title: KOC-7c, 72 hour suspension, replicate 2

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

description:
Library name: Sample 8
KOC7C_SPH_rep2

data_processing:
Galaxy Platform
Raw sequences were confirmed to be of high-quality by analyzing per base sequence quality, GC content, N content, overrepresented sequences and adapter content using FastQC. Reads were mapped to the human genome (hg38) using HISAT2 using default settings and read counts were annotated to genomic features using featureCounts with default settings and built-in gene annotation file.
Differential analysis was performed using limma, genes without more than 0.5 CPM in at least 2 samples are insignificant and filtered out.
TMM was the method used to normalize library sizes, eBayes was used with "robust" settings.
Assembly: hg38
Supplementary files format and content: limma normalized counts

growth_protocol: Briefly, cell lines were cultured in Dulbecco’s Modified Eagle medium/Ham’s F12 supplemented with 10% FBS. Cells lines were maintained as monolayer cultures grown at 37°C with a 5% CO2. Once cells reached 80-90% confluency, media was aspirated, cells were washed with Phosphate Buffered Saline (PBS) (Wisent, catalogue #311-425-CL), treated with tryp-sin/EDTA to induce detachment, and replated at 1:3 – 1:5 dilution.

extract_protocol:
To obtain RNA from cell lines grown as monolayer or in suspension the 105C and KOC-7c cell lines were grown for 3 days on either tissue culture plastic or ULA plates. On day 3, RNA was extracted and purified using RNEasy Kit (Qiagen, cat. 74106). Concentration and purity were measured using NanoDrop One Microvolume UV-Vis spectrophotometer (Thermo Scientific).
VAHTS Total RNA-Seq (H/M/R) Library Prep Kit for Illumina (PN NR603) from Vazyme Biotech Co. Ltd. was used to create indexed libraries which were sequenced using the Illumina NextSeq platform (150-bp; single-end reads).

treatment_protocol: To drive spheroid for-mation cells were seeded to Ultra-Low Attachment plates

value: Ovarian clear cell carcinoma

value: 72 hour suspension


title: d2 replicated, bmem, tbx21neg, mdln+other, d30, adt

status: Public on Jun 18 2025

type: SRA

city: Birmingham

first: Frances

last: Lund

state: AL

address: 1720 2nd Ave. South

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

description:
Library name: d2_mixed_adt
10X genomics, s11

library_source: other

data_processing:
GEX and ADT libraries were processed using Cellranger Count (v4.0.0) for matrix construction
VDJ libraries were processed using Cellranger (v4.0.0) and filtered_contig_fasta files were submitted to IMGT HighVQuest for VDJ call refinement.
processed data were imported into seurat and then merged
GEX were demultiplexed with Seurat(v4.3.0) HTODemux()
Assembly: mm10 + gene encoding ZsGreen
Supplementary files format and content: tab separated values and matrix files
Library strategy: CITE-seq

molecule: protein

organism: Mus musculus

source_name: lymph nodes

extract_protocol:
Memory B cells from lymph nodes of D30 influenza-infected mice were stained with NP tetramers, fluorophore-labeled Abs, and Abs conjugated with TotalSeq C oligomer hashtags and other protein targets. NP+ and Npneg Bmem cells (CD4negCD8negLIVE/DEADnegCD19+IgDnegGL-7negPNAnegCD138negCD93negCD38+NP-PE-OligonegNP-APCneg) cells were sort-purified.
Chromium Single Cell 5’ Library and Gel Bead Kit (Next GEM 5’ Kit v 2) as well as the Single Cell 5’ Feature Barcode Library Kit (10XGenomics) and mouse BCR amplification Library Kit (10XGenomics)

tag: tissue

value: lymph nodes

tag: cell line

tag: cell type

value: memory B cell

tag: genotype

tag: treatment

value: D30 post influenza infection


title: 18_CTX_Rotenone_B11

city: London

first: Maria

last: Tsalenchuk

address: Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Initial screening for sample anomalies was performed with FastQC (version 0.11.9). Adapter sequences were trimmed using Trim Galore! (version 0.6.7). For RNA-seq, FASTQ files were aligned, and transcripts were quantified using Salmon (version V1.10.0).
Assembly: Rn7
Supplementary files format and content: quant.sf files

molecule: total RNA

organism: Rattus norvegicus

source_name: cortex

extract_protocol:
Samples were homogenised in 1 mL of Trizol reagent (Thermofisher Scientific, Waltham, MA) and total RNA was extracted using the Life Technologies min-RNA purification kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were constructed using the 3’QuantSeq kit (Lexogen) with the following modifications. To enable the removal of PCR duplications, a custom oligo-dT primer was designed using a 12-bp unique molecular identifier.

treatment_protocol: Male Lewis rats aged 8-10 months received either rotenone at a dose of 2.8 mg/kg or a vehicle solution (Miglyol) administered intraperitoneally once daily for 21 days.24 hours after the final rotenone injection, rats were perfused using a saline-buffered solution. The cortex and SN were microdissected and immediately placed on dry ice

value: cortex

value: Rotenone


title: KOC-7c, 72 hour suspension, replicate 1

description:
Library name: Sample 7
KOC7C_SPH_rep1

organism: Homo sapiens

value: WT

tag: batch


title: H-R1

city: Dalian

first: Xiaofeng

last: Tian

address: Zhongshan Road NO.467

department: General Surgery

country: China

institute: The Second Hospital of Dalian Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath 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 genomic benchwork
Supplementary files format and content: The xls format file contains the FPKM value of gene in every sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).

value: intestinal epithelial cells

value: hypoxia/reoxygenation


title: d2 replicated, bmem, tbx21neg, mdln+other, d30, vdj

description:
Library name: d2_mixed_vdj
10X genomics, s3

library_source: transcriptomic single cell

data_processing:
GEX and ADT libraries were processed using Cellranger Count (v4.0.0) for matrix construction
VDJ libraries were processed using Cellranger (v4.0.0) and filtered_contig_fasta files were submitted to IMGT HighVQuest for VDJ call refinement.
processed data were imported into seurat and then merged
GEX were demultiplexed with Seurat(v4.3.0) HTODemux()
Assembly: mm10 + gene encoding ZsGreen
Supplementary files format and content: tab separated values and matrix files


title: TIL_285

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

description: CD3+ lymphocytes were isolated from a primary melanoma tumor

data_processing:
DNBseq-G400 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include gene ID and FPKM values for each sample

source_name: Skin melanoma

growth_protocol: Cells were cultured in 10% STF RPMI in a 37ºC and 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA purification kit from Macherey-Nagel
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: CD14+ monocytes were isolated from PBMCs of healthy donors. BLM and A375 melanoma cell lines were cocultured with these monocytes for 24h before negative selection with CD14 beads and RNA purification. Tumor cells and tumor-infiltrated lymphocytes were isolated from human skin melanoma.

value: Skin melanoma

value: CD14-CD3+ Tumor infiltrating lymphocytes


title: 3_CTX_Vehicle_A5

value: PBS


title: d2 replicated, bmem, tbx21neg, mdln+other, d30, gex

description:
Library name: d2_mixed_gex
10X genomics, s7


title: KOC-7c, 72 hour monolayer, replicate 2

description:
Library name: Sample 6
KOC7C_ML_rep2

value: 72 hour monolayer


title: TIL_279


title: 2_CTX_Vehicle_A3


title: Huvecs_control_2

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

description: Library name: PU01002

data_processing:
FASTQ files were generated with bcl2fastq (v2.19.1.403, Illumina).
Adapter trimming and quality filtering, including poly(A) tail removal and exclusion of reads containing ambiguous bases (N), were conducted using cutadapt (v1.15). Each sample initially yielded approximately 8 million reads; to ensure uniform sequencing depth across samples, all datasets were downsampled to 5 million reads.
Reads were aligned to the human reference genome GRCh38  with Gencode v29 annotations  using the STAR aligner (v2.6.1a).
Assembly: Reference genome GRCh38 with Gencode v29 annotations
Supplementary files format and content: raw_gene_counts_GeneSymbols_GeneTypes.tsv: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner; Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)

source_name: Umbilical Cord

growth_protocol: HUVECs were grown on gelatin pre-coated cell culture dishes in M199-based medium supplemented with 20% FBS, 0.4% endothelial cell growth supplement with heparin (ECGS/H), 2 mM L-glutamine, 0.1% penicillin, 0.1% streptomycin and 0.25 μg/mL fungizone in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using the PeqGOLD Total RNA kit (VWR) and stored at -80°C
Sequencing libraries were prepared from total RNA at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq FWD protocol (Lexogen). The optimal number of PCR amplification cycles was determined by quantitative PCR, according to the manufacturer's instructions. Library quality control was performed using the Agilent Bioanalyzer 2100 with the High Sensitivity DNA Kit to confirm the expected insert size. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (Invitrogen). Pooled libraries were sequenced on an Illumina NextSeq500 system in 1×75 bp single-end mode.

