title: Heart_PBS_rep1

city: Changsha

first: Weizhi

state: Hunan

address: Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, Hunan, 410011, China.

department: Department of Cardiovascular Surgery

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: GRCm39
Supplementary files format and content: Spreadsheet file includes FPKM value, TPM value, read count and average FPKM value for each Sample

source_name: heart

growth_protocol: 10-week-old healthy, specific pathogen-free, and wild-type C57BL/6 male mice were provided by Hunan SJA Laboratory Animal Co., Ltd. (Changsha, China) and raised at the Laboratory Animal Center of the Second Xiangya Hospital, Central South University (Changsha, China). All mice were placed in 12-hour light/dark cycle surroundings with standard ambient temperature, humidity, and oxygen concentrations and were provided with freely available food and water.

extract_protocol:
After 12 hours of treatment, heart tissues were collected from the mice. Total RNA was extracted from myocardial tissue samples using TRIzol reagent and purified with chloroform, isopropyl alcohol, and ethanol. The quality of RNA samples was evaluated by concentration, 28S/18S ratio, and RNA quality number (RQN) measured by a fragment analyzer with the Standard Sensitivity RNA Analysis Kit (15 nt) (DNF-471).
mRNAs were enriched from high-quality RNA samples (RQN＞7.0, 28S/18S＞1.0), fragmented and used as templates for synthesizing cDNAs. cDNAs were subjected to end-repair, add a single ‘A’ nucleotide to the 3’ ends, set up to ligate adaptors with the cDNAs, and finally be amplified to construct libraries. After quality control, cDNAs were circularized to generate DNA nanoballs via rolling cycle amplification, which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis.

treatment_protocol: 10-week-old healthy, specific pathogen-free, and wild-type C57BL/6 male mice were randomly assigned to the PBS group and the LPS group (n=5/group). In order to construct mouse models of sepsis-induced myocardial dysfunction, the LPS group were given a single intraperitoneal injection of 10 mg/kg LPS, while the PBS group were given an equal volume of PBS as controls.

value: heart

value: male

value: wild type

value: an equal volume of PBS


title: PTBP1-immunoprecipitated RNAseq Primar culture Sertoli cell_1

status: Public on Dec 31 2025

type: SRA

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description:
Library name: Sertoli_cell_PTBP1-IP_1
SC_RIP_1_1

library_source: transcriptomic

data_processing:
For RNAseq of FACSed Sertoli cells,Paired-end reads (2 × 36 bases) were obtained by sequencing on NextSeq 500 (Illumina) at Tsukuba i-Laboratory LLP (Tsukuba, Japan). Raw sequencing data files were processed in FASTQ format and imported into CLC Genomics Workbench (CLC GW, Version 10.1.1, Qiagen). Sequences were mapped to the mouse genome (mm10) and quantified using the 49,585 annotated genes provided in CLC GW. Total count values were used for pairwise comparison using the Empirical Analysis of DGE tool in CLC GW. For PTBP1-immunoprecipitated RNAseq,The fastq files were generated using bcl2fastq-2.20. Adapter sequences and low-quality bases were trimmed from the raw reads using cutadapt(59) ver v1.18. The trimmed reads that mapped to mouse rRNA and tRNA using Bowtie2 (version 2.3.5.1) were filtered out. The remaining reads were then aligned to the mouse reference genome (mm10) using STAR(60) ver 2.6.0c with the GENCODE (gencode.vM23) gtf file. Uniquely mapped reads were counted and summarized at the gene level (protein coding) using htseq-count(61) v0.11.2 with the GENCODE gtf file. The immunoprecipitated RNAs (genes) were identified as differentially expressed genes (DEGs) relative to the input as the control by calculating fold changes and false discovery rates (FDR) using DESeq2(62) v1.30.0.
Assembly: mm10
Supplementary files format and content: .txt formatted CPM values or .xlsx formatted FPKM values

molecule: total RNA

organism: Mus musculus

source_name: Testis

extract_protocol:
NucleoSpin RNA plus (TaKaRa).
For RNAseq of FACSed Sertoli cells, Poly-A RNA was isolated from 100 ng of total purified RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490), and converted into a sequencing library using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7420). For PTBP1-immunoprecipitated RNAseq, RNA-seq libraries from total RNA were generated using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB).

tag: tissue

value: Testis

tag: cell type

tag: genotype

value: WT


title: 2mATF3KO_skin [replicate_3]

city: Tokyo

first: Jiancheng

last: Liang

state: Bunkyo

department: Graduate school of Agricultural and Life Sciences

data_processing:
Raw reads with low-quality bases and adapters were removed using BBTools (parameters: minlen=50 qtrim=rl trimq=20 ref=adapters.fa ktrim=r k=25 mink=11 hdist=1 tbo tpe). STAR for genome mapping and alignment to the Danio rerio GRCz11 reference genome (Ensembl.Danio.rerio.GRCz11.112), (parameters: STAR –genomeDir --runThreadN 16  --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c). RSEM for quantifying the expression (parameters: rsem-calculate-expression --alignments --paired-end -p 30 --append-names --estimate-rspd). DESeq2 for differential expression analysis.
Assembly: Ensembl.Danio.rerio.GRCz11.112
Supplementary files format and content: tab-delimited text file includes expected counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Danio rerio

source_name: Skin

extract_protocol:
Zebrafish were euthanized using Tricaine, dissected, and gathered the corresponding organs kept in NucleoProtect RNA (TAKARA) solution. Total RNA was extract using NucleoSpin RNA Clean-up Kit (TAKARA) following the manufacturer's protocols and verified the RNA quality and concentration using TapeStation RNA ScreenTape (Agilent).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following the manufacture’s protocols.

value: Skin

tag: time

value: 2 month

value: ATF3 knockout


title: L3

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

country: China

institute: Weifang University

description: Library name: CY-M3

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The paired-end raw reads with 150-bp were generated through Illumina sequencing. The clean reads were obtained by filtering the low-quality reads through processing the raw reads with fastq format using FASTQ preprocessor [19] and then mapped to the reference genome database on NCBI GenBank with accessions JAVRBK000000000 using HISAT2. The FPKM measure was used to calculate expression of each gene of which read counts were determined by HTSeq-count. The biological duplication of samples was evaluated by principal component analysis (PCA) with R (v 3.2.0).
The FPKM measure was used to calculate expression of each gene of which read counts were determined by HTSeq-count. The biological duplication of samples was evaluated by principal component analysis (PCA) with R (v 3.2.0).
Assembly: NCBI GenBank, accession number: JAVRBK000000000.
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Pyrocoelia pectoralis

source_name: luminous organ

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: luminous organ

tag: Sex


title: RNAseq Primar culture Sertoli cell_3

description:
Library name: Sertoli_cell_3
SC_Input_2_1


title: L2

description: Library name: CY-M2


title: 2mATF3KO_muscle [replicate_3]

source_name: Muscle

value: Muscle


title: 2mATF3KO_intestine [replicate_3]

source_name: Intestine

value: Intestine


title: RNAseq Primar culture Sertoli cell_2

description:
Library name: Sertoli_cell_2
SC_Input_1_2


title: ATF2 Cut & Tag c1

city: Beijing

first: Zhimin

last: He

address: No. 1 Qinghuayuan Street

department: School of Medicine

institute: Tsinghua University

description: Cut & Tag

library_source: genomic

data_processing:
Base calling using bcl2fastq2
clean reads were generated using Trimmomatic software version:0.36, by setting ILLUMIACLIP:Adapter.fa:2:30:10, SLIDINGWINDOW:4:15, LEADING: 3, TRAILING:3, MINLEN:36.
reads aligne to the mm10 genome using bowtie2 version 2.1.0
peak calling using MACS2
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bedGraphToBigWig sorftware.
Library strategy: Cut&Tag

molecule: genomic DNA

source_name: ATF2 c1

extract_protocol:
Cut& Tag assay using Hyperactive In-Situ ChIP Library Prep Kit for Illumina, Vazyme, TD901, following the manuscfacturer's insutrction
Library were constructed with index from TruePrep Index Kit V2/v3 fro Illumina (Vazyme #TD202)

treatment_protocol: Cut & Tag were proformed in WT AMs or HDAC3-KO AMs (as negative control)

value: control

value: alveolar macrophages

tag: strain

tag: chip antibody


title: ATF2 Cut & Tag c2

description: Cut & Tag

source_name: ATF2 c2


title: L1

description: Library name: CY-M1


title: RNAseq Primar culture Sertoli cell_1

description:
Library name: Sertoli_cell_1
SC_Input_1_1


title: HDAC3 Cut & Tag c2

description: Cut & Tag

source_name: HDAC3 c2


title: 2mATF3KO_heart [replicate_3]

source_name: Heart

value: Heart


title: Lin-Sca1+c-Kit+ cell, WT, 5weeks, rep2

city: Hangzhou

first: Liyun

last: Chen

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina Casava 1.7 software used for basecalling
Assembly: mm9
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
RNA was havested using Trizol reagent,1.3ug of total RNA was used for the constructon of  sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

value: bone marrow

tag: cell line

value: hematopoietic cell


title: HDAC3 Cut & Tag c1

description: Cut & Tag

source_name: HDAC3 c1


title: 2mATF3KO_eyes [replicate_4]

source_name: Eyes

value: Eyes


title: 2mATF3KO_gills [replicate_3]

source_name: Gills

value: Gills


title: RNAseq FACS sorted Ptbp1 cKO Sertoli cell_3

description: Library name: Ptbp1_cKO_Sertoli_cell_3

molecule: polyA RNA

value: AmhCre; Ptbp1 flox/flox; mTmG;wt


title: NL2

description: Library name: CY-N2

source_name: non-luminous organ

value: non-luminous organ

value: male


title: HDAC3 Cut & Tag KO1

description: Cut & Tag

source_name: HDAC3 HDAC3KO1

value: HDAC3 KO

value: ab7030 (abcam)


title: RNAseq FACS sorted Ptbp1 cKO Sertoli cell_2

description: Library name: Ptbp1_cKO_Sertoli_cell_2

value: Testis


title: RNAseq FACS sorted Ptbp1 cKO Sertoli cell_1

description: Library name: Ptbp1_cKO_Sertoli_cell_1


title: HDAC3 Cut & Tag Ctrl2

description: Cut & Tag

source_name: HDAC3 Ctrl2


title: 2mATF3KO_eyes [replicate_3]

value: 2 month

value: ATF3 knockout


title: 2mATF3KO_brain [replicate_3]

source_name: Brain

value: Brain


title: HDAC3 Cut & Tag ko

description: Cut & Tag

source_name: HDAC3 HDAC3ko


title: HG001, Total RNA-seq associated to RNase 1 Ribo-seq, Ret, rep2 sample

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

country: France

institute: CNRS

description: Library name: Sample TR 8

data_processing:
Sequencing data were analyzed with the workflow described in Kohl et al. 2024 (Methods Mol Biol.) with slight modifications.
Briefly, raw reads were filtered and trimmed using Skewer v.0.2.2, with the following parameters: -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -Q 10 -l 35 -L 51.
Bowtie v.1.2.2 was then applied to discard any contaminating reads mapping to tRNA or rRNA sequences, using the following parameters: -v 2 -y -m 1 -a — best —strata.
The remaining reads were uniquely mapped to the S. aureus HG001 reference genome, allowing up to two mismatches with Bowtie v.1.2.2 using the same parameters as above.
Mapped reads between 35 and 51 nt were used in subsequent analyses.
The raw read densities of all RNA-seq samples were assigned to the 3′ end of reads, and normalized densities were calculated for each strand and genomic position in reads per million mapped reads (RPM).
Assembly: S. aureus HG001 reference genome
Supplementary files format and content: Normalized read densities are provided in a wiggle track format as two separate files, *_plus.wig and *_minus.wig.

