfluidic experiments organoids were passaged 1 day before a 72h experiment, 2 days before 48h experiment and 3 days before a 24h experiment. The day of the experiment, two wells of a 24-well plate were harvested and washed with ice cold Advanced DMEM/F12 supplemented with GlutaMAX (2 mM; Life Technologies), Hepes (10 mM; Life Technologies), and penicillin-streptomycin (100 U/ml; 100 μg/ml; Life Technologies) to remove the BME. Organoids are resuspended in BME to a final concentration of 50% and carefully loaded into the microfluidic chip which was pre-filled with ENR culture media. After loading organoids on the chip, all tubing (4x inlet tubing of 3 meters, and 2x outlet tubing of 1 meter) was connected and during the experiment the organoids were cultured under a flow rate of 200 µl/h, using a microfluidic pump (Harvard apparatus #70-45060). After approximately 30 min culturing in culture medium, pumping program to induce drug pulses was started. For the bulk RNAseq and immunofluorescence microfluidic experiments, organoids were removed by aspirating the organoids out of the chip with a 200ul pipet via the organoid inlets and follow-up methods were performed as described.

value: duodenum-derived organoids

value: Non-enriched for cell type

tag: strain

value: DMSO control

value: 72 hours


title: WT_Rep1

value: spleen

value: CD4+ T cells

value: cocultured with APCs sorted from the spleens of 8-week-old F1 (BALB/c x C57BL/6) mice.

value: 3 day


title: RNA from criollo seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep3

value: primed seeds

value: Biol rep 3

value: water


title: dmso-72h-n-2


title: cut_130_24h_1

value: whole organism


title: iBAT from cold exposed C57BL/6N ADCY3∆AT, HFD, replicate 3

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Transcriptome assembly was done using StringTie and determined Adcy3-at transcript was added manually to Ensembl reference
Quantification of transcripts done using Salmon on Ensembl GRCm38 reference including Adcy3-at transcript
Normalisation and differential gene expression analysis was done using EdgeR
Assembly: GRCm38
Supplementary files format and content: Raw Salmon gene counts are provided in iBAT_WT_atKO_HFD_cold.cts.txt. The Gene summarization was done using summarizeToGene() from tximport package for R.

source_name: Interscapular Brown Adipose Tissue (iBAT)

extract_protocol:
Tissues were homogenised and lysed in TRIZol using FastPrep24 homogenizer. Total RNA was isolated using EconoSpin All-In-One Mini Spin Columns (EconoSpin 1920-250).
Paired end libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s protocol.
Paired-end Total RNA

treatment_protocol: Mice were fed chow diet (Ssniff V1554) up to the age of 8 weeks, where the respective cohorts were put on HFD (Ssniff D12492 (I) mod.) for 12 weeks and kept at 4degree celcius for 24 h.

value: HFD diet, cold


title: dmso-72h-n-1


title: iBAT from cold exposed C57BL/6N ADCY3∆AT, HFD, replicate 2

value: Interscapular Brown Adipose Tissue (iBAT)


title: cut_130_3h_3

value: WT

value: 3 hours after cut the caudal fin with 130mM glucose


title: RNA from criollo seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep1

value: Biol rep 1

value: mature seed (re-dried 48h after seed priming)

value: Criollo


title: cut_130_3h_2


title: iBAT from cold exposed C57BL/6N ADCY3∆AT, HFD, replicate 1


title: RNA from microtom seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep3

value: uTom

value: MeJA 48h


title: RNA from criollo seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep2

value: Biol rep 2


title: iBAT from cold exposed C57BL/6N WT, HFD, replicate 3

value: wt/wt


title: RNA from microtom seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep2


title: RNA from criollo seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep3


title: cut_130_3h_1


title: cut_130_24h_2

value: 24 hours after cut the caudal fin with 130mM glucose


title: dmso-24h-n-3

value: duodenum-derived organoids

value: Non-enriched for cell type

value: DMSO control

value: 24 hours


title: dmso-48h-n-1

value: 48 hours


title: RNA from microtom seeds treated with osmopriming and MeJA 2 mM (PEG 8000 -1MPa) for 48h rep1

value: primed seeds


title: C_cut_48h_3

value: whole organism

value: 48 hours after cut the caudal fin with regular culture medium


title: iBAT from cold exposed C57BL/6N WT, HFD, replicate 1

value: Interscapular Brown Adipose Tissue (iBAT)

value: HFD diet, cold


title: C_cut_48h_2

value: WT


title: iBAT from cold exposed C57BL/6N WT, HFD, replicate 2


title: RNA from microtom seeds treated with osmopriming (PEG 8000 -1MPa) for 48h rep3

value: Biol rep 3

value: mature seed (re-dried 48h after seed priming)

value: water


title: dmso-24h-n-1