treatment_protocol: Replicative senescent HUVECs were generated by continuos passaging for more than 35 times in a 1:3 ratio. Irradiation-induced premature senescent HUVECs were created by exposure to 10 Gy of ionizing irradiation and subsequent 10 day recovery period. Control HUVECs were cells of early passage.

value: Umbilical Cord

value: HUVEC

value: Endothelial Cells

tag: Stage

value: control


title: d1 replicated, bmem, tbx21pos, mdln, d30, adt

description:
Library name: d1_mdlnpos_adt
10X genomics, s10


title: KOC-7c, 72 hour monolayer, replicate 1

description:
Library name: Sample 5
KOC7C_ML_rep1

value: Ovarian clear cell carcinoma


title: 4_CTX_Vehicle_A7


title: TIL_278


title: 19_CTX_Rotenone_B13


title: Huvecs_control_1

description: Library name: PU01001


title: 1_CTX_Vehicle_A1


title: TC_285

description: CD14-CD3- tumor cells were isolated from a primary melanoma tumor

value: CD14-CD3- Tumor cells


title: 105C, 72 hour suspension, replicate 2

description:
Library name: Sample 4
105C_SPH_rep2

value: 72 hour suspension


title: d1 replicated, bmem, tbx21pos, mdln, d30, vdj

description:
Library name: d1_mdlnpos_vdj
10X genomics, s2

value: lymph nodes

value: memory B cell

value: D30 post influenza infection


title: 17_CTX_Rotenone_B9

value: cortex

value: Rotenone


title: 105C, 72 hour suspension, replicate 1

description:
Library name: Sample 3
105C_SPH_rep1

value: WT


title: TC_279

value: Skin melanoma


title: 105C, 72 hour monolayer, replicate 2

description:
Library name: Sample 2
105C_ML_rep2


title: TC_278


title: d1 replicated, bmem, tbx21neg, mdln+other, d30, adt

description:
Library name: d1_mixed_adt
10X genomics, s9


title: 105C, 72 hour monolayer, replicate 1

description:
Library name: Sample 1
105C_ML_rep1


title: BLM_MoD135

description: Human melanoma BLM cell line cocultured for 24h with healthy donor monocytes

source_name: BLM

value: BLM

value: human melanoma

value: Coculture with healthy donor monocytes for 24h


title: 6_CTX_Vehicle_A11

value: PBS


title: 7_CTX_Vehicle_A13


title: d1 replicated, bmem, tbx21neg, mdln+other, d30, gex

description:
Library name: d1_mixed_gex
10X genomics, s5


title: kidney biopsy, NADIR_28

city: Bellinzona

first: Anna

last: Rinaldi

address: Zorzi

country: Switzerland

institute: EOC

data_processing:
The sequencing data were processed using CellRanger (version 6.0.0), with reads aligned to the human reference genome (GRCh38-2020).
The Cell Ranger cellranger count function output filtered gene–cell expression matrices, removing cell barcodes not represented in cells.
UMI count table utilizing both exonic and intronic reads was generated for downstream analysis.
Assembly: human reference genome (GRCh38-2020).
Supplementary files format and content: X_13.09.2024.RDS includes renal cells, a seurat object is provided for each sample
Supplementary files format and content: PTFig8_13.09.2024.RDS includes the subset of proximal tubular cells of all patients

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Frozen samples were cut into small pieces and transferred into a 2-ml Dounce homogenizer (Sigma, Cat#D8938) loaded with 1 ml of NEZ Lysis Buffer (Sigma, Cat#N3408) with RNase inhibitor (NEB, Cat#M0314) at final concentration of 0.4U/μl on ice. Samples were then Dounce homogenized on ice with five strokes of the looser pestle every 2 min for 8 min (25 strokes in total). Samples were then slowly Dounce homogenized 25 times with the tighter pestle on ice. The homogenized sample was filtered through a 40-μm Falcon Nylon Cell Strainer, then the filter was washed with 8 ml of 1% BSA PBS, and the nuclear suspension spin in a precooled (4°C) centrifuge at 650g for 8 min. Supernatant was removed, the pellet re-suspended in 2% BSA PBS with RNase inhibitor and nuclei from human biopsies further filtered by 20-μm and 10-μm strainers and moved to a low-bind Eppendorf tube. Nuclei from murine samples were sorted as DAPI and EDU positive on a BD Aria into 2% BSA solution with RNA inhibitor after 40um filtering. Nuclear quality and number were assessed with trypan blue staining.
Barcoded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions

value: kidney

tag: condition

value: proteinuric nephropathies


title: 20_CTX_Rotenone_B15


title: BLM_MoD134


title: kidney biopsy, NADIR_21


title: 10_CTX_Vehicle_A19


title: lead acetate-exposed mice with METTL3 cKO, B_3_(Ip)

city: Hefei

first: guo

middle: Xiao

last: Suo

address: No. 81 Meishan Road, Shushan District, Hefei City, Anhui Province

institute: anhui medical university

description: Library name: B_3_Ip_CleanData

data_processing:
Libraries were qualified using Agilent 2100 bioanalyzer and then subjected to 150-bp paired_x005F_x005f_x005f_x005F_x0002_end sequencing on an Illumina NovaSeq 6000 sequencer, and were controlled by Q30.  After 30 adaptor-trimming and removing low quality reads using cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4).
Paired-end reads were harvested and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome by STAR software. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS software.
Differentially binding sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.GO and Pathway enrichment analysis were performed by the differentially binding mRNA coding genes.
Assembly: hg19
Supplementary files format and content: some tabular files which contains information about called peaks and differential genes expression analysis
Supplementary files format and content: tab-delimited text files include different transcript for each group

source_name: renal tissue

growth_protocol: Mice with or without METTL3 cKO were were maintained under constant humidity and temperature at standard facilities under specific pathogen-free conditions with free access to water.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol, The quantity and integrity of RNA yield was assessed by using the K5500(Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. m6A antibody immunoprecipitation RNA was quality control with Qubit(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA).
mRNA was enriched from total RNA using the DynabeadsTM mRNA Purification Kit (Invitrogen) and then subjected to immunoprecipitation with the GenSeqTM m6A-IP Kit (GenSeq, China). RNA was randomly fragmented into 100–200 nt fragments using RNA fragmentation reagents, and protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4 °C for 4 h to obtain immunoprecipitated RNA fragments. Both the input and m6A IP samples were prepared for the next-generation sequencing.RNA libraries for IP and input samples were then generated with the NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: Mice with or without METTL3 cKO were induced with lead acetate.

value: renal tissue


title: lead acetate-exposed mice with METTL3 cKO, B_3_(Input)

description: Library name: B_3_Input_CleanData


title: d1 replicated, bmem, tbx21pos, mdln, d30, gex

description:
Library name: d1_mdlnpos_gex
10X genomics, s6


title: BLM_MoD133


title: BLM_GCSF_24h

description: Human melanoma BLM cell line stimulated with 500ng/ml of G-CSF for 24h

value: Control


title: lead acetate-exposed mice with METTL3 cKO, B_2_(Ip)

description: Library name: B_2_Ip_CleanData


title: kidney biopsy, NADIR_20


title: 11_CTX_Rotenone_A21


title: kidney biopsy, NADIR_17


title: A375_MoD135

description: Human melanoma A375 cell line cocultured for 24h with healthy donor monocytes


title: 14_VM_Rotenone

source_name: ventral midbrain

value: ventral midbrain


title: kidney biopsy, NADIR_13


title: A375_MoD134


title: kidney biopsy, NADIR_08


title: d1 replicated, bmem, tbx21neg, mdln+other, d30, vdj

description:
Library name: d1_mixed_vdj
10X genomics, s1


title: A375

description: Human melanoma A375 cell line


title: 2_VM_Vehicle


title: 8_VM_Vehicle


title: 9_VM_Vehicle


title: lead acetate-exposed mice with METTL3 cKO, B_1_(Input)

description: Library name: B_1_Input_CleanData


title: ChIP p63 FaDu

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

country: Italy

institute: University of Rome "Tor Vergata"

description: ChIP antibody: : anti-ΔNp63α (D2K8X, Rabbit mAb #13109, CellSignaling)

library_source: genomic

data_processing:
The libraries were sequenced using the NextSeq 500 system from Illumina, CA. Reads were quality controlled with FastQC v0.11.9 and aligned to the human hg19 reference using bowtie v2.3.4.3 The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools v1.7 p63 and ZNF148 peaks were called with MACS2 v2.2.6 (command-line parameters: -callpeak -B --SPMR --call-summits -q 0.001 -g hs) using matched input DNA as a control. QC statistics of the whole workflow were obtained with multiqc v1.12 Assembly: hg19 Supplementary files format and content: bigwig and narrow peaks (excluded input samples)
Assembly: hg19
Supplementary files format and content: bigwig and narrow peaks

molecule: genomic DNA

source_name: FaDu

growth_protocol: FaDu cells, a pharyngeal squamous cell carcinoma cell line, were obtained from ATCC and were cultured in Eagle’s Minimum Essential Medium (EMEM, Corning 10-009-CV).