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: S. aureus HG001 was plated and grown at 37°C o/n on BHI agar plates. Single colonies were used to inoculate 3 mL of BHI and pre-cultures were grown, shaking at 180 rpm, o/n at 37°C. The following day, pre-cultures were diluted to an optical density A600 (OD) of 0.05 in 50 mL of BHI in 250 mL flasks. Bacterial cultures were grown, shaking at 180 rpm at 37°C, to an OD of 3.5.

extract_protocol:
Cultures were subjected to rapid cooling by swirling in an ice-bath for 3 min, before 40 mL of each sample (split into two 50 mL falcon tubes) were harvested by centrifugation. Another 10 mL of each culture were flash frozen in liquid nitrogen and reserved for total RNA sequencing. For Ribo-seq and Ribo-Ret, cell pellets were resuspended in 550 μL of pre-chilled lysis buffer A (20 mM Tris-HCl pH 8, 50 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 0.4 % Triton X-100, 0.1 % NP-40, 100 U/mL DNase 1, 1 mM GMPPNP). Mechanical lysis was performed by two rounds of ‘fastprep’ bead-beating at 6 m/s for 40 seconds in 2 mL fastprep tubes containing Lysing Matrix B. Subsequently, samples were centrifuged at 16,000 g for 5 min at 4°C and supernatants were carefully retrieved. Measurement of absorbance at 260 nm in a Nanodrop spectrophotometer served to adjust nuclease concentration for subsequent digestion by either MNase or RNase 1. For MNase digestion, 750 U of MNase and 50 U of SUPERase-In (does not inhibit MNase) were added per 40 absorbance units (AU). After 1 h shaking at 1400 rpm and 25°C, the reactions were quenched by addition of 5 mM EGTA (f.c.). For the alternative digestion by RNase 1, 250 U of RNase 1 were added per 40 AU of sample concentration. The digestion was performed for 20 min shaking at 800 rpm and 37°C, before it was stopped by addition of 100 U of SUPERase-In. All samples were kept strictly on ice prior to loading onto a 5-50 % sucrose gradient for isolation of 70S monosome peaks. Ribosome protected fragments (RPFs) were extracted using acidic hot phenol and size selected on a 15% polyacrylamide- 8 M Urea gel (PAGE). RPFs were gel eluted via passive elution in RNA elution buffer (0.5 M NH4Ac pH 6.5, 1 mM EDTA, 0.1 % SDS) o/n at 4°C shaking at 700 rpm prior to acidic PCI (phenol/chloroform/isoamyl alcohol, 25/24/1) extraction and ethanol RNA precipitation.
All samples were subjected to ribosomal RNA depletion employing a commercially available rRNA depletion kit (siTOOLs) according to the manufacturer’s protocol. Associated total RNA sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer's instructions.

treatment_protocol: For Ribo-Ret, cultures were briefly (5 min before harvesting) treated with 25 μL of 25 mg/mL Retapamulin (12.5 μg/mL f.c.). Ret-treated and non-treated samples were processed in parallel for cell harvest and lysis.

value: bacterial cells

value: wild-type

tag: treatment

value: Retapamulin treated


title: HDAC3 Cut & Tag Ctrl1

description: Cut & Tag

source_name: HDAC3 Ctrl1

value: control

value: alveolar macrophages


title: RNAseq FACS sorted Control Sertoli cell_3

description: Library name: Control_Sertoli_cell_3

source_name: Testis

value: AmhCre; Ptbp1 flox/wt; mTmG;wt


title: 2mATF3KO_skin [replicate_2]

source_name: Skin

value: Skin


title: RNAseq FACS sorted Control Sertoli cell_2

description: Library name: Control_Sertoli_cell_2


title: HG001, Total RNA-seq associated to RNase 1 Ribo-seq, Ret, rep1 sample

description: Library name: Sample TR 7


title: 2mATF3KO_muscle [replicate_2]

source_name: Muscle

value: Muscle


title: 2mATF3KO_intestine [replicate_2]

source_name: Intestine

value: Intestine


title: NL3

description: Library name: CY-N3

value: non-luminous organ


title: female_E85, scRNAseq

last: Wang

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1
Assembly: ARS1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Capra hircus

source_name: ovary

extract_protocol:
For the collection of the testicular germ cells and somatic cells, testes were dissected under a dissection microscope and transferred to a 15 mL tube digested with 1 mg/mL collagenase IV, 1 mg/mL hyaluronidase, 0.25% trypsin, and 1 mg/mL DNase I for 30 min at 37C. To prepare the single-cell suspension for 10x Genomics single-cell RNA-seq, the cell suspension was repeatedly pipetted after adding serum, filtered through a 40 mm membrane, and resuspended in 0.1% serum/PBS.
The cell suspension (1000 living cells per microliter determined by CountStar) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53C for 45 min, followed by 85C for 5 min, and hold at 4C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200. According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 30 Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: ovary

value: F

tag: developmental stage


title: female_E125, scRNAseq

description: 10x Genomics


title: RNAseq FACS sorted Control Sertoli cell_1

description: Library name: Control_Sertoli_cell_1


title: HG001, Total RNA-seq associated to RNase 1 Ribo-seq, no drug, rep1 sample

description: Library name: Sample TR 5

value: untreated


title: DL_rep_4

city: Kunming

first: Jiahong

last: Duan

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences

institute: Yunnan University

description: Library name: DL_rep_4

data_processing:
RNA was converted into Illumina-compatible libraries via poly(A) selection, fragmentation, cDNA synthesis (random hexamers), end repair/adapter ligation, and size selection (300–400 bp, AMPure XP beads), followed by PCR amplification.
Clean reads were aligned to the C. elegans genome (WBcel235) using HISAT2, retaining only uniquely mapped, properly paired reads (MAPQ≥10). Gene-level counts were generated with HTSeq, quantifying exonic reads while excluding multi-mapping and low-quality alignments.
Assembly: WBcel235
Supplementary files format and content: FPKMs_all_samples.txt
Supplementary files format and content: column 1 = WormBase Gene_ID, columns 2-9 = FPKM values for 8 experimental samples

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized L1 larvae cultured on NGM/OP50 at 20°C for 40 h to young adult stage.

extract_protocol:
Total RNA was extracted from synchronized C. elegans using TRIzol reagent (Invitrogen，USA) following the manufacturer's protocol.
PolyA-selected mRNA was used for library preparation with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530). mRNA was fragmented, reverse-transcribed, and converted to double-stranded cDNA. After end repair, A-tailing, and adapter ligation (NEB Next Multiplex Oligos), libraries were size-selected (250–300 bp) using AMPure XP beads and PCR-amplified

treatment_protocol: Young adult C. elegans were exposed to 12h-light (8,000 lux, LED)/12h-dark cycles in 20°C incubators (DL group) or constant darkness (NL control).

value: whole organism

value: wild-type (N2)

value: 12h-light/12h-dark (DL)

tag: batch


title: 2mATF3KO_heart [replicate_2]

source_name: Heart

value: Heart

value: 2 month

value: ATF3 knockout


title: HG001, Total RNA-seq associated to MNase Ribo-seq, Ret, rep2 sample

description: Library name: Sample TR 4

value: bacterial cells

value: wild-type

value: Retapamulin treated


title: DL_rep_3

description: Library name: DL_rep_3


title: BMDM_M2+JQ1_BRD4-ChIP

city: Houston

first: Ge

last: Deng

state: Texas

address: 6670 Bertner Avenue, R7-217

country: USA

institute: Houston Methodist Hospital and Houston Methodist Research Institute

description: Library name: BMDM_M2+JQ1_BRD4-ChIP

data_processing:
Reads were mapped to the mouse genome (mm10) using the BWA algorithm with default settings and stored in BAM format. Low mapping quality reads and duplicated reads were discarded from downstream analysis. Putative binding sites were determined using MACS algorithm (v1.4.2) with a cutoff of P value of 10 -7. Differential peaks among different conditions were determined by the unique peaks of a specific condition and average peak values fold change (> or < mean unique peak values). Genomic annotation of peaks was calculated and plotted with ChIPseeker program in R. For visualization, coverage profiles were firstly calculated using deepTools bamCoverage (--binSize 10 –normalizeUsing RPKM), then output files (normalized BigWig files) were visualized in Integrative Genomics Viewer (IGV). Chip-seq read density profiles were calculated using deepTools computeMatrix (--referencePoint center -b 5000 -a 5000 –binSize 10) and plotHeatmap functions.
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: Mouse primary macrophages

growth_protocol: Bone marrow cells were extracted from wild type C57/BL6 mice and cultured in DMEM high glucose medium containing 10% FBS, 1% pen-strep and 20ng/ml M-CSF (Peprotech, 315-02). Medium was replaced on day3 and cells were matured into mature macrophages on day6.

extract_protocol:
ChIP was performed using a ChIP-IT PBMC Kit (Active Motif, 53042).  Briefly, BMDMs were harvested and fixed with formaldehyde, quenched and subjected to sonication to fragment the genomic chromatin to designated lengths. Immunoprecipitation of chromatin was performed using BRD4 (Bethyl Laboratories, A301-985A50) or H3K27ac (Active Motif, 39133). The DNA/protein complexes were washed, eluted and reverse crosslinked with proteinase K treatment. The purified DNA was harvested for further sequencing.
The ChIP and input DNA were used for Illumina sequencing library construction following the standard consecutive enzymatic steps for end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: Matured BMDM were stimulated with 20ng/ml IL-4 (Peprotech, 214-14) to polarize into M2 with or without 200nM JQ1 (Sigma-Aldrich, SML-1524) treatment for 24 hours. Otherwise, BMDM was maintained in DMEM high glucose medium without any other stimulations as M0.

value: Mouse primary macrophages

value: Bone marrow derived macrophages

value: wild type

value: 20ng/ml IL-4 and 200nM JQ1 stimulated for 24 hours


title: NL1

description: Library name: CY-N1

value: non-luminous organ

value: male


title: BMDM_M2_BRD4-ChIP

description: Library name: BMDM_M2_BRD4-ChIP

value: 20ng/ml IL-4 stimulated for 24 hours


title: DL_rep_2

description: Library name: DL_rep_2


title: BMDM_M0_BRD4-ChIP

description: Library name: BMDM_M0_BRD4-ChIP

value: unstimulated


title: HG001, Total RNA-seq associated to MNase Ribo-seq, Ret, rep1 sample

description: Library name: Sample TR 3


title: 2mATF3KO_eyes [replicate_2]

source_name: Eyes

value: Eyes


title: HG001, Total RNA-seq associated to MNase Ribo-seq, no drug, rep2 sample

description: Library name: Sample TR 2

value: untreated


title: BMDM_M2_H3K27Ac-ChIP

description: Library name: BMDM_M2_H3K27Ac-ChIP


title: DL_rep_1

description: Library name: DL_rep_1

value: whole organism

value: wild-type (N2)

value: 12h-light/12h-dark (DL)


title: 2mATF3KO_brain [replicate_2]

value: Brain

value: 2 month

value: ATF3 knockout


title: 2mATF3KO_skin [replicate_1]

value: Skin


title: NL_rep_4

description: Library name: NL_rep_4

value: constant dark (NL)


title: BMDM_M0_H3K27Ac-ChIP

description: Library name: BMDM_M0_H3K27Ac-ChIP

value: Mouse primary macrophages

value: Bone marrow derived macrophages


title: HG001, Total RNA-seq associated to MNase Ribo-seq, no drug, rep1 sample

description: Library name: Sample TR 1

value: bacterial cells

value: wild-type


title: HG001, Total RNA-seq associated to RNase 1 Ribo-seq, no drug, rep2 sample

description: Library name: Sample TR 6


title: HG001, RNase 1 Ribo-seq, Ret, rep2

description: Library name: Sample RP 8

library_source: other

data_processing:
Sequencing data were analyzed with the workflow described in Kohl et al. 2024 (Methods Mol Biol.) with slight modifications.
Briefly, raw reads were filtered and trimmed using Skewer v.0.2.2, with the following parameters: -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -Q 10 -l 15 -L 51.
Bowtie v.1.2.2 was then applied to discard any contaminating reads mapping to tRNA or rRNA sequences, using the following parameters: -v 2 -y -m 1 -a — best —strata.
The remaining reads were uniquely mapped to the S. aureus HG001 reference genome, allowing up to two mismatches with Bowtie v.1.2.2 using the same parameters as above.
Mapped reads between 15 and 45 nt were used in subsequent analyses.
The raw ribosome densities of all ribo-seq samples were assigned to the 3′ end of reads, and normalized densities were calculated for each strand and genomic position in reads per million mapped reads (RPM).
Assembly: S. aureus HG001 reference genome
Supplementary files format and content: Normalized ribosome densities are provided in a wiggle track format as two separate files, *_plus.wig and *_minus.wig.
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
Cultures were subjected to rapid cooling by swirling in an ice-bath for 3 min, before 40 mL of each sample (split into two 50 mL falcon tubes) were harvested by centrifugation. Another 10 mL of each culture were flash frozen in liquid nitrogen and reserved for total RNA sequencing. For Ribo-seq and Ribo-Ret, cell pellets were resuspended in 550 μL of pre-chilled lysis buffer A (20 mM Tris-HCl pH 8, 50 mM MgCl2, 100 mM NH4Cl, 5 mM CaCl2, 0.4 % Triton X-100, 0.1 % NP-40, 100 U/mL DNase 1, 1 mM GMPPNP). Mechanical lysis was performed by two rounds of ‘fastprep’ bead-beating at 6 m/s for 40 seconds in 2 mL fastprep tubes containing Lysing Matrix B. Subsequently, samples were centrifuged at 16,000 g for 5 min at 4°C and supernatants were carefully retrieved. Measurement of absorbance at 260 nm in a Nanodrop spectrophotometer served to adjust nuclease concentration for subsequent digestion by either MNase or RNase 1. For MNase digestion, 750 U of MNase and 50 U of SUPERase-In (does not inhibit MNase) were added per 40 absorbance units (AU). After 1 h shaking at 1400 rpm and 25°C, the reactions were quenched by addition of 5 mM EGTA (f.c.). For the alternative digestion by RNase 1, 250 U of RNase 1 were added per 40 AU of sample concentration. The digestion was performed for 20 min shaking at 800 rpm and 37°C, before it was stopped by addition of 100 U of SUPERase-In. All samples were kept strictly on ice prior to loading onto a 5-50 % sucrose gradient for isolation of 70S monosome peaks. Ribosome protected fragments (RPFs) were extracted using acidic hot phenol and size selected on a 15% polyacrylamide- 8 M Urea gel (PAGE). RPFs were gel eluted via passive elution in RNA elution buffer (0.5 M NH4Ac pH 6.5, 1 mM EDTA, 0.1 % SDS) o/n at 4°C shaking at 700 rpm prior to acidic PCI (phenol/chloroform/isoamyl alcohol, 25/24/1) extraction and ethanol RNA precipitation.
All samples were subjected to ribosomal RNA depletion employing a commercially available rRNA depletion kit (siTOOLs) according to the manufacturer’s protocol. Prior to library preparation, RPFs were de-phosphorylated by the use of Antarctic phosphatase and subsequently phosphorylated with T4 polynucleotide kinase. RPF libraries were then prepared using the NEBNext Small RNA Library Prep Set from Illumina, following the kit’s instructions.

value: Retapamulin treated


title: BMDM_Input

description: Library name: BMDM_Input

value: wild type


title: Klf9-ChIP-seq in TAC mouse hearts of 12-14wks of age

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

description: Library name: Klf9-ChIP-seq-TAC

data_processing:
ChIP-Seq: Sequence analysis – 75-nt sequence generated by sequencing reads were mapped to the genome using BWA algorithm, and the information stored in BAM format. Only reads which align with no more than two mismatches and map uniquely are used in analysis. Peak Finding – Genomic regions with enrichments in tag numbers are termed ‘intervals', and defined by the chromosome number, start and end coordinate. 24237848 normalized tags were used for peak calling using MACS 2.1.0 algorithm with default cutoff p value 1e-7. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist. Merged region analysis – To compare peak metrics between two samples, overlapping Intervals are grouped into ‘Merged Regions', which are defined by start coordinate of the most upstream interval and end coordinate of the most downstream interval (=union of overlapping intervals; “merged peaks”). In locations where only one sample has an interval, this interval defines Merged Region. The MaxTags filter out the regions with low signal values, which are expected to be more variable and therefore lead to unreliable, often exaggerated ratios. To calculate the maximum number of tags (reads) multiply the average value of the tag per sample with the length of the regions and divide by constant 224. The 224 value represents the average length of the sequenced fragment in base pairs.
RNAseq:- Sequenced reads were processed through fastp software to remove possible adapter sequences and nucleotides with poor quality to obtain clean reads. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Alignment information for each read was stored in the BAM format. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Distribution of read counts in libraries was examined before and after normalization. The original read counts were normalized to adjust for various factors such as variations of sequencing yield between samples. These normalized read counts were used to accurately determine differentially expressed genes using DESeq2 R package (1.20.0). Log2 fold change between the groups was calculated and the Wald test was used to determine statistical significance (p-value). Adjusted p values were calculated using Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: Klf9-ChIP-Seq: Excel sheet with merged regions, MaxTags
Supplementary files format and content: RNAseq: Excel sheet with all comparisons

source_name: heart

extract_protocol:
Mice were saced and hearts were snapped forzen in liquid nitorgen and sent to Active Motif, Inc for processing and Klf9-ChIP-Seq. For RNAseq, hearts were extracted from Wt-Cre (control) and Klf9KI mice and send for RNA extraction and RNAseq to Novogene, Inc
library construction for ChIP-seq was performed by Active motif, InC. RNAseq libraries were prepared by Novogene. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non-strand specific library or dUTP for strand specific library. These libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: ChIP-Seq: Mice were subjected to sham ot Transconstrictive operations (TAC) for 2wks

value: heart

value: TAC


title: 2mATF3KO_intestine [replicate_1]

value: Intestine


title: NL_rep_2

description: Library name: NL_rep_2

value: whole organism


title: HG001, RNase 1 Ribo-seq, Ret, rep1

description: Library name: Sample RP 7


title: HG001, RNase 1 Ribo-seq, no drug, rep2

description: Library name: Sample RP 6

value: untreated


title: 2mATF3KO_gills [replicate_2]

source_name: Gills

value: Gills


title: NL_rep_1

description: Library name: NL_rep_1

value: wild-type (N2)


title: HG001, RNase 1 Ribo-seq, no drug, rep1

description: Library name: Sample RP 5


title: Set_2_3

city: Zunyi

first: yan

last: Zhang

state: Guizhou

address: Honghuagang

department: College of Basic Medicine

institute: Zunyi Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole worm

extract_protocol:
Total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

value: whole worm


title: 2mATF3KO_heart [replicate_1]

value: Heart

value: 2 month

value: ATF3 knockout


title: Klf9-ChIP-seq in adult (Sham) mouse hearts of 12-14wks of age

description: Library name: Klf9-ChIP-seq-Sham

value: Sham


title: Input samples for Klf9 ChIP-Seq

description: Library name: Input, ChIP-seq

value: Pooled sampoles from Sham and TAC


title: 2mATF3KO_gills [replicate_1]


title: 2mATF3KO_eyes [replicate_1]

value: Eyes


title: ATAC_B6_HFD_7

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
For ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.6.1) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools v 1.9. Duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with HMMRATAC (v1.2.10) using ‘--means 75,200,400,600 --upper 20 --lower 10’.
Assembly: mm10
Supplementary files format and content: Sample-wise peaks: Summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary files format and content: Raw counts: Consensus peak set was formed from the peak centers using modified kernel density estimation -based approach (Tuoresmäki et al. PLoS One 2014;9(4):e96105). Reads were shortened to 1bp tags at 5’-ends and counted using csaw (v1.28.0).
Supplementary files format and content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.
Supplementary files format and content: Normalized counts: Counts normalized using csaw LOESS CPM and batch correction applied with limma::removeBatchEffect

source_name: eWAT

extract_protocol:
Nuclei were isolated using a Dounce homogenizer and 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 1 mM β-mercaptoethanol). After homogenization, the samples were filtered through a 100 µm nylon mesh filter, and nuclei were recovered by OptiPrep/iodixanol (Sigma-Aldrich) density gradient centrifugation.
Libraries were generated following Omni-ATAC protocol (Corces MR. et al. Nat Methods. 2017;14(10):959-962) with minor adjustments. Nuclei were resuspended in transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). After the transposition reaction, DNA was purified with DNA Clean & Concentrator-5 Kit (Zymo Research). Ten microliters of purified transposed DNA were amplified for 9-11 cycles (predetermined) using 25µl of 2 × Ultra II Q5 Master Mix (New England BioLabs) and 1 µl of both amplification primers (Buenrostro JD et al. Nat Methods. 2013;10(12):1213-1218; 1.25 μM final concentration). For cleanup and to remove primer dimers and large (>1,000 bp) fragments from the libraries, SPRIselect beads (Beckman Coulter) were used.