extract_protocol:
DNA fragments from three independent ChIP assays were purified with QIAquick PCR Purification Kit (QIAGEN #28106).
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

value: FaDu

value: Pharyngeal squamous cell carcinoma

value: untreated


title: ChIP ZNF148 FaDu

description: ChIP antibody: anti-ZNF148 (ab227076, Abcam)


title: lead acetate-exposed mice, A_3_(Ip)

description: Library name: A_3_Ip_CleanData

value: lead acetate-exposed mice


title: RIB40, Vanillin treated, 24h, rep3

city: Espoo

first: Miika-Erik

last: Korpioja

address: Tekniikantie 21

country: Finland

institute: VTT Technical Research Centre of Finland

description:
Library name: RNA_S8825Nr95
Van_24h_3

data_processing:
RNA-seq data were analyzed using the bioinformatic toolbox at the Chipster virtual interface at the IT Center for Science (CSC), Finland. Adapters were trimmed with Skewer (version 0.2.2) and low-quality sequencing reads were trimmed using Trimmomatic (version 0.33). The quality of the sequencing data was checked using FastQC. Trimmed paired-end sequencing reads were mapped to the A. oryzae RIB40 genome retrieved with GFF from EmsemblFungi. using HISAT2 (version 2.2.1). BAM files were used as input files to quantify the number of short reads with HTSeq (version 0.6.1), which resulted in the aligned read counts for all sequenced gene transcripts. Differential expression analysis was performed using DESeq2 (version 1.26.0).
Assembly: NITE Aspergillus oryzae RIB40
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Aspergillus oryzae

source_name: mycelia

growth_protocol: Aspergillus oryzae RIB40 was grown in 250 mL shake flasks with Czapek-Dox with 2 % D-fructose.

extract_protocol:
Total RNA was extracted from mycelia using TRIzol (Thermo Fisher Scientific) according to manufacturer’s instructions with small modifications. Mycelium samples were ground using cooled mortars under liquid nitrogen into fine powder and about 50 µL of powder was transferred into a 2 mL tube, after which 1 mL of TRIzol was immediately added. Mixture was vortexed and incubated at room temperature for 5 minutes, after which it was centrifuged (12000 x g, 4 °C, 10 minutes) and the supernatant was transferred to a new tube. After this, the protocol was continued according to manufacturer’s instructions. RNA was then purified using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions.
After purification samples were sent for RNA sequencing, that was performed by CeGaT GmbH (Tübingen, Germany) using the Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA). Library was prepared with TruSeq Stranded mRNA (Illumina) kit.

treatment_protocol: Mycelia was harvested on Miracloth and washed with Czapek-Dox. Equal portions of mycelia were transferred to flasks containing 50 mL Czapek-Dox with 2 % D-fructose and the selected inhibitors.

value: mycelia

value: Vanillin (Van)

tag: strain

tag: time

tag: concentration


title: lead acetate-exposed mice with METTL3 cKO, B_2_(Input)

description: Library name: B_2_Input_CleanData


title: lead acetate-exposed mice, A_2_(Ip)

description: Library name: A_2_Ip_CleanData


title: 1_VM_Vehicle


title: RIB40, Vanillin treated, 24h, rep1

description:
Library name: RNA_S8825Nr93
Van_24h_1

value: WT


title: NZ-P3

city: Xuzhou

first: Dianshuang

last: Zhou

state: Jiangsu

address: 209 Tongshan Road

institute: Xuzhou Medical University

data_processing:
Sequencing quality is examined by FastQC, and trimmed reads (pass Illumina quality filter, trimmed 5', 3’-adaptor bases by cutadapt) are aligned, allowing for one mismatch only to miRNA reference sequences with miRDeep2. The abundance of miRNAs is evaluated using their sequencing counts and is normalized as counts per million (CPM) of total aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes cpm for each Sample

source_name: plasma

extract_protocol:
Total RNA was extracted from exosomes using the Total Exosome RNA & Protein Isolation Kit (Invitrogen, Cat. No: 4478545, USA). The "Isolate RNA–Purify the RNA" part was performed according to the manufacturer's instructions. Before the sequencing experiment, agarose electrophoresis was used to check the integrality of total RNA samples. Then the samples were quantified on the NanoDrop ND-1000 instrument (Thermo Fisher Scientific, USA).
Library preparation for small RNAs was performed with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, Cat. No: E7300, USA). The main procedures are as follows: total RNA samples were first pretreated as follows to remove some RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged) deacylation to 3’-OH for 3' adaptor ligation, 3’-cP (2', 3’-cyclic phosphate) removal to 3’-OH for 3' adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. After the pretreatment, 3’-adapter ligation, 5’-adapter ligation, cDNA synthesis, and PCR amplification were sequentially carried out. Then, ∼134-160bp PCR amplified fragments (corresponding to ∼14-40nt small RNAs) were selected. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument.

value: plasma

value: normal


title: lead acetate-exposed mice, A_2_(Input)

description: Library name: A_2_Input_CleanData


title: lead acetate-exposed mice with METTL3 cKO, B_1_(Ip)

description: Library name: B_1_Ip_CleanData


title: 16_VM_Rotenone

value: Rotenone


title: A375(MoD133)

value: human melanoma

value: Coculture with healthy donor monocytes for 24h


title: NZ-P2


title: lead acetate-exposed mice, A_3_(Input)

description: Library name: A_3_Input_CleanData


title: Input FADU

description: ChIP antibody: none


title: 18_VM_Rotenone


title: RIB40, Levulinic acid treated, 24h, rep3

description:
Library name: RNA_S8825Nr92
LA_24h_3

value: Levulinic acid (LA)


title: RIB40, Levulinic acid treated, 24h, rep2

description:
Library name: RNA_S8825Nr91
LA_24h_2


title: lead acetate-exposed mice, A_1_(Ip)

description: Library name: A_1_Ip_CleanData


title: NZ-P1


title: 7_VM_Vehicle

value: PBS


title: OA-X8

value: obstructive azoospermia


title: lead acetate-exposed mice, A_1_(Input)

description: Library name: A_1_Input_CleanData

value: renal tissue


title: Mouse Heart, LPS

city: xiamen

first: XiaoQiang

last: Chen

address: 2999 Jinshan Road,Huli District,Xiamen,Fujian Province

institute: Xiamen Cardiovascular Hospital, Xiamen University School of Medicine

description:
Library name: Sample2
MobiCube Single-Cell 3' RNA-seq

data_processing:
The MobiVision software pipeline (version 2.1) was provided by MobiDrop. Subsequently, the unique molecular identifier (UMI) count matrix was processed using the R package Seurat (version 4.4)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
The fresh mouse heart tissues were quick-frozen in liquid nitrogen for 1 h upon receipt of samples and stored in a refrigerator at -80 °C. We used the Nuclei Isolation Kit (BioYou) to prepare nuclei suspension. Nuclei were counted using Countess II.Automated Cell Counter and concentration adjusted to 700-1200 nuclei/μL.
Single-cell (nucleus) suspensions were loaded into the MobiNova-100 platform.The MobiCube Single-Cell 3′ RNA-seq Kit v1.0 (MobiDrop) was used to prepare the library, which was subsequently sequenced using Illumina NovaSeq 6000 Systems.

treatment_protocol: We administered lipopolysaccharide (LPS, 10 mg/kg) or saline to mice via intraperitoneal injection to establish a septic cardiomyopathy model, and collected the hearts 18 hours post-administration.