value: eWAT

value: HFD


title: Set_2_1


title: HG001, MNase Ribo-seq, Ret, rep2

description: Library name: Sample RP 4

value: bacterial cells

value: wild-type

value: Retapamulin treated


title: ATAC_B6_HFD_6


title: HG001, MNase Ribo-seq, Ret, rep1

description: Library name: Sample RP 3


title: 2mATF3KO_brain [replicate_1]

source_name: Brain

value: Brain


title: Set_2_2


title: HG001, MNase Ribo-seq, no drug, rep2

description: Library name: Sample RP 2


title: WT_3


title: ATAC_B6_HFD_5


title: unvariegated centre leaves, replicate 3 [UC3]

city: Beaucouzé

first: Laurence

middle: Hibrand

last: Saint oyant

state: Please choose a country or region

address: 42 rue G. Morel, INRA-IRHS-GDO

department: BAP

institute: INRAe

data_processing:
quality control : base quality and Phred score (Illumina CASAVA v1.8 software) : error rate (0.04%), clean data, Q20 and Q30 % (>97 and 93% respectively), GC content >50%
transcript length distribution : cleans reads are de novo assembled by Trinity to get assembly transcriptome. Then Corset will perform Hierarchical Clustering to remove redundence. Afterwards the longest trasncripts of each cluster will be selected as unigenes.
gene functionnal annotation : to achieve gene functionnal annotation, seven databases are applied by Novogene : Nr (NCBI non-redundant protein seuqence), Nt (NCBI nucleotide sequence), Pfam (Protein family), KOG/COG (Cluster of Orthologous Groups of protein), Swiss-prot, KEGG (Kyoto Encyclopedia of Genes nad Genome), GO( Gene ontology).
quantification results : De Novo transcriptome is used as a reference. RSEM (Li et al, 2011) will map reads back to transcriptome and quantify the expression level. To calculate the gene expression level, RSEM analysed the mapping results of Bowtie2, and then got the read count for each gene of each sample. Furthermore, converted them into FPKM value. In RNA-seq, FPKM, short for the expected number of Fragment Per kilobase of transscript sequence per Millions base pairs sequenced, is the most common method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments.
differential expression analysis was perfoirmed using DEGseq2 (Love MI et al., 2014)
transcriptome reconstruction : in the absence of a reference genome, cleans reads need to be assembled to get a reference sequence for the following analysis. Trinity (Grabherr et al, 2011) is the software chosen to complete the trasncriptome reconstruction process.
Assembly: Trinity.fasta, Unigene.fasta
Supplementary files format and content: read.counts

organism: Yucca flaccida

source_name: center of in vitro leaves

growth_protocol: Variegated and unvariegated plants were multiplied and maintained in in vitro conditions (see Rouinsard et al., 2021).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Plus kit according to the manufacturer’s instructions (Macherey-Nagel, Duren, Germany), with minus modifications (2% PVP40 in lysis buffer) (en attente quantité ARNm pour libraiire - quesiton posée à novogene)
After QC procedures, mRNA is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamer and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H, and Escherichia coli polymerase I to generate strand by nick-translation. The final cDNA libnrary is ready after a round of purification, terminal-repair, A-tailing, ligation of sequenciing adpaters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorescent (Life technologies), then diluted to 1ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accurancy by quantitative PCR(Q-PCR).

treatment_protocol: no treatment

value: center of in vitro leaves

value: Golden Sword

tag: phenotype

value: unvariegated leaf

tag: development stage

value: second youngest leaf of a plant

tag: date of_sampling


title: NL_rep_3

description: Library name: NL_rep_3

value: whole organism

value: wild-type (N2)

value: constant dark (NL)


title: HG001, MNase Ribo-seq, no drug, rep1

description: Library name: Sample RP 1

source_name: bacterial cells

value: untreated


title: 2mATF3KO_muscle [replicate_1]

value: Muscle

value: 2 month

value: ATF3 knockout


title: WT_2

value: whole worm


title: unvariegated centre leaves, replicate 2 [UC2]


title: CP9 strain, planktonic, 24 hr, rep 3

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

description: Library name: CP9_3_planktonic_24hr

data_processing:
The paired-end reads were assessed for quality using FastQC (v0.11.9).
The reference genome was indexed using the subread-buildindex function in subread (v2.0.6). We then mapped the paired-end reads to the reference genome using the subread-align function in subread (v2.0.6), including multi-mapped reads, mapping to the best 10 genomic loci (parameters: –multiMapping, -B 10)
Transcript abundance for each gene was computed using the featureCounts function in subread (v2.0.6), counting only read-pairs where both ends map to the same chromosome (parameters: -B, -C, –countReadPairs). The transcript abundance table was generated by consolidating all serial isolates, biological replicates, time point (90 minutes, 8 hours and 24 hours) and growth condition (biofilm and planktonic growth condition) using a custom Python script (v3.8.18) and were used for subsequent differential expression analyses.
Differential expression analysis was performed using DESeq2 (v1.44.0).
Assembly: ASM18276v2
Supplementary files format and content: tab-delimited txt file contains transcript abundance counts for all samples.

organism: Candida parapsilosis

source_name: planktonic

growth_protocol: Biofilms were harvested by gently pipetting up and down along the bottoms of the 12-well plates and combining the biofilm slurry of the same strain from each well of one 12-well plate into a 50 mL conical tube. Planktonic cultures of a given biological replicate were combined in a 50 mL conical tube.

extract_protocol:
The conical tubes were centrifuged at 4,000 x g for 5 minutes and the supernatant was aspirated. Pellets were snap-frozen and stored at -80°C until RNA extraction. Total RNA was extracted using the Ribopure RNA Purification Kit for Yeast (AM1926). mRNA was separated from total RNA using the NEBNext Poly(A) mRNA Isolation Module (E7490L).
500 ng of purified mRNA were made into cDNA libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7775L).

value: planktonic

value: 24 hr


title: ATAC_B6_HFD_3

value: eWAT

value: HFD


title: unvariegated centre leaves, replicate 1 [UC1]


title: WT_1


title: Wdr_5_3


title: ATAC_B6_HFD_4


title: CP9 strain, planktonic, 8 hr, rep 3

description: Library name: CP9_3_planktonic_8hr

value: 8 hr


title: unvariegated edge leaves, replicate 3 [UE3]

source_name: edged of in vitro leaves

value: edged of in vitro leaves


title: ATAC_B6_HFD_1


title: Wdr_5_2


title: ATAC_B6_HFD_2


title: Wdr_5_1


title: unvariegated edge leaves, replicate 2 [UE2]

value: Golden Sword


title: CP9 strain, planktonic, 24 hr, rep 2

description: Library name: CP9_2_planktonic_24hr


title: CP9 strain, planktonic, 90 min, rep 3

description: Library name: CP9_3_planktonic_90min

value: 90 min


title: ATAC_SV_HFD_6


title: PS_CON_P0_3

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: Excel file includes fpkm and raw counts for each Sample

source_name: whole animal

treatment_protocol: This study exposed Caenorhabditis elegans to a culture medium containing polystyrene plastic particles at a concentration of 1000 μ g/L to detect its healthy

value: whole animal


title: unvariegated edge leaves, replicate 1 [UE1]

value: unvariegated leaf

value: second youngest leaf of a plant


title: CP9 strain, planktonic, 90 min, rep 2

description: Library name: CP9_2_planktonic_90min


title: CP9 strain, planktonic, 8 hr, rep 2

description: Library name: CP9_2_planktonic_8hr


title: variegated centre leaves, replicate 3 [VC3]

value: center of in vitro leaves

value: variegated leaf


title: ATAC_SV_HFD_5


title: PS_CON_P0_1


title: PS_CON_P0_2


title: variegated centre leaves, replicate 2 [VC2]


title: CP9 strain, planktonic, 24 hr, rep 1

description: Library name: CP9_1_planktonic_24hr


title: ATAC_SV_HFD_3


title: variegated centre leaves, replicate 1 [VC1]


title: CP9 strain, planktonic, 8 hr, rep 1

description: Library name: CP9_1_planktonic_8hr


title: PS_1K_P0_3


title: PS_1K_P0_2


title: ATAC_SV_HFD_2


title: variegated edge leaves, replicate 2 [VE2]


title: CP12 strain, planktonic, 24 hr, rep 3

description: Library name: CP12_3_planktonic_24hr


title: ATAC_SV_HFD_1


title: PS_1K_P0_1


title: variegated edge leaves, replicate 1 [VE1]


title: Control_3

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts and FPKM values for each Sample

value: Control


title: ATAC_B6_Chow_6

value: Chow


title: ATAC_B6_Chow_5


title: Persister rep 3

city: W 120 St

first: Brent

middle: R

last: Stockwell

state: New york

department: Biology

institute: Columbia University

description: Library name: BER006

data_processing:
Libraries are then sequenced using Element AVITI at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 75bp reads reads for each sample.
Core use bases2fastq version 1.1.0 for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p13) using kallisto (0.46.1). Further downstream analysis performed via Sleuth (0.30.0) and clusterProfiler (4.6.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file of est kallisto counts for all samples by gene
Supplementary files format and content: tab-delimited text file of est kallisto counts for all samples by transcript

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from cells using the AllPrep DNA/RNA Isolation Kit (Qiagen). Quality was assessed with Bioanalyzer (RIN for all samples = 10) and 2-3 ug per sample were submitted to the genome center for library construction.
Core uses poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry

value: NSCLC

value: persister


title: Control_2


title: ATAC_SV_HFD_4


title: Persister rep 2

description: Library name: BER005


title: Control_1


title: ATAC_B6_Chow_3


title: ATAC_B6_Chow_4


title: CP12 strain, planktonic, 8 hr, rep 2

description: Library name: CP12_2_planktonic_8hr

value: planktonic


title: CP9 strain, planktonic, 90 min, rep 1

description: Library name: CP9_1_planktonic_90min


title: ASP_3

value: ASP


title: CP12 strain, planktonic, 90 min, rep 2

description: Library name: CP12_2_planktonic_90min


title: variegated edge leaves, replicate 3 [VE3]


title: Parental rep 3

description: Library name: BER003

value: parental


title: Persister rep 1

description: Library name: BER004


title: ASP_2


title: ATAC_B6_Chow_2

value: eWAT


title: ATAC_B6_Chow_1


title: Parental rep 2

description: Library name: BER002


title: Parental rep 1

description: Library name: BER001


title: CP12 strain, planktonic, 24 hr, rep 1

description: Library name: CP12_1_planktonic_24hr

value: 24 hr


title: ASP_1


title: CP12 strain, planktonic, 8 hr, rep 1

description: Library name: CP12_1_planktonic_8hr

value: 8 hr


title: ATAC_SV_Chow_5


title: ATAC_SV_Chow_4


title: 22Rv1 cells, WCF-598

city: Guangzhou

first: Hong

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

description:
Library name: sample2
fpkm_Rv1_WCF598

data_processing:
sample1-2:single sequencing was performed with Illumina HiSeq 3000 (RiboBio Co, Ltd). TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome. Differential analysis of the RNA-seq data was performed using DESeq2 analysis.
Assembly: hg38
Supplementary files format and content: sample1-2:tab-delimited text files include TPM values for each Sample

source_name: Homo sapiens

growth_protocol: 22Rv1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample1-2:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
sample1-2:DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (E7420L). RNA libraries were prepared for paired-end sequencing using standard Illumina protocols.

treatment_protocol: 22Rv1 cells were treated with HX531 for 48 h.

value: tumor cells


title: CP12 strain, planktonic, 8 hr, rep 3

description: Library name: CP12_3_planktonic_8hr


title: 4 GEX multiplexed samples group H

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

institute: Assistance Publique des Hôpitaux de Paris

description:
Library name: H-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and aligned using GRCh38 genome assembly as reference data.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes2.tsv.gz, features2.tsv.gz, matrix2.mtx.gz
Library strategy: CITE-seq

source_name: Peripheric blood

extract_protocol:
Library was prepared using Chromium Single Cell 3ʹ version CG000769 rev A protocol (10x Genomics) with on chip multiplexing technology. Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ version  CG000769 rev A protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA and the antibody-derived tagged cDNAs. For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ version CG000317 rev B protocol (10x Genomics).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq X (100 cycles cartridge).

value: Peripheric blood

value: PBMC

value: mRNA derived cDNA

value: Haetopoietic stem cell transplant


title: CP12 strain, planktonic, 90 min, rep 1

description: Library name: CP12_1_planktonic_90min

value: 90 min


title: CP12 strain, planktonic, 90 min, rep 3

description: Library name: CP12_3_planktonic_90min


title: CP12 strain, planktonic, 24 hr, rep 2

description: Library name: CP12_2_planktonic_24hr


title: 22Rv1 cells, Con

description:
Library name: sample1
fpkm_Rv1_Con

value: control


title: 4 GEX multiplexed samples group G

description:
Library name: G-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: 4 feature barcode multiplexed samples group H

description:
Library name: H-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

molecule: protein

value: ADT derived cDNA


title: SK-MEL-28-siLINC01291

city: Guangzhou City

first: Minna

last: Xu

state: Guangdong Province

address: 1838 Guangzhou Avenue North

institute: Southern Medical University

description:
Library name: XMN_4
XMN_4_FPKM

data_processing:
Based on the TPM quantification results, we calculated the correlation between each pair of samples. According to the standards recommended by the ENCODE project, two samples designated as biological replicates should have a squared Pearson correlation coefficient (R²) ≥ 0.92. Differentially expressed genes (DEGs) between the experimental group and the control group were analyzed using DESeq2 / edgeR software. Under the default conditions, genes with P-value < 0.05 and |log2(fold change)| > 1 are defined as significantly differentially expressed genes. Genes with log2(fold change) > 1 are labeled as upregulated genes (Up), while those with log2(fold change) < -1 are labeled as downregulated genes (Down). Genes not meeting these criteria are classified as Not DEGs (non-significantly differentially expressed genes). We ranked genes by P-value, selected the top 15 genes from both upregulated and downregulated gene sets, and used their TPM values to plot a heatmap. The differentially expressed genes were then subjected to GO and KEGG enrichment analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

growth_protocol: A375 and SK-MEL-28 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
1.Extract total RNA from the sample and perform quality control; after passing the quality check, use Oligo(dT) magnetic beads to enrich eukaryotic mRNA (for prokaryotes, use a kit to remove rRNA); 2.Add fragmentation reagents and incubate the mRNA at an appropriate temperature in a thermomixer to fragment it into short pieces; 3.Use the fragmented mRNA as a template to synthesize single-stranded cDNA, then prepare a reaction system to synthesize double-stranded cDNA; 4.Use a kit to purify and recover the cDNA, repair sticky ends, add an “A” base to the 3' end, and ligate adapters; 5.Perform size selection and PCR amplification to construct the library; 6.After the constructed library passes quality control using the Agilent 2100 Bioanalyzer and Qubit, sequence it with the Illumina sequencer.
The raw data from the sequencing machine is in FASTQ format. Fastp (https://github.com/OpenGene/fastp) software is used to perform quality control on the raw data, including removing adapters, duplicate sequences, and low-quality sequences, resulting in CleanData in FASTQ format. FastQC (https://github.com/s-andrews/FastQC) is then used to perform quality control analysis on the processed data. Next, ribosomal RNA is removed, and the Clean reads data are aligned to the reference genome using HISAT2 software. The quality-controlled sequences are mapped to the reference genome using HISAT2, and new transcripts are assembled with StringTie. These newly assembled transcripts are then merged with known genes, and HTSeq software is used for gene expression quantification analysis.

treatment_protocol: A375 and SK-MEL-28 cells were treated with EL,siNC and siLINC01291

value: cell line

value: human melanoma cells


title: CP11 strain, planktonic, 24 hr, rep 3

description: Library name: CP11_3_planktonic_24hr


title: SK-MEL-28-siNC

description:
Library name: XMN_3
XMN_3_FPKM


title: ATAC_SV_Chow_1

value: Chow


title: CP11 strain, planktonic, 90 min, rep 3

description: Library name: CP11_3_planktonic_90min

value: planktonic


title: 4 feature barcode multiplexed samples group G

description:
Library name: G-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: ATAC_SV_Chow_3


title: A375-siLINC01291

description:
Library name: XMN_2
XMN_2_FPKM


title: bone_ko 3

city: Toon

first: Aoi

last: Ikedo

state: Ehime

address: Shitsukawa

institute: Ehime University

description: B_Expression Browser.txt

data_processing:
CLC Genomic Workbench
Seqence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench (Quality scores limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomics workbench (Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.8, Similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomics workbench.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using QuantSeq 3'mRNA-seq Library Prep Kit for Illumina (LEXOGEN) following manufacturer's protocols.

value: Bone

value: CD45-, CD31-, PDGFR{alpha}+ cells


title: CP11 strain, planktonic, 8 hr, rep 2

description: Library name: CP11_2_planktonic_8hr


title: CP11 strain, planktonic, 24 hr, rep 2

description: Library name: CP11_2_planktonic_24hr


title: 4 feature barcode multiplexed samples group F

description:
Library name: F-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: bone_ko 1

description: B_Expression Browser.txt


title: 4 GEX multiplexed samples group E

description:
Library name: E-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: noT2D_HAM_72h +Mtb biol rep 4

city: San Antonio

first: Larry

last: Schlesinger

state: TX

address: 8715 W Military Dr

institute: Texas Biomedical Research Institute

description:
Library name: LS_181_noT2D_HAM_72h +Mtb
LS_181_noT2D_HAM_72h +Mtb

data_processing:
CLC Genomics Workbench v 20.0
Low-quality sequences and adapters were trimmed.
Trimmed reads were mapped to the human hg38 reference genome.
The reads were assigned to the transcripts using the EM algorithm.
The TMM normalization  in EdgeR and multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM) were carried out for differential expression analysis.
Assembly: hg38
Supplementary files format and content: RawCounts.xlsx
Supplementary files format and content: This file contains the raw counts of all the samples

source_name: Bronchoalveolar lavage fluid

extract_protocol:
Cells were retrieved from plates using 5mM EDTA (Sigma) and incubating the cells on ice for 30mins. Cells were stored in RNALater (Invitrogen) at -80C. Prior to shipment the cells were spun down and RNALater replaced with Trizol. RNA was isolated using Quick-RNA Microprep Kit (R1050; Zymo Research) as per the manufacturer’s instructions. Isolated RNA was quantified using the Qubit RNA High Sensitivity Assay Kit (Q32852) and Qubit 4 Fluorometer (both from ThermoFisher Scientific).
RNA sequencing libraries were prepared from 25-500ng of Total RNA using the NEB Next directional RNA library preparation Kit with poly (A) enrichment module (Ipswich, MA).
stranded RNA-seq

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

tag: donor number

tag: diabetes status

value: No Type 2 diabetes (noT2D)

value: Mtb infected

value: 72h post infection


title: CP11 strain, planktonic, 90 min, rep 2

description: Library name: CP11_2_planktonic_90min

value: 24 hr


title: noT2D_HAM_72h +Mtb biol rep 3

description:
Library name: LS_145_noT2D_HAM_72h +Mtb
LS_145_noT2D_HAM_72h +Mtb


title: 4 feature barcode multiplexed samples group E

description:
Library name: E-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: Peripheric blood

value: PBMC


title: bone_con 3

description: B_Expression Browser.txt

value: PDGFR{alpha}-CreER


title: noT2D_HAM_72h +Mtb biol rep 2

description:
Library name: LS_125_noT2D_HAM_72h +Mtb
LS_125_noT2D_HAM_72h +Mtb


title: CP11 strain, planktonic, 8 hr, rep 3

description: Library name: CP11_3_planktonic_8hr

value: 8 hr


title: ATAC_SV_Chow_2

value: eWAT


title: bone_con 2

description: B_Expression Browser.txt


title: CP10 strain, planktonic, 24 hr, rep 3

description: Library name: CP10_3_planktonic_24hr


title: bone_con 1

description: B_Expression Browser.txt


title: 4 feature barcode multiplexed samples group D

description:
Library name: D-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: ADT derived cDNA

value: Haetopoietic stem cell transplant


title: CP11 strain, planktonic, 90 min, rep 1

description: Library name: CP11_1_planktonic_90min

value: 90 min


title: A375-siNC

description:
Library name: XMN_1
XMN_1_FPKM

value: cell line

value: human melanoma cells


title: 4 GEX multiplexed samples group F

description:
Library name: F-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: mRNA derived cDNA


title: noT2D_HAM_72h +Mtb biol rep 1

description:
Library name: LS_113_noT2D_HAM_72h +Mtb
LS_113_noT2D_HAM_72h +Mtb

value: Bronchoalveolar lavage fluid


title: bone_ko 2

description: B_Expression Browser.txt

value: Bone

value: CD45-, CD31-, PDGFR{alpha}+ cells


title: 4 GEX multiplexed samples group C

description:
Library name: C-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: CP10 strain, planktonic, 8 hr, rep 3

description: Library name: CP10_3_planktonic_8hr

value: planktonic


title: muscle_ko 3

description: M_Expression Browser.txt

source_name: Muscle

value: Muscle

value: CD45-, CD31-, Vcam1-, PDGFR{alpha}+ cells


title: noT2D_HAM_72h -Mtb biol rep 4

description:
Library name: LS_182_noT2D_HAM_72h -Mtb
LS_182_noT2D_HAM_72h -Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)