value: Heart

tag: age

value: 8 weeks old

tag: Sex

value: male

value: lipopolysaccharide


title: RIB40, HMF treated, 24h, rep3

description:
Library name: RNA_S8825Nr89
HMF_24h_3

value: Hydroxymethylfurfural (HMF)


title: RIB40, Levulinic acid treated, 24h, rep1

description:
Library name: RNA_S8825Nr90
LA_24h_1

value: mycelia


title: OA-X4


title: Mouse Heart, NC

description:
Library name: Sample1
MobiCube Single-Cell 3' RNA-seq

value: saline


title: RIB40, Vanillin treated, 24h, rep2

description:
Library name: RNA_S8825Nr94
Van_24h_2

value: WT

value: Vanillin (Van)


title: 4_VM_Vehicle

value: ventral midbrain


title: RIB40, HMF treated, 24h, rep1

description:
Library name: RNA_S8825Nr87
HMF_24h_1


title: RIB40, HMF treated, 24h, rep2

description:
Library name: RNA_S8825Nr88
HMF_24h_2


title: 15_VM_Rotenone

value: Rotenone


title: NOA-X6

value: plasma

value: Non obstructive azoospermia


title: 11_VM_Rotenone


title: RIB40, Furfural treated, 24h, rep3

description:
Library name: RNA_S8825Nr86
FF_24h_3

value: Furfural (FF)


title: NOA-X9


title: HCC_N, scRNA-seq

city: Guangzhou

first: Xue-Jia

last: Lin

state: Guangdong

address: Xin Gang Xi Road 135#

institute: Sun Yat-sen University

description:
Library name: Sample3
liver paracancerous tissues from HCC mice

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: liver paracancerous tissues

extract_protocol:
Tissues were finely minced and subjected to enzymatic digestion at 37°C for 30 minutes with gentle shaking at 200 rpm in a digestion buffer. After digestion, cell suspensions were filtered through a 100 μm cell strainer and subsequently washed with 1× phosphate-buffered saline (PBS) containing 2% FBS and 2 mM EDTA. The washed cell suspensions from liver/tumor were further applied for immunocyte purification by using 35% Percoll. Red blood cells were removed by Red Cell lysis buffer. Afterwards, the cells were then stained with fluorochrome-conjugated surface antibodies in 1× PBS containing 2 mM EDTA. Viable cells were identified by using Live/Dead Fixable Viability Dye. Cell sorting from mouse liver/tumor tissues was performed on BD FACSAria, and the viable CD45+ cells (immunocytes) were sorted for scRNA-seq.
Libraries were prepared with Chromium Next GEM Single cell 3’ Reagent v3.1 Kits according to the manufacturer's protocol.

value: liver paracancerous tissues

value: immune cells


title: 20_VM_Rotenone


title: NOA-X2


title: MASH, scRNA-seq

description:
Library name: Sample2
liver tissues from MASH mice

source_name: liver tissues

value: liver tissues


title: RIB40, Furfural treated, 24h, rep2

description:
Library name: RNA_S8825Nr85
FF_24h_2


title: total RNA, CAG

city: Ithaca

first: Andrew

middle: William

last: Grimson

state: NY

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
A custom python script was used to count barcodes in all libraries. The barcode sequence was extracted from the constant region of reads and each barcode was counted.
Barcode count tables were imported into R, each barcode was linked to its cognate 3′UTR, and normalized for library depth (counts per million, CPM).
Assembly: Not applicable
Supplementary files format and content: A count matrix with barcode counts for 3′UTR is included (utrome_barcode_counts.tsv). The first column is "position," which specifies the 3′UTR and its position (plate and well) within the cloned library, and the second column is "barcode" which specifies the 12 nt barcode for that 3′UTR. The remaining 81 columns correspond to the 81 samples.
Library strategy: Barcode amplicon sequencing

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
For barcode libraries derived from RNA, Trizol was used for extraction. Genomic DNA was extracted using the Qiagen Gentra Puregene Cell DNA Extraction Kit. For polysome libraries, cells were treated with 100 μg/mL cycloheximide and lysed. The lysate was run over a 15 45% (w/v) sucrose gradient to separate polysomes. RNA was extracted from each fraction.
For RNA libraries and RNA extracted from polysome fractions, cDNA was generated using RevertAid Reverse Transcriptase and RT primer 5′CTCCACTTTGTACAAGAAAG. The cDNA was purified and concentrated with the Zymo DNA Clean & Concentrator Kit and all was used as template in PCRI. For DNA libraries, all genomic DNA was used in PCRI. For both assays, three PCR cycles were performed with ExTaq polymerase (primers 5′GTCAACCACCGCGGTCTC and 5′ACGACGCTCTTCCGATCTNNNNNNNNNNcactttgtacaagaaagttgaacg). Reactions were then purified with SPRIselect beads (Beckman Coulter) using a 0.7x one sided size selection protocol and used in PCRII (primers 5′CGTGTGCTCTTCCGATCTcgaccactaccagcagaaca and 5′ACACTCTTTCCCTACACGACGCTCTTCCGATCT), which was then purified with SPRIselect beads using a 0.6x to 1.2x two sided size selection protocol. A portion of this reaction was used for a final (PCRIII) reaction to add Illumina-compatible sequences (index primers from the NEBNext Multiplex Oligos for Illumina Kit). The final libraries were purified and concentrated with SPRIselect beads using a 0.5x to 1x two sided size selection protocol, quantified and submitted for Illumina sequencing.

value: CAG landing pad


title: NC, scRNA-seq

description:
Library name: Sample1
normal liver tissues from 8-week-old mice


title: 10_VM_Vehicle

value: PBS


title: 3_VM_Vehicle


title: 17_VM_Rotenone


title: RIB40, Furfural treated, 24h, rep1

description:
Library name: RNA_S8825Nr84
FF_24h_1


title: OA-X5

value: obstructive azoospermia


title: iWAT, HFD, male, LFABP-/-, rep2

city: Newark

first: Adriana

last: Messyasz

address: 185 South Orange Avenue

institute: Rutgers-New Jersey Medical School

description: G3OLF_M59iWAT_S17_R1_001 (GE) - RPKM

data_processing:
CLC Genomics Workbench v 20.0.4
Low quality bases were trimmed and remaining reads were mapped to GRCm38 (ENSEMBLE release.92)
Aligned reads were obtain using the default settings of the RNA-Seq Analysis Tool of the CLC Genomics Workbench.
Statistical analysis of differentially expressed genes was carried out based on a negative binomial model tool in the CLC Genomic Workbench
Assembly: Mus musculus GRCm38
Supplementary files format and content: Tab-delimited text file with RPKM normalized counts of sequencing reads for genes from each sample. Includes gene names, chromosome coordinates, and Ensembl gene IDs

source_name: iWAT

growth_protocol: Mice were maintained on a 12-h light/dark cycle and had unrestricted access to standard rodent chow. At 2 months of age, male LFABP-/-, and WT mice were housed 2-3 per cage and fed a 45 kcal % fat diet high in saturated fat (D10080402, Research Diets, Inc., New Brunswick, NJ) for 12 weeks. At the end of the HF feeding, mice were food deprived for 4 hours and anesthetized with ketamine/xylazine/acepromazine (80:100:150 mg/kg, intraperitoneally, respectively), prior to collection of blood and tissues.

extract_protocol:
At the end of the feeding period, mice were food deprived for 4 hours and anesthetized with ketamine/xylazine/acepromazine (80:100:150 mg/kg, intraperitoneally, respectively), and tissues collected. Mice were euthanized under anesthesia. Inguinal white and interscapular brown adipose tissue (iWAT and iBAT, respectively) depots and the liver from mice fasted for 4h were treated with RNAlaterTM stabilization solution (InvitrogenTM, Thermo Fisher Scientific, Waltham, MA) upon excision before snap freezing in liquid nitrogen (N2) and storage at -80oC. Total mRNA was extracted from iWAT and iBAT depots and the liver using the PureLinkTM RNA Mini Kit (InvitrogenTM, Thermo Fisher Scientific, Waltham, MA). All tissue samples were first homogenized using TRIzolTM reagent (InvitrogenTM, Thermo Fisher Scientific, Waltham, MA) for total RNA isolation. RNA abundance and quality were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
Total cellular mRNA extracts derived from the iWAT of WT and LFABP-/- mice were submitted for RNA-Sequencing (RNA-Seq) analysis to Rutgers Genomics Center (Rutgers University, Newark, NJ). RNA quality was first checked for integrity using an Agilent 2200 TapeStation (Agilent Technologies); samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). Illumina compatible RNA-seq library was prepared using a NEB next ultra RNA-seq library preparation kit. The cDNA libraries were purified using AmpureXP beads and quantified on an Agilent TapeStation and Qubit 4 Fluorometer (Thermo Fisher Scientific). An equimolar amount of barcoded libraries was pooled and sequenced on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA) using the 1X100 cycles configuration.

value: iWAT

value: male

value: LFABP-/-


title: total genomic DNA, CAG


title: 13_VM_Rotenone


title: 6_VM_Vehicle


title: unsorted, genomic DNA, CAG


title: iBAT, HFD, male, WT, rep5

description: G32WT_M89iBAT_S10_R1_001 (GE) - RPKM

source_name: iBAT

treatment_protocol: At 2 months of age, male LFABP-/-, and WT mice were housed 2-3 per cage and fed a 45 kcal % fat diet high in saturated fat (D10080402, Research Diets, Inc., New Brunswick, NJ) for 12 weeks.