value: Uninfected

value: 72h post culture


title: noT2D_HAM_72h -Mtb biol rep 3

description:
Library name: LS_146_noT2D_HAM_72h -Mtb
LS_146_noT2D_HAM_72h -Mtb


title: muscle_ko 1

description: M_Expression Browser.txt


title: 4 GEX multiplexed samples group B

description:
Library name: B-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: Peripheric blood

value: PBMC


title: 4 feature barcode multiplexed samples group C

description:
Library name: C-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: ADT derived cDNA

value: Haetopoietic stem cell transplant


title: CP10 strain, planktonic, 90 min, rep 3

description: Library name: CP10_3_planktonic_90min

value: 90 min


title: muscle_ko 2

description: M_Expression Browser.txt


title: CP10 strain, planktonic, 24 hr, rep 2

description: Library name: CP10_2_planktonic_24hr

value: 24 hr


title: 4 feature barcode multiplexed samples group B

description:
Library name: B-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: 4 GEX multiplexed samples group D

description:
Library name: D-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: mRNA derived cDNA


title: CP11 strain, planktonic, 8 hr, rep 1

description: Library name: CP11_1_planktonic_8hr

value: 8 hr


title: noT2D_HAM_24h +Mtb biol rep 5

description:
Library name: LS_163_noT2D_HAM_24h +Mtb
LS_163_noT2D_HAM_24h +Mtb

value: Bronchoalveolar lavage fluid

value: Mtb infected

value: 24h post infection


title: CP10 strain, planktonic, 90 min, rep 2

description: Library name: CP10_2_planktonic_90min

value: planktonic


title: 4 GEX multiplexed samples group A

description:
Library name: A-GEX
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.


title: muscle_con 1

description: M_Expression Browser.txt

value: Muscle

value: CD45-, CD31-, Vcam1-, PDGFR{alpha}+ cells

value: PDGFR{alpha}-CreER


title: CP10 strain, planktonic, 24 hr, rep 1

description: Library name: CP10_1_planktonic_24hr


title: noT2D_HAM_24h +Mtb biol rep 3

description:
Library name: LS_143_noT2D_HAM_24h +Mtb
LS_143_noT2D_HAM_24h +Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)


title: 4 feature barcode multiplexed samples group A

description:
Library name: A-FB
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.

value: Peripheric blood


title: noT2D_HAM_24h +Mtb biol rep 4

description:
Library name: LS_151_noT2D_HAM_24h +Mtb
LS_151_noT2D_HAM_24h +Mtb


title: H34_IH_Tu

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

data_processing:
Alignment: The sequenced reads from the raw sequence (.fastq files) were aligned on the UCSC rn6 genome using the STAR software (2.7.1a) (Dobin et al. 2013) [PMID:23104886] to produce bam files.
Counts: The aligned reads (.bam files) were counted using HTSeq framework (0.11.2) (Anders et al. 2015) [PMID:25260700], with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none.
Assembly: rn6
Supplementary files format and content: Tab-delimited text files

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNA was extracted from rat liver tissue samples preserved with an RNA stabilization solution (Thermo scientific, USA). RNA purification was performed with RNeasy Mini Kit® (Qiagen, USA) according to the instructions provided by the manufacturer. Quality assessment for the RNA Integrity Number (RIN) was performed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
The stranded mRNA library was prepared with 1 μg total RNA (RIN>7).
The normalized and pooled libraries were sequenced on DNBseqTM platform (MGI).

tag: rat

tag: condition

value: Intermittent hypoxia

value: Liver

value: Tu

value: Male

value: Fischer 344

tag: disease

value: DEN-induced model of HCC


title: CP10 strain, planktonic, 8 hr, rep 1

description: Library name: CP10_1_planktonic_8hr

tag: cell type

tag: genotype

value: 8 hr


title: noT2D_HAM_24h +Mtb biol rep 2

description:
Library name: LS_123_noT2D_HAM_24h +Mtb
LS_123_noT2D_HAM_24h +Mtb

tag: tissue

value: Bronchoalveolar lavage fluid

tag: time


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 2

city: Cleveland

first: Brian

last: Kim

state: OHIO

address: 10900 Euclid Ave

institute: Case Western Reserve University

data_processing:
Sequence reads were trimed then aligned to mm10 genome build using kallisto v0.46.1. The transcripts were quantified in TPM, which was further processed into gene-level TPM abundance using tximport.
Assembly: mm10
Supplementary files format and content: excel file that shows counts for each gene and sample

source_name: Cell line

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen). 1ug of total RNA was used for construction of sequencing libraries.
rRNA was depleted using NEBNext rRNA Depletion Kit v2 (NEB), then RNA library was constructed using NEBNext Ultra II Directional RNA Library Prep kit (NEB)

value: Cell line

value: adipocyte

value: WT

value: Tgf-b1, Tgf-b1 Free


title: noT2D_HAM_72h -Mtb biol rep 2

description:
Library name: LS_126_noT2D_HAM_72h -Mtb
LS_126_noT2D_HAM_72h -Mtb

value: Uninfected

value: 72h post culture


title: noT2D_HAM_72h -Mtb biol rep 1

description:
Library name: LS_114_noT2D_HAM_72h -Mtb
LS_114_noT2D_HAM_72h -Mtb

value: Alveolar macrophage


title: H34_IH_NT

value: NT

tag: Sex

tag: strain


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate1

tag: cell line

tag: treatment


title: noT2D_HAM_24h +Mtb biol rep 1

description:
Library name: LS_111_noT2D_HAM_24h +Mtb
LS_111_noT2D_HAM_24h +Mtb

value: No Type 2 diabetes (noT2D)

value: Mtb infected

value: 24h post infection


title: CP12 strain, biofilm, 8 hr, rep 3

description: Library name: CP12_3_biofilm_8hr

source_name: biofilm

value: biofilm


title: CP10 strain, planktonic, 8 hr, rep 2

description: Library name: CP10_2_planktonic_8hr

value: planktonic


title: 3T3-L1 cells, Tgf-b1 treated, 4 Days, duplicate 2


title: muscle_con 3

description: M_Expression Browser.txt

value: Muscle

value: CD45-, CD31-, Vcam1-, PDGFR{alpha}+ cells


title: H32_IH_NT

value: Intermittent hypoxia

value: Liver

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: muscle_con 2

description: M_Expression Browser.txt

value: PDGFR{alpha}-CreER


title: CP12 strain, biofilm, 90 min, rep 3

description: Library name: CP12_3_biofilm_90min

value: 90 min


title: noT2D_HAM_24h -Mtb biol rep 5

description:
Library name: LS_164_noT2D_HAM_24h -Mtb
LS_164_noT2D_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Uninfected

value: 24h post culture


title: noT2D_HAM_24h -Mtb biol rep 4

description:
Library name: LS_152_noT2D_HAM_24h -Mtb
LS_152_noT2D_HAM_24h -Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)


title: CP12 strain, biofilm, 24 hr, rep 2

description: Library name: CP12_2_biofilm_24hr

value: 24 hr


title: H31_IH_Tu

value: Tu


title: noT2D_HAM_24h -Mtb biol rep 3

description:
Library name: LS_144_noT2D_HAM_24h -Mtb
LS_144_noT2D_HAM_24h -Mtb


title: 3T3-L1 cells, Tgf-b1 treated, 4 Days, duplicate 1

value: Cell line

value: adipocyte

value: WT


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 3

value: Tgf-b1, Tgf-b1 Free


title: 3T3-L1 cells, PBS treated, duplicate 2

value: PBS


title: CP12 strain, biofilm, 8 hr, rep 2

description: Library name: CP12_2_biofilm_8hr

value: biofilm

value: 8 hr


title: CP12 strain, biofilm, 90 min, rep 2

description: Library name: CP12_2_biofilm_90min


title: H29_IH_Tu

value: Intermittent hypoxia

value: Liver

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: H31_IH_NT

value: NT


title: noT2D_HAM_24h -Mtb biol rep 1

description:
Library name: LS_112_noT2D_HAM_24h -Mtb
LS_112_noT2D_HAM_24h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: Uninfected

value: 24h post culture


title: CP12 strain, biofilm, 24 hr, rep 3

description: Library name: CP12_3_biofilm_24hr

value: 24 hr


title: 3T3-L1 cells, PBS treated, duplicate 1

value: Cell line

value: adipocyte


title: H32_IH_Tu

value: Tu


title: H29_IH_NT


title: H27_No_Tu

value: Normoxia


title: noT2D_HAM_2h +Mtb biol rep 8

description:
Library name: LS_183_noT2D_HAM_2h +Mtb
LS_183_noT2D_HAM_2h +Mtb

value: No Type 2 diabetes (noT2D)

value: Mtb infected

value: 2h post infection


title: CP12 strain, biofilm, 24 hr, rep 1

description: Library name: CP12_1_biofilm_24hr

value: biofilm


title: CP12 strain, biofilm, 8 hr, rep 1

description: Library name: CP12_1_biofilm_8hr

value: 8 hr


title: Old_3_Cecum

city: Jena

first: Jing

last: Lu

state: Thuringia

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging – Fritz Lipmann Institute (FLI)

description: Single cell RNA sequencing

data_processing:
The fastq files are mapped against mm10.e87 genome following by counting the UMI and removing duplicates for single cells using 'cellranger count' (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count ) with default parameters.
Assembly: mm10.e87
Supplementary files format and content: epithelialF_single_F3.rds, the processed data is an rds file denoting the seurat object of quantitative matrix

source_name: cecum

growth_protocol: 3 Young (about 12week) and 6 old (about 108week) female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility

extract_protocol:
Crypts from different sections of intestine were isolated as described previously(Asad A Ahmad et al., 2014). After centrifugation, the crypts were re-suspended in 3ml of Single-Cell Isolation Solution (TrypLE supplemented with: 1mg/ml DNaseI, 5mM MgCl2, 80μM Y27) and incubated at 37°C for 20min, vortexing for 5 seconds after first 10min. Reaction was quenched by addition of 27ml ice-cold PBS and cells were centrifuged at 1000g for 5minutes at 4°C. Cell pellet was re-suspended in FACS staining medium (FSM - PBS supplemented with 2% Fetal Bovine Serum, 80μM Y27, 3mM EDTA) and treated with CD326 (EpCAM) (G8.8), PE-Cyanine7 coupled rat monoclonal antibody and a TotalSeq Hashtag antibody for 30min on ice in the dark. The cells were then centrifuged at 450g for 5min at 4°C and re-suspended in 500μl fresh FSM. An input of 10000 EpCAM positive FACS sorted single cells per compartment was added to each 10X Chromium Controller channel.
The 10X Single Cell 3’ v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction.