value: iBAT


title: HCC_T, scRNA-seq

description:
Library name: Sample4
liver tumor tissues from HCC mice

source_name: liver tumor tissues

value: liver tumor tissues

value: WT


title: Liver, HFD, male, WT, rep5

description: G32WT_M89Liver_S15_R1_001 (GE) - RPKM

source_name: Liver

value: Liver

value: 45 kcal % fat diet high in saturated fat (D10080402, Research Diets, Inc., New Brunswick, NJ) for 12 weeks


title: 19_VM_Rotenone

value: ventral midbrain

value: Rotenone


title: sorted GFP bin, 0-100, CAG


title: 12_VM_Rotenone


title: RIB40, Ferulic acid treated, 24h, rep1

description:
Library name: RNA_S8825Nr81
FA_24h_1

value: mycelia

value: Ferulic acid (FA)


title: Liver, HFD, male, WT, rep4

description: G32WT_M88Liver_S14_R1_001 (GE) - RPKM


title: sorted GFP bin, 90-100, CAG


title: RIB40, Control, 24h, rep4

description:
Library name: RNA_S8825Nr80
CTRL_24h_4


title: iBAT, HFD, male, WT, rep4

description: G32WT_M88iBAT_S9_R1_001 (GE) - RPKM


title: sorted GFP bin, 70-80, CAG


title: RIB40, Control, 24h, rep3

description:
Library name: RNA_S8825Nr79
CTRL_24h_3


title: 5_VM_Vehicle


title: sorted GFP bin, 40-60, CAG


title: RIB40, Ferulic acid treated, 24h, rep3

description:
Library name: RNA_S8825Nr83
FA_24h_3


title: RIB40, Control, 24h, rep2

description:
Library name: RNA_S8825Nr78
CTRL_24h_2


title: sorted GFP bin, 20-30, CAG


title: iBAT, HFD, male, LFABP-/-, rep5

description: G32OLF_M64iBAT_S25_R1_001 (GE) - RPKM


title: sorted GFP bin, 0-10, CAG


title: iWAT, HFD, male, LFABP-/-, rep5

description: G32OLF_M64iWAT_S20_R1_001 (GE) - RPKM


title: RIB40, Ferulic acid treated, 24h, rep2

description:
Library name: RNA_S8825Nr82
FA_24h_2


title: Liver, HFD, male, LFABP-/-, rep4

description: G32OLF_M63Liver_S29_R1_001 (GE) - RPKM


title: RIB40, Vanillin treated, 5h, rep2

description:
Library name: RNA_S8825Nr75
Van_5h_2

value: Vanillin (Van)


title: total RNA, PGK

value: PGK landing pad


title: iWAT, HFD, male, LFABP-/-, rep4

description: G32OLF_M63iWAT_S19_R1_001 (GE) - RPKM


title: total genomic DNA, PGK


title: RIB40, Vanillin treated, 5h, rep1

description:
Library name: RNA_S8825Nr74
Van_5h_1


title: iBAT, HFD, male, LFABP-/-, rep4

description: G32OLF_M63iBAT_S24_R1_001 (GE) - RPKM


title: RIB40, HMF treated, 5h, rep3

description:
Library name: RNA_S8825Nr70
HMF_5h_3

value: Hydroxymethylfurfural (HMF)


title: unsorted, genomic DNA, PGK


title: Liver, HFD, male, LFABP-/-, rep5

description: G32OLF_M64Liver_S30_R1_001 (GE) - RPKM


title: Liver, HFD, male, LFABP-/-, rep3

description: G32OLF_M62Liver_S28_R1_001 (GE) - RPKM


title: RIB40, Control, 24h, rep1

description:
Library name: RNA_S8825Nr77
CTRL_24h_1


title: sorted GFP bin, 90-100, PGK


title: RIB40, HMF treated, 5h, rep2

description:
Library name: RNA_S8825Nr69
HMF_5h_2


title: iWAT, HFD, male, LFABP-/-, rep3

description: G32OLF_M62iWAT_S18_R1_001 (GE) - RPKM


title: sorted GFP bin, 70-80, PGK


title: RIB40, Vanillin treated, 5h, rep3

description:
Library name: RNA_S8825Nr76
Van_5h_3


title: PBMC_OLD_RM211-15_male_Tp 1

type: genomic

city: Pittsburgh

middle: J

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Macaca mulatta

source_name: PBMC

label_protocol: Standard Illumina Protocol, Cy3 and Cy5

extract_protocol: AllPrep DNA/RNA (Qiagen)

tag: gender

tag: dpi

tag: age day


title: RIB40, HMF treated, 5h, rep1

description:
Library name: RNA_S8825Nr68
HMF_5h_1


title: PBMC_OLD_RM211-15_male_Tp 2


title: iBAT, HFD, male, LFABP-/-, rep3

description: G32OLF_M62iBAT_S23_R1_001 (GE) - RPKM


title: RIB40, Furfural treated, 5h, rep3

description:
Library name: RNA_S8825Nr67
FF_5h_3

value: Furfural (FF)


title: sorted GFP bin, 40-60, PGK


title: PBMC_YOUNG_RM241-15_male_Tp 4


title: PBMC_YOUNG_RM243-15_female_Tp 2

value: female


title: iWAT, HFD, male, WT, rep5

description: G30WT_M89iWAT_S5_R1_001 (GE) - RPKM

value: iWAT


title: PBMC_YOUNG_RM243-15_female_Tp 3


title: PBMC_OLD_RM211-15_male_Tp 3

value: male


title: PBMC_OLD_RM213-15_female_Tp 4


title: sorted GFP bin, 20-30, PGK


title: RIB40, Furfural treated, 5h, rep2

description:
Library name: RNA_S8825Nr66
FF_5h_2


title: PBMC_YOUNG_RM243-15_female_Tp 1


title: PBMC_YOUNG_RM241-15_male_Tp 3


title: iWAT, HFD, male, WT, rep4

description: G30WT_M88iWAT_S4_R1_001 (GE) - RPKM


title: sorted GFP bin, 0-10, PGK


title: RIB40, Furfural treated, 5h, rep1

description:
Library name: RNA_S8825Nr65
FF_5h_1


title: Liver, HFD, male, WT, rep3

description: G30WT_M85Liver_S13_R1_001 (GE) - RPKM


title: PBMC_OLD_RM213-15_female_Tp 3


title: polysome, fraction 20, rep2, pilot

value: Tet-On landing pad


title: iWAT, HFD, male, WT, rep3

description: G30WT_M85iWAT_S3_R1_001 (GE) - RPKM


title: RIB40, Control, 5h, rep4

description:
Library name: RNA_S8825Nr61
CTRL_5h_4


title: polysome, fraction 18, rep2, pilot


title: iBAT, HFD, male, WT, rep3

description: G30WT_M85iBAT_S8_R1_001 (GE) - RPKM

value: iBAT


title: RIB40, Control, 5h, rep3

description:
Library name: RNA_S8825Nr60
CTRL_5h_3


title: polysome, fraction 15, rep2, pilot


title: RIB40, Control, 5h, rep2

description:
Library name: RNA_S8825Nr59
CTRL_5h_2


title: PBMC_OLD_RM213-15_female_Tp 2


title: Liver, HFD, male, WT, rep2

description: G30WT_M84Liver_S12_R1_001 (GE) - RPKM


title: PBMC_YOUNG_RM241-15_male_Tp 1


title: PBMC_YOUNG_RM241-15_male_Tp 2


title: polysome, fraction 12, rep2, pilot


title: RIB40, Control, 5h, rep1

description:
Library name: RNA_S8825Nr58
CTRL_5h_1


title: PBMC_OLD_RM213-15_female_Tp 1


title: polysome, fraction 8, rep2, pilot


title: RIB40, Vanillin treated, 3h, rep3

description:
Library name: RNA_S8825Nr57
Van_3h_3


title: polysome, cytoplasmic fraction, rep2, pilot


title: iWAT, HFD, male, WT, rep2

description: G30WT_M84iWAT_S2_R1_001 (GE) - RPKM


title: Liver, HFD, male, WT, rep1

description: G30WT_M83Liver_S11_R1_001 (GE) - RPKM


title: PBMC_YOUNG_RM242-15_male_Tp 4


title: iWAT, HFD, male, WT, rep1

description: G30WT_M83iWAT_S1_R1_001 (GE) - RPKM


title: polysome, fraction 18, rep1, pilot


title: RIB40, Vanillin treated, 3h, rep1

description:
Library name: RNA_S8825Nr55
Van_3h_1


title: iBAT, HFD, male, WT, rep1

description: G30WT_M83iBAT_S6_R1_001 (GE) - RPKM


title: PBMC_OLD_RM237-15_female_Tp 4


title: polysome, fraction 16, rep1, pilot


title: PBMC_YOUNG_RM242-15_male_Tp 3


title: RIB40, HMF treated, 3h, rep3

description:
Library name: RNA_S8825Nr51
HMF_3h_3


title: iBAT, HFD, male, WT, rep2

description: G30W_M84iBAT_S7_R1_001 (GE) - RPKM


title: polysome, fraction 13, rep1, pilot


title: PBMC_YOUNG_RM242-15_male_Tp 2


title: RIB40, HMF treated, 3h, rep1

description:
Library name: RNA_S8825Nr49
HMF_3h_1


title: Liver, HFD, male, LFABP-/-, rep2

description: G30OLF_M59Liver_S27_R1_001 (GE) - RPKM

value: LFABP-/-


title: PBMC_OLD_RM176-10_female_Tp 3


title: polysome, fraction 10, rep1, pilot


title: iBAT, HFD, male, LFABP-/-, rep2

description: G30OLF_M59iBAT_S22_R1_001 (GE) - RPKM


title: RIB40, Furfural treated, 3h, rep3

description:
Library name: RNA_S8825Nr48
FF_3h_3

value: WT


title: RIB40, Vanillin treated, 3h, rep2

description:
Library name: RNA_S8825Nr56
Van_3h_2


title: polysome, fraction 6, rep1, pilot


title: PBMC_YOUNG_RM242-15_male_Tp 1


title: PBMC_OLD_RM176-10_female_Tp 2


title: RIB40, Furfural treated, 3h, rep2

description:
Library name: RNA_S8825Nr47
FF_3h_2


title: Liver, HFD, male, LFABP-/-, rep1

description: G30OLF_M56Liver_S26_R1_001 (GE) - RPKM

value: Liver


title: total RNA, rep3, pilot


title: iBAT, HFD, male, LFABP-/-, rep1

description: G30OLF_M56iBAT_S21_R1_001 (GE) - RPKM

value: 45 kcal % fat diet high in saturated fat (D10080402, Research Diets, Inc., New Brunswick, NJ) for 12 weeks


title: RIB40, Furfural treated, 3h, rep1

description:
Library name: RNA_S8825Nr46
FF_3h_1


title: iWAT, HFD, male, LFABP-/-, rep1

description: G30OLF_M56iWAT_S16_R1_001 (GE) - RPKM


title: RIB40, HMF treated, 3h, rep2

description:
Library name: RNA_S8825Nr50
HMF_3h_2


title: total RNA, rep2, pilot


title: RIB40, Control, 3h, rep4

description:
Library name: RNA_S8825Nr42
CTRL_3h_4


title: RIB40, Control, 3h, rep3

description:
Library name: RNA_S8825Nr41
CTRL_3h_3


title: PBMC_OLD_RM176-10_female_Tp 4


title: total RNA, rep1, pilot


title: PBMC_OLD_RM176-10_female_Tp 1


title: PBMC_YOUNG_RM245-15_female_Tp 3


title: FAC-sorted cells, DNMT1 knockout, rep 2

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Neuroepigenetics

country: Germany

institute: RWTH Aachen University

data_processing:
FASTQ files were generated using bcl2fastq (Illumina, U.S.A.). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/rnaseq pipeline version 3.1210 implemented in Nextflow 23.10.011 with the minimal command. In brief, lane-level reads were trimmed using Trim Galore 0.6.712 and aligned to the mouse genome (GRCm39) using STAR 2.7.9a13. Gene-level and transcript-level quantification was done by Salmon v1.10.114. All analysis was performed using custom scripts in R version 4.3.2 using the DESeq2 v.1.32.0 framework15.
Assembly: GRCm39
Supplementary files format and content: Comma-separated table listing the normalized counts of detected genes per sample

source_name: Basal telencephalon

extract_protocol:
The basal telencephalons  were collected in cold HBSS (w/ phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose; 4 µg/µL (600 U) of DNAse I (AppliChem GmbH, Germany). After treatment with 0.04% trypsin for 17 min at 37 °C, HBSS was replaced by DMEM with additional L-glutamine and 4.5 g/L D-glucose, 10% FBS and 1% P/S to stop the trypsinization. Subsequently, the cells were pelletized, resuspended and triturated in cold HBSS (w/o phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose, before being filtered through a nylon gauze (pore size 140 µm, Merck, U.S.A.) for FACS. Respective parameters for the procedure using a BD FACS Aria Fusion (BD Biosciences, U.S.A) were defined as follows: 5-laser (FCS, SSC, PE, BV421), 18-color (3-6-2-4-3). TdTomato-positive cells were collected in 100 µL of cold TRIzol™ (Thermo Fisher Scientific, U.S.A.) for subsequent RNA sequencing. Samples were mixed by inversion and stored at -80°C until processing. RNA was isolated from 50,000 cells pooled per genotype. The samples were filled up to 1 ml with TRIzol™ and dounced 25 times in a glass homogenizer using the small-clearance pestle. Samples were incubated for 5 min at room temperature, supplemented with 200 µL chloroform and mixed by shaking vigorously until a homogenous milky solution appeared. Following another incubation at room temperature (until a visible phase separation appeared) samples were centrifuged at 13,000x g and 4°C for 15 min in a tabletop centrifuge with cooling function. For precipitation, the clear upper phase was collected and mixed with 70% ethanol. Samples were bound onto RNeasy mini columns (Qiagen, Germany) and washed according to the instructions in the manual. RNA was eluted with 30 µL nuclease-free water.
Prior to library preparation, samples were digested with HL dsDNAseI (ArcticZymes Technologies ASA, Norway) for 10 min at 37°C to remove traces of gDNA. To avoid a digestion of the newly generated cDNA during library preparation, the dsDNAseI was heat inactivated for 5 min at 58°C. Thereafter, samples were subjected to library preparation using the TAKARA SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian for Illumina (Takara Bio, Japan). Fragmentation was done at 94°C for 4 min. Illumina adaptors and indices were ligated to cDNA in a PCR reaction with 5 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). RRNA depletion was performed on the amplified libraries. Final libraries were subjected to an upscale PCR with 13 cycles (98°C for 15 s, 55°C for 15 s and 68°C for 30 s). Amplified libraries were cleaned with magnetic AMPure XP beads (Beckman Coulter, U.S.A.). Library concentration was determined with a Qubit™ 4 fluorometer using the 1x dsDNA HS reagent (Thermo Fisher Scientific, U.S.A.). Library size was assessed on a Tape Station 4200 using the DNA D1000 kit (Agilent Technologies, U.S.A.). Libraries were diluted, equimolarly pooled, denatured, and loaded for clustering onto an Illumina NovaSeq 6000 SP (200 cycles) flow cell (Illumina, U.S.A.) in conjunction with 1% PhiX control library, and run on an Illumina NovaSeq machine (Illumina, U.S.A.) in 75 bp paired-end mode. The 1% PhiX control library was spiked in to improve base calling accuracy.

value: Basal telencephalon

tag: developmental stage

value: Sst interneuron

value: Sst-Cre/tdTomato/Dnmt1 loxP2


title: PBMC_YOUNG_RM245-15_female_Tp 4


title: FAC-sorted cells, DNMT1 knockout, rep 1

tag: tissue


title: total genomic DNA, rep2, pilot

tag: cell line


title: polysome, cytoplasmic fraction, rep1, pilot


title: FAC-sorted cells, DNMT1 control, rep 2

tag: cell type

value: Sst-Cre/tdTomato


title: RIB40, Control, 3h, rep1

description:
Library name: RNA_S8825Nr39
CTRL_3h_1

value: mycelia

tag: genotype


title: RIB40, Control, 3h, rep2

description:
Library name: RNA_S8825Nr40
CTRL_3h_2


title: total genomic DNA, rep1, pilot


title: PBMC_OLD_RM237-15_female_Tp 3


title: Spleen_OLD_RM213-15_female_Nx

source_name: Spleen

extract_protocol: Tri Reagent (Sigma-Aldrich) with column purification (Zymo)


title: RIB40, Vanillin treated, 1h, rep3

description:
Library name: RNA_S8825Nr38
Van_1h_3

tag: treatment

value: Vanillin (Van)


title: FAC-sorted cells, DNMT1 control, rep 1


title: sorted GFP bin, 0-100, rep2, pilot


title: sorted GFP bin, 90-100, rep2, pilot


city: Beijing

first: Yao

last: Lv

state: Beijing

address: No. 7 Science Park Road, Zhongguancun Life Science Park, Changping District,   Beijing 102206, P.R. China

institute: National Institute of Biological Sciences,Beijing

description:
mouse lung epithelial cells, seq3 aegl KO ALT_2, 6h
Lungepi_III-CKOALT.txt
III-aeglKOALT-2

data_processing:
Raw sequencing data were processed using Fastp (version 0.19.7) to remove adaptors and low-quality reads according to the following criteria: (1) paired reads were discarded if either read contained adapter contamination; (2) paired reads were discarded if more than 10% of bases were uncertain in either read; (3) paired reads were discarded if the proportion of low-quality bases (Phred quality < 5) exceeded 50% in either read.
Filtered reads were then aligned to the mouse reference genome (mm10) or the human reference genome (hg19) using HISAT2 (v2.2.1)
The resulting SAM files were converted to sorted BAM files using Samtools
Gene annotations were based on the GENCODE mouse release M25 and GENCODE human release 19 comprehensive gene annotation files.Rawcounts were extracted with featureCounts (v2.0.2)
Read count normalization and differential gene expression analysis were performed using DESeq2 (v1.36.0) in the R environment (v4.2.2)
Assembly: mm10, hg19
Supplementary files format and content: format:txt, content:raw counts of each sample in the experiment

source_name: lung

growth_protocol: Mice were bred and maintained in the animal facility under specific pathogen-free conditions.Cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (GEMINI Cat 900-108), 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco), and were maintained in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNAprep Pure Cell/Bacteria Kit (TIANGEN, Cat: DP430)
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocols.