value: cecum

value: old (about 108week)

value: female

value: Aging


title: Old_3_DistCol

description: Single cell RNA sequencing

source_name: distal colon

value: distal colon


title: noT2D_HAM_2h +Mtb biol rep 7

description:
Library name: LS_177_noT2D_HAM_2h +Mtb
LS_177_noT2D_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage


title: H26_No_Tu

value: Liver

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: CP12 strain, biofilm, 90 min, rep 1

description: Library name: CP12_1_biofilm_90min

value: 90 min


title: Old_3_ProxCol

description: Single cell RNA sequencing

source_name: proximal colon

value: proximal colon


title: noT2D_HAM_2h +Mtb biol rep 5

description:
Library name: LS_161_noT2D_HAM_2h +Mtb
LS_161_noT2D_HAM_2h +Mtb

value: No Type 2 diabetes (noT2D)

value: Mtb infected


title: Old_3_IntSI

description: Single cell RNA sequencing

source_name: intermediate small intestine

value: intermediate small intestine


title: H26_No_NT

value: Normoxia

value: NT


title: noT2D_HAM_2h +Mtb biol rep 4

description:
Library name: LS_149_noT2D_HAM_2h +Mtb
LS_149_noT2D_HAM_2h +Mtb

value: 2h post infection


title: H27_No_NT


title: Old_3_DistSI

description: Single cell RNA sequencing

source_name: distal small intestine

value: distal small intestine

value: old (about 108week)

value: female


title: noT2D_HAM_2h +Mtb biol rep 6

description:
Library name: LS_169_noT2D_HAM_2h +Mtb
LS_169_noT2D_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid


title: CP11 strain, biofilm, 90 min, rep 3

description: Library name: CP11_3_biofilm_90min

value: biofilm


title: CP11 strain, biofilm, 24 hr, rep 3

description: Library name: CP11_3_biofilm_24hr

value: 24 hr


title: CP11 strain, biofilm, 8 hr, rep 2

description: Library name: CP11_2_biofilm_8hr

value: 8 hr


title: Old_2_ProxCol

description: Single cell RNA sequencing

value: Aging


title: H20_No_Tu

value: Liver

value: Tu

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: noT2D_HAM_24h -Mtb biol rep 2

description:
Library name: LS_124_noT2D_HAM_24h -Mtb
LS_124_noT2D_HAM_24h -Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)

value: Uninfected

value: 24h post culture


title: CP11 strain, biofilm, 8 hr, rep 3

description: Library name: CP11_3_biofilm_8hr


title: noT2D_HAM_2h +Mtb biol rep 3

description:
Library name: LS_141_noT2D_HAM_2h +Mtb
LS_141_noT2D_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: H23_No_Tu

value: Normoxia


title: Old_2_Cecum

description: Single cell RNA sequencing

value: cecum

value: old (about 108week)

value: female


title: noT2D_HAM_2h +Mtb biol rep 1

description:
Library name: LS_109_noT2D_HAM_2h +Mtb
LS_109_noT2D_HAM_2h +Mtb

value: Bronchoalveolar lavage fluid


title: Old_2_DistSI

description: Single cell RNA sequencing

value: distal small intestine

value: Aging


title: CP11 strain, biofilm, 90 min, rep 2

description: Library name: CP11_2_biofilm_90min

value: biofilm

value: 90 min


title: CP11 strain, biofilm, 24 hr, rep 1

description: Library name: CP11_1_biofilm_24hr

value: 24 hr


title: H20_No_NT

value: Liver

value: NT

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: no T2D_HAM_2h -Mtb biol rep 3

description:
Library name: LS_170_no T2D_HAM_2h -Mtb
LS_170_no T2D_HAM_2h -Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)

value: Uninfected

value: 2h post culture


title: Old_3_ProxSI

description: Single cell RNA sequencing

source_name: proximal small intestine

value: proximal small intestine

value: old (about 108week)


title: CP11 strain, biofilm, 90 min, rep 1

description: Library name: CP11_1_biofilm_90min


title: Old_2_DistCol

description: Single cell RNA sequencing

value: distal colon

value: female


title: no T2D_HAM_2h -Mtb biol rep 4

description:
Library name: LS_178_no T2D_HAM_2h -Mtb
LS_178_no T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid


title: Old_1_ProxCol

description: Single cell RNA sequencing

value: proximal colon

value: Aging


title: CP11 strain, biofilm, 8 hr, rep 1

description: Library name: CP11_1_biofilm_8hr

value: biofilm

value: 8 hr


title: Old_2_IntSI

description: Single cell RNA sequencing

value: intermediate small intestine


title: CP10 strain, biofilm, 24 hr, rep 3

description: Library name: CP10_3_biofilm_24hr

value: 24 hr


title: noT2D_HAM_2h +Mtb biol rep 2

description:
Library name: LS_121_noT2D_HAM_2h +Mtb
LS_121_noT2D_HAM_2h +Mtb

value: Mtb infected

value: 2h post infection


title: H23_No_NT

value: Normoxia

value: Liver

value: NT

value: Male

value: Fischer 344

value: DEN-induced model of HCC


title: no T2D_HAM_2h -Mtb biol rep 2

description:
Library name: LS_142_no T2D_HAM_2h -Mtb
LS_142_no T2D_HAM_2h -Mtb

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)

value: Uninfected

value: 2h post culture


title: zhengchang, replicate 1, scRNAseq

city: Beijing

first: Xiasang

last: Chen

address: 2 Yuanmingyuan West Road. Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

institute: State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: Amel_HAv3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apis mellifera

source_name: Mushroom bodies

extract_protocol:
Whole dissociation was placed in the ice-cold phosphate-buffered solution plate, removed the coating membrane and the optic lope, antennal lobe, then the mushroom bodies were fetched into the tube, washed double times using cold PBS solution, added the tissue into the 300 μL activated enzyme blended solution and brain dissociation kit enzyme mix overall, incubated in the automated dissociator by the 37℃, 200 rpm, 30 min, every 10 minutes used a wide-bore pipette tip to mix the cells gently and thoroughly, Used a 40 μm cell strainer to remove any remaining cell debris and large clumps, Centrifuged cells at 300 rcf for 10 min, 4℃. Removed supernatant without disrupting the cell pellet. Using a wide-bore pipette tip, add 1 ml 1× PBS with 0.04% BSA to the tube. Gently mixed 5 times and inverted tubes to re-suspend the cell pellet. Centrifuged the cells at 300 rcf for 10 min. Removed supernatant without disrupting the cell pellet, used DMEM + 10% FBS to re-suspend, and fitted the volume to obtain the target cell concentration.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics).Briefly,Mushroom body cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selectes with SPRIselect reagent for subsequent library construction. During the library construction. During the library construction llumina R2 Primer sequences, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Mushroom bodies

value: newly emerged workers

value: mainly Kenyon cells

value: wild type

value: control


title: T2D_MDM_72h +Mtb biol rep 3

description:
Library name: LS_81_T2D_MDM_72h +Mtb
LS_81_T2D_MDM_72h +Mtb

source_name: Blood

value: Blood

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)

value: Mtb infected

value: 72h post infection


title: Old_2_ProxSI

description: Single cell RNA sequencing

value: proximal small intestine

value: old (about 108week)

value: female

value: Aging


title: Old_1_Cecum

description: Single cell RNA sequencing

value: cecum


title: T2D_MDM_72h +Mtb biol rep 1

description:
Library name: LS_11_T2D_MDM_72h +Mtb
LS_11_T2D_MDM_72h +Mtb


title: CP10 strain, biofilm, 8 hr, rep 2

description: Library name: CP10_2_biofilm_8hr

value: biofilm

value: 8 hr


title: tumor 8M

type: RNA

city: Tokyo

first: Manabu

last: Takamatsu

address: 3-8-31 Ariake Koto-ku

department: Pathology

institute: Cancer Institute

description: surgically resected

hyb_protocol: Hybridization was performed using the NanoString nCounter protocol, incubated at 65°C for 18 hours.

scan_protocol: Post-hybridization processing was performed, and data were collected using the analyzer SPRINT.

data_processing: Raw RCC files were analyzed using NanoString nSolver v4.0. Background correction and normalization were performed using positive controls and housekeeping genes.

source_name: primary pancreatic cancer

label_protocol: Not applicable

extract_protocol: Total RNA was extracted from fresh frozen tissue using the RNeasy Kit (Qiagen) per manufacturer’s instructions. RNA integrity was confirmed by Bioanalyzer (Agilent).

tag: clusterid

value: M


title: tumor 8O

description: surgically resected

value: O


title: tumor 7M

description: surgically resected


title: no T2D_HAM_2h -Mtb biol rep 1

description:
Library name: LS_122_no T2D_HAM_2h -Mtb
LS_122_no T2D_HAM_2h -Mtb

value: Bronchoalveolar lavage fluid

value: Alveolar macrophage

value: No Type 2 diabetes (noT2D)

value: Uninfected

value: 2h post culture


title: Old_1_DistCol

description: Single cell RNA sequencing

value: distal colon


title: CP10 strain, biofilm, 90 min, rep 3

description: Library name: CP10_3_biofilm_90min

value: 90 min


title: CP10 strain, biofilm, 8 hr, rep 3

description: Library name: CP10_3_biofilm_8hr


title: T2D_MDM_72h +Mtb biol rep 2

description:
Library name: LS_47_T2D_MDM_72h +Mtb
LS_47_T2D_MDM_72h +Mtb

value: Blood

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)

value: Mtb infected

value: 72h post infection


title: tumor 7Q

description: surgically resected

value: Q


title: tumor 7G

description: surgically resected

value: G


title: T2D_MDM_72h -Mtb biol rep 3

description:
Library name: LS_82_T2D_MDM_72h -Mtb
LS_82_T2D_MDM_72h -Mtb

value: 72h post culture


title: Old_1_ProxSI

description: Single cell RNA sequencing

value: proximal small intestine

value: old (about 108week)

value: female

value: Aging


title: CP10 strain, biofilm, 8 hr, rep 1

description: Library name: CP10_1_biofilm_8hr

value: biofilm

value: 8 hr


title: T2D_MDM_72h -Mtb biol rep 2

description:
Library name: LS_48_T2D_MDM_72h -Mtb
LS_48_T2D_MDM_72h -Mtb

value: Uninfected


title: Old_1_IntSI

description: Single cell RNA sequencing

value: intermediate small intestine


title: Young_3_DistCol

description: Single cell RNA sequencing

value: distal colon

value: Young (about 12week)


title: Old_1_DistSI

description: Single cell RNA sequencing

value: distal small intestine


title: Young_3_ProxCol

description: Single cell RNA sequencing

value: proximal colon


title: CP10 strain, biofilm, 90 min, rep 1

description: Library name: CP10_1_biofilm_90min

value: 90 min


title: T2D_MDM_72h -Mtb biol rep 1

description:
Library name: LS_12_T2D_MDM_72h -Mtb
LS_12_T2D_MDM_72h -Mtb

value: Blood

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)