value: lung

value: lung epithelial cell


title: RIB40, Vanillin treated, 1h, rep2

description:
Library name: RNA_S8825Nr37
Van_1h_2


title: sorted GFP bin, 70-80, rep2, pilot


description:
mouse lung epithelial cells, seq3 aegs KO ALT_2, 6h
Lungepi_III-CKOALT.txt
III-aegsKOALT-2


title: RIB40, Vanillin treated, 1h, rep1

description:
Library name: RNA_S8825Nr36
Van_1h_1


title: sorted GFP bin, 40-60, rep2, pilot


title: Liver_OLD_RM213-15_female_Nx

value: female


title: RIB40, Levulinic acid treated, 1h, rep2

description:
Library name: RNA_S8825Nr34
LA_1h_2

value: Levulinic acid (LA)


title: sorted GFP bin, 20-30, rep2, pilot


description:
mouse lung epithelial cells, seq3 WT ALT_2, 6h
Lungepi_III-CKOALT.txt
III-WTALT-2


title: sorted GFP bin, 0-10, rep2, pilot


title: RIB40, Levulinic acid treated, 1h, rep1

description:
Library name: RNA_S8825Nr33
LA_1h_1


title: Cerebellum_OLD_RM213-15_female_Nx

source_name: Cerebellum


title: Spleen_YOUNG_RM244-15_female_Nx


description:
mouse lung epithelial cells, seq3 WT ALT_1, 6h
Lungepi_III-CKOALT.txt
III-WTALT-1


title: unsorted, genomic DNA, rep1, pilot


title: RIB40, HMF treated, 1h, rep2

description:
Library name: RNA_S8825Nr31
HMF_1h_2

value: Hydroxymethylfurfural (HMF)


description:
mouse lung epithelial cells, seq3 DPBS ctrl2, 6h
Lungepi_III-CKOALT.txt
III-PBS-2


title: sorted GFP bin, 0-100, rep1, pilot

value: Tet-On landing pad


description:
mouse lung epithelial cells, seq3 DPBS ctrl1, 6h
Lungepi_III-CKOALT.txt
III-PBS-1


description:
mouse lung epithelial cells, seq3 aegl KO ALT_1, 6h
Lungepi_III-CKOALT.txt
III-aeglKOALT-1


title: sorted GFP bin, 90-100, rep1, pilot


title: RIB40, HMF treated, 1h, rep1

description:
Library name: RNA_S8825Nr30
HMF_1h_1


title: Heart_OLD_RM213-15_female_Nx


title: RIB40, Levulinic acid treated, 1h, rep3

description:
Library name: RNA_S8825Nr35
LA_1h_3


title: Heart_YOUNG_RM244-15_female_Nx


title: sorted GFP bin, 70-80, rep1, pilot


title: RIB40, Furfural treated, 1h, rep3

description:
Library name: RNA_S8825Nr29
FF_1h_3

value: Furfural (FF)


title: Liver_YOUNG_RM244-15_female_Nx


title: Cerebellum_YOUNG_RM244-15_female_Nx


title: Colon_YOUNG_RM244-15_female_Nx

source_name: Colon


description:
mouse lung epithelial cells, seq3 aegs KO ALT_1, 6h
Lungepi_III-CKOALT.txt
III-aegsKOALT-1


title: RIB40, HMF treated, 1h, rep3

description:
Library name: RNA_S8825Nr32
HMF_1h_3


title: sorted GFP bin, 40-60, rep1, pilot


title: Colon_OLD_RM213-15_female_Nx


title: Spleen_OLD_RM211-15_male_Nx

value: male


title: RIB40, Furfural treated, 1h, rep2

description:
Library name: RNA_S8825Nr28
FF_1h_2

value: WT


title: sorted GFP bin, 20-30, rep1, pilot


description:
mouse lung epithelial cells, seq2 Aeg-L_2, 6h
Lungepi_II-AegSL.txt
II-AegL-2


title: RIB40, Furfural treated, 1h, rep1

description:
Library name: RNA_S8825Nr27
FF_1h_1


description:
mouse lung epithelial cells, seq2 Aeg-L_1, 6h
Lungepi_II-AegSL.txt
II-AegL-1


title: sorted GFP bin, 0-10, rep1, pilot


title: Liver_OLD_RM211-15_male_Nx


title: RIB40, Ferulic acid treated, 1h, rep3

description:
Library name: RNA_S8825Nr26
FA_1h_3

value: Ferulic acid (FA)


description:
mouse lung epithelial cells, seq2 Aeg-S/L_2, 6h
Lungepi_II-AegSL.txt
II-AegSL-2


description:
mouse lung epithelial cells, seq2 Aeg-S_2, 6h
Lungepi_II-AegSL.txt
II-AegS-2


title: CAG, small RNA-seq, rep2

data_processing:
Raw reads were mapped to miRBase miRNA annotations (version 22.1) using mapper.pl (parameters -m -e -h -i -j -v -k AGATCGGA -l 18) from the miRDeep2 package (version 2.0.0.7).
MicroRNAs were quantified with quantifier.pl (parameters -W  -j) from the miRDeep2 package (version 2.0.0.7).
Reads from miRNAs in the same miRNA families (defined as containing the same extended seed region, nt position 2-8 of miRNA) were combined and subsequent analysis performed on a family-level basis.
Assembly: miRBase version 22.1
Supplementary files format and content: The miRNA count table from miRDeep2 mapping and quantification is provided (mirna_counts.tsv).
Supplementary files format and content: The collapsed miRNA family count table is provided (mirnaFamily_counts.tsv).

extract_protocol:
Cells were scraped from 70% confluent 10 cm plates in ice-cold PBS, pelleted, and Trizol was added. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Small RNA-seq libraries were prepared by the RNA Sequencing Core and the Transcriptional Regulation and Expression Facility at Cornell University with the NEBNext Small RNA Library Prep Kit.

value: CAG landing pad


title: RIB40, Ferulic acid treated, 1h, rep2

description:
Library name: RNA_S8825Nr25
FA_1h_2


description:
mouse lung epithelial cells, seq2 Aeg-S_1, 6h
Lungepi_II-AegSL.txt
II-AegS-1


title: CAG, small RNA-seq, rep1


title: RIB40, Ferulic acid treated, 1h, rep1

description:
Library name: RNA_S8825Nr24
FA_1h_1


description:
mouse lung epithelial cells, seq2 Aeg-S/L_1, 6h
Lungepi_II-AegSL.txt
II-AegSL-1


title: PGK, small RNA-seq, rep2

value: PGK landing pad


description:
mouse lung epithelial cells, seq2 DPBS ctrl2, 6h
Lungepi_II-AegSL.txt
II-PBS-2


title: RIB40, Control, 1h, rep4

description:
Library name: RNA_S8825Nr23
CTRL_1h_4


title: Heart_OLD_RM211-15_male_Nx


title: RIB40, Control, 1h, rep3

description:
Library name: RNA_S8825Nr22
CTRL_1h_3


description:
mouse lung epithelial cells, seq2 DPBS ctrl1, 6h
Lungepi_II-AegSL.txt
II-PBS-1