title: tumor 6M

description: surgically resected

value: M


title: T2D_MDM_24h +Mtb biol rep 3

description:
Library name: LS_91_T2D_MDM_24h +Mtb
LS_91_T2D_MDM_24h +Mtb

value: Mtb infected

value: 24h post infection


title: CP10 strain, biofilm, 24 hr, rep 2

description: Library name: CP10_2_biofilm_24hr

value: 24 hr


title: T2D_MDM_24h +Mtb biol rep 2

description:
Library name: LS_45_T2D_MDM_24h +Mtb
LS_45_T2D_MDM_24h +Mtb


title: CP9 strain, biofilm, 8 hr, rep 3

description: Library name: CP9_3_biofilm_8hr


title: CP9 strain, biofilm, 24 hr, rep 3

description: Library name: CP9_3_biofilm_24hr


title: tumor 4M

description: surgically resected


title: T2D_MDM_24h +Mtb biol rep 1

description:
Library name: LS_33_T2D_MDM_24h +Mtb
LS_33_T2D_MDM_24h +Mtb


title: Young_3_Cecum

description: Single cell RNA sequencing

value: cecum

value: female

value: Aging


title: T2D_MDM_24h -Mtb biol rep 3

description:
Library name: LS_92_T2D_MDM_24h -Mtb
LS_92_T2D_MDM_24h -Mtb

value: Uninfected

value: 24h post culture


title: Young_3_DistSI

description: Single cell RNA sequencing


title: tumor 3M

description: surgically resected


title: Young_3_IntSI

description: Single cell RNA sequencing

value: intermediate small intestine


title: CP9 strain, biofilm, 90 min, rep 3

description: Library name: CP9_3_biofilm_90min

value: biofilm


title: CP10 strain, biofilm, 90 min, rep 2

description: Library name: CP10_2_biofilm_90min


title: CP9 strain, biofilm, 24 hr, rep 2

description: Library name: CP9_2_biofilm_24hr


title: T2D_MDM_24h -Mtb biol rep 2

description:
Library name: LS_46_T2D_MDM_24h -Mtb
LS_46_T2D_MDM_24h -Mtb


title: tumor 6O

description: surgically resected

value: O


title: Young_3_ProxSI

description: Single cell RNA sequencing

value: proximal small intestine

value: Young (about 12week)


title: T2D_MDM_24h -Mtb biol rep 1

description:
Library name: LS_34_T2D_MDM_24h -Mtb
LS_34_T2D_MDM_24h -Mtb

value: Blood


title: tumor 2M

description: surgically resected


title: tumor 5M

description: surgically resected


title: CP9 strain, biofilm, 90 min, rep 2

description: Library name: CP9_2_biofilm_90min

value: 90 min


title: Young_2_DistCol

description: Single cell RNA sequencing

value: distal colon


title: Young_2_ProxCol

description: Single cell RNA sequencing

value: proximal colon


title: T2D_MDM_2h +Mtb biol rep 6

description:
Library name: LS_89_T2D_MDM_2h +Mtb
LS_89_T2D_MDM_2h +Mtb

value: Monocyte-derived Macrophage

value: Type 2 diabetes (T2D)

value: Mtb infected

value: 2h post infection


title: tumor 9Q

description: surgically resected

value: Q


title: T2D_MDM_2h +Mtb biol rep 5

description:
Library name: LS_77_T2D_MDM_2h +Mtb
LS_77_T2D_MDM_2h +Mtb


title: Young_2_Cecum

description: Single cell RNA sequencing

value: cecum

value: female

value: Aging


title: CP9 strain, biofilm, 8 hr, rep 1

description: Library name: CP9_1_biofilm_8hr

value: 8 hr


title: CP9 strain, biofilm, 24 hr, rep 1

description: Library name: CP9_1_biofilm_24hr

value: biofilm

value: 24 hr


title: tumor 16Q

description: surgically resected


title: T2D_MDM_2h +Mtb biol rep 4

description:
Library name: LS_63_T2D_MDM_2h +Mtb
LS_63_T2D_MDM_2h +Mtb


title: Young_2_DistSI

description: Single cell RNA sequencing

value: distal small intestine


title: tumor 16M

description: surgically resected

value: M


title: Young_2_IntSI

description: Single cell RNA sequencing

value: intermediate small intestine

value: Young (about 12week)


title: CP9 strain, biofilm, 90 min, rep 1

description: Library name: CP9_1_biofilm_90min

value: 90 min


title: 3C-seq of S. muelleri plate with 25 ug/ml Chloramphenicol for 30 min

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Raw contact maps were built as described previously (Lioy and Cournac 2018). Briefly, each read was assigned to a restriction fragment. Non- informative events such as self-circularized restriction fragments, or uncut co- linear restriction fragments were discarded. The chromosome of each bacterium was divided into 5 kb bins and the frequencies of contacts between genomic loci for each bin were assigned. Contact frequencies were visualized as heatmaps. Raw contact maps used for comparative analyses were built using 1 million valid reads. Raw contact maps were normalized using Iterative correction and eigenvector decomposition (ICE; Imakaev, et all 2012 https://pubmed.ncbi.nlm.nih.gov/22941365/). To facilitate visualization, normalized contact matrices are visualized as log matrices. A Gaussian filter of H=0.5 is used when plotting the matrices. To quantify the frequency of interactions in the secondary diagonals (Supplementary Figure 4), we applied to our data a method based on the filtering of significant 3C contacts and developed as described (Wang et al, science, 2015).
Assembly: CP083930.1
Supplementary files format and content: raw and ICE-normalized matrices
Library strategy: 3C-Seq

organism: Simonsiella muelleri

source_name: bacterial cell culture

extract_protocol:
3C libraries were prepared as previously described (Lioy et al., 2021b, 2018; Marbouty et al., 2015b). Cells were plated from glycerol stock onto agar plates and grown at 37C for 24 hours and 48 hours, after which they were scraped off and transferred to BSTSY/FBS containing 6% f.c formaldehyde, fully resuspended, and fixed at room temperature at 120 rpm, followed by 30 min more at 4C. Glycine (250 mM f.c.) was added, and the cells incubated 30 min at 4C at 120 rpm. After fixation, cells were collected by centrifugation for 10 min at 3,500 g at 4C, resuspended in fresh medium, collected again by centrifugation, and resuspended in 1 ml fresh medium before final collection by centrifugation. Cell pellets were stored at -70C. For digestion, cell pellets were thawed on ice for 10 min, resuspended in 500 l Tris 10 mM EDTA 0.5 mM (TE) (pH 8), and lysed using 4 l Ready-lyse lysozyme (Epicentre) for 20 min at 37C, 300 rpm. SDS (0.5% f.c.) was added and incubated for 10 min at room temperature. 500 l lysed cells were then transferred to a tube containing 4.5 ml digestion buffer (1% Triton X-100, 1x Cutsmart buffer (New England Biolabs)), and 100 l cells (non-digested control) were transferred to a tube containing 0.9 ml of digestion buffer. 100U of HpaII (New England Biolabs) were added to the 5 ml digestion mix. Both tubes were incubated for 3 h at 37C. After digestion, 1 ml of digestion mix was put on ice (digested control) together with the non-digested control. The remaining digestion mix was split into 4 parts, centrifuged for 20 min at 20,000 g, and pellets were carefully resuspended in 1 ml water each, and pooled into 7 ml ligation buffer (1X ligation buffer 3 (New England Biolabs; without ATP), 1mM ATP, 1 mg/ml BSA, 500 U of T4 DNA ligase 5 U/l (ThermoFisher)). Ligation was carried out at 16C for 4 h, followed by incubation together with the two control tubes overnight at 65C with proteinase K (0.25 mg/ml f.c.) and EDTA (6 mM f.c.). The next day, DNA of the ligated sample was precipitated with 1/10 volume of 3 M sodium acetate (pH 5.2) and 2 volumes of isopropanol, and after one hour at -80C, DNA was pelleted by centrifugation for 30 min at 10,000 g at 4C, and resuspended in 500 l 1X TE buffer. DNA in all tubes (ligation and two controls) were extracted once with 400 l phenol-chloroform pH 8.0 (vortexed for 1 min and centrifuged for 5 min 16,000 g at 4C), precipitated (see above; 30 min at -80C, followed by centrifugation for 20 min at 16,000 x g at 4C), washed with 400 l 80% cold ethanol, and diluted in 30 l 1X TE buffer supplemented with RNase A (1 mg/ml f.c.; ThermoFisher). Tubes containing ligated DNA were pooled. A 1% agarose gel was run with aliquots of the ligated and two control DNA to check for efficiency of digest and ligation. Ligated DNA was adjusted with water for 130 l with approx. 5 g, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 l elution buffer; Quiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37C before inactivation for 20 min at 65C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 dNTPs, 0.2 M Illumina primers PE1.0 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA) and PE2.0 (CAAGCAGAAGACGGCATACGAGAT), 3 l of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 C 30 s, 12 cycles of 65C 30 s, and 72C 30 s, and 72C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads. Reads have been trimmed of adapter sequences and deduplicated (see paper for details).
Ligated DNA (5 µg) was adjusted with water to 130 µl, and sheared using a Covaris S220 (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 s for 4 cycles), and the DNA purified using the QIAquick PCR purification kit (40 µl elution buffer; Qiagen), and DNA end-repaired with 1X T4 DNA ligase buffer (New England Biolabs), 0.4 mM dNTP mix, 15 U T4 polynucleotide kinase (New England Biolabs), 5 U Klenow DNA polymerase (Roche), and incubated for 30 min at RT. DNA was purified using MinElute columns (Qiagen). A-tailing was done with 1X NEBuffer 2 (New England Biolabs), 0.2 mM dATP, and 15 U Klenow exo (New England Biolabs), for 30 min at 37°C before inactivation for 20 min at 65°C, and DNA again purified using MinElute columns (Qiagen). Sequencing adapters were ligated with 0.5 mM custom-made adapters, 2.106 U T4 DNA ligase, and 1X T4 DNA ligase buffer, for 2 hours at RT, followed by inactivation for 20 min at 65°C. DNA fragments were purified in a size from 400 to 900 bp using a PippinPrep apparatus (SAGE Science). Each library was amplified in 12 cycles with 1X Phusion Buffer (ThermoFisher) , 0.2 mM dNTPs, 0.2 µM Illumina primers PE1.0 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3’) and PE2.0 (5’-CAAGCAGAAGACGGCATACGAGAT-3’), 3 µl of 3C library, and 1U of Taq Phusion polymerase (ThermoFisher; 98 °C 30 s, 12 cycles of 65°C 30 s, and 72°C 30 s, and 72°C for 7 min). The PCR reaction was purified using MinElute PCR purification kit (Qiagen), and libraries sequenced on an Illumina NextSeq500 with 75 bp paired-end reads.

value: bacterial cell culture

tag: group


title: T2D_MDM_2h +Mtb biol rep 2

description:
Library name: LS_31_T2D_MDM_2h +Mtb
LS_31_T2D_MDM_2h +Mtb

value: Blood

value: Monocyte-derived Macrophage


title: tumor 15N

description: surgically resected

value: N