title: CAG, PRO-seq, rep3

data_processing:
Illumina pipeline software was used for base calling.
The fastp program (version 0.23.2, with parameters --umi --umi_loc=per_read --umi_len=7 --disable_adapter_trimming --disable_quality_filtering --disable_length_filtering --disable_trim_poly_g) was used to add the unique molecular identifiers (UMIs) to the read name for later removal of PCR duplicates.
Cutadapt was used to remove adapters (parameters -q 20 --poly-a   minimum-length=10 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC)
Reads mapping to PhiX or ribosomal DNA were removed using bowtie2 (version 2.5.1) with parameters --fast-local --dovetail --un-conc.
Reads were mapped to the human genome (hg19) with hisat2 (version 2.2.1) using default parameters.
PCR duplicates were removed using the dedup tool from the UMI-tools program (parameters --umi-separator=":" -paired).
Gene body reads (excluding 200 bp  downstream from the TSS and upstream to the TES) were counted for each gene using Gencode (v19) annotations and featureCounts (version 2.0.3) with parameters -s 2 -p --countReadPairs -F SAF.
Assembly: hg19
Supplementary files format and content: The featureCounts output, a matrix with gene counts for all six samples, is provided (proseq_gene_counts.tsv).
Library strategy: PRO-seq

extract_protocol:
To prepare nuclei, cells were scraped from 70% confluent 10 cm plates in ice-cold PBS. A portion (20%) was taken for RNA-seq library preparation. Cells were then pelleted (700g, 4°C, 3 min), resuspended in permeabilization buffer (10 mM Tris Cl pH 7.5, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1mM EGTA, 0.05% Tween 20, 0.5 mM DTT), incubated on ice for 10 min, pelleted, washed (10 mM Tris Cl pH 7.5, 10 mM KCl, 150 mM sucrose, 5 mM MgCl2, 0.5 mM CaCl2, 0.008% Tween 20, 0.5 mM DTT), resuspended in storage buffer (50 mM Tris Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT), snap frozen and stored at -80°C.
The nascent RNA was generated using biotin run-on reactions, extracted using the Norgen Total RNA Purification Kit, and hydrolyzed using NaOH. A 3′ adapter (rUrNrNrNrNrNGATCGTCGGACTGTAGAACTCTGAAC/3InvdT/ ) was ligated to the nascent RNA, purified with streptavidin beads, 5′ ends were modified, and a 5′ adapter (/5InvddT/CCTTGGCACCCGAGAATTCCANrNrNrNrNrNrC) ligated. RNA was purified with Trizol, reverse transcribed, PCR amplified, and PAGE-purified.


title: Heart_OLD_RM176-10_female_Nx


title: PGK, small RNA-seq, rep1


title: Liver_OLD_RM176-10_female_Nx


description:
mouse lung epithelial cells, seq1 ALT2, 6h
Lungepi_I-PBS-ALT.txt
I-ALT-2


title: RIB40, Control, 1h, rep2

description:
Library name: RNA_S8825Nr21
CTRL_1h_2


title: RIB40, Control, 1h, rep1

description:
Library name: RNA_S8825Nr20
CTRL_1h_1


description:
mouse lung epithelial cells, seq1 ALT3, 6h
Lungepi_I-PBS-ALT.txt
I-ALT-3


title: Colon_OLD_RM176-10_female_Nx


description:
mouse lung epithelial cells, seq1 ALT1, 6h
Lungepi_I-PBS-ALT.txt
I-ALT-1


title: CAG, PRO-seq, rep2


title: RIB40, Vanillin treated, 0h, rep3

description:
Library name: RNA_S8825Nr19
Van_0h_3


title: CAG, PRO-seq, rep1


title: RIB40, Vanillin treated, 0h, rep2

description:
Library name: RNA_S8825Nr18
Van_0h_2


title: PGK, PRO-seq, rep2


description:
mouse lung epithelial cells, seq1 DPBS ctrl3, 6h
Lungepi_I-PBS-ALT.txt
I-PBS-3


title: Spleen_OLD_RM176-10_female_Nx


description:
mouse lung epithelial cells, seq1 DPBS ctrl2, 6h
Lungepi_I-PBS-ALT.txt
I-PBS-2


title: Cerebellum_OLD_RM176-10_female_Nx


title: PGK, PRO-seq, rep1


title: RIB40, Vanillin treated, 0h, rep1

description:
Library name: RNA_S8825Nr17
Van_0h_1


description:
mouse lung epithelial cells, seq1 DPBS ctrl1, 6h
Lungepi_I-PBS-ALT.txt
I-PBS-1


title: Colon_OLD_RM211-15_male_Nx


title: Heart_YOUNG_RM245-15_female_Nx


title: fat_YOUNG_RM245-15_female_Nx

source_name: fat


title: RIB40, Levulinic acid treated, 0h, rep3

description:
Library name: RNA_S8825Nr16
LA_0h_3


title: bone marrow 231005BM 1

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

data_processing:
Before aligning each fastq file to the mouse genome, reads were trimmed using Trimmomatic version 0.36 with reference to the 'TruSeq3.fa' adapter sequence file. The specific parameters applied were as follows: ILLUMINACLIP:TruSeq3.fa:2:30:10:2:keepBothReads, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36
The trimmed reads were aligned to the Mus musculus genome assembly GRCm38 using the STAR aligner , version 2.5.3a, with the parameter 'outFilterMismatchNmax' set to 2 to specify  the number of mismatched bases permitted. STAR has been shown to perform well compared to other RNA-seq aligners .
Gene counts were subsequently generated by the STAR aligner
Assembly: STAR aligner (v2.7.10b_alpha_220111) RNA-SeQC

source_name: CD11b positive cells from mouse bone marrow

extract_protocol:
total RNA was isolated from CD11b+ cells using Trisol
Libraries were prepared from 200 nanograms of total RNA using the TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: Female mice were fed by either a regualr or a high fat diet for eight weeks before pregnancy and during pregnancy and lactation.. Mice were bred with control males and offspring weaned at 4 weeks.WE isolated bone marrow cells from 4 week old offspring of mothers fed a regular or high fat diet (Off-RD/Off-HFD), and purified the CD11b+ cells from those bone marrow cells

value: tissue

value: myeloid cells

value: FVB/NJ

value: Offspring of RD fed mother


title: RIB40, Levulinic acid treated, 0h, rep2

description:
Library name: RNA_S8825Nr15
LA_0h_2

source_name: mycelia

value: mycelia


title: RIB40, Levulinic acid treated, 0h, rep1

description:
Library name: RNA_S8825Nr14
LA_0h_1


title: bone marrow 230829BM 2

value: CD11b positive cells from mouse bone marrow


title: bone marrow 230828BM 6


title: RIB40, HMF treated, 0h, rep3

description:
Library name: RNA_S8825Nr13
HMF_0h_3


title: RIB40, HMF treated, 0h, rep2

description:
Library name: RNA_S8825Nr12
HMF_0h_2


title: bone marrow 230828BM 4


title: Colon_YOUNG_RM245-15_female_Nx


title: RIB40, HMF treated, 0h, rep1

description:
Library name: RNA_S8825Nr11
HMF_0h_1


title: Cerebellum_YOUNG_RM245-15_female_Nx


title: Spleen_YOUNG_RM245-15_female_Nx


title: bone marrow 230828BM 3


title: RIB40, Furfural treated, 0h, rep3

description:
Library name: RNA_S8825Nr10
FF_0h_3


title: X8C_KI_MIA_D21_F

type: RNA

city: Salamanca

first: Juan Carlos

last: Arevalo

address: C/ Pintor Fernando Gallego, 1

department: INCyL

institute: University of Salamanca

description: Gene expression in L3-5 DRGs from KI mice 21 days after MIA injection

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (SurePrint G3 Unrestricted GE 8x60K, Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C.

data_processing: Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE) version 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09 for FE version 10.7).

label: Cyanine 3-CTP

source_name: L3-5 DRGs, KI mouse, MIA injection, 21 days

label_protocol: 200 ng of RNA was labelled using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Input Linear Amplification Kit and purified with Quiagen´s Rneasy mini spin columns.

growth_protocol: Mice were housed in Specific Pathogen Free Animal Facility of the University of Salamanca with a maximum of 5 animals per cage. They were fed ad libitum in a 12-hours-light/dark cycle, constant temperature of 20-22ºC and a relative humidity of 55-65%.

extract_protocol: Isilateral L3 to 5 DRGs were collected at day 5 and 21 post-injection. RNA was extracted with RNA/DNA Purification Micro Kit (Norgen Biotek Corp.). RNA concentration was quantified with NanoDrop 2000c spectrophotometer (ThermoScientific) and only samples with an absorbance ratio of 1.8<OD260/280<2.0 were subsequently analyzed. Each sample was then quality checked for integrity using the Agilent BioAnalyzer 2100 (Agilent G2938C, RNA 6000 nano kit) and those samples with an RNA Integrity Number (RIN) index higher than 8.0 were processed further.

treatment_protocol: Mice were injected with saline or 0.7mg MIA (Sigma-Aldrich, #I2512) in 10 ul of salinie solution in the left knee joint as previously described (Sousa-Valente et al., 2018).

value: KI

value: MIA

tag: day

value: Female


title: Cerebellum_OLD_RM211-15_male_Nx


title: bone marrow 230828BM 2


title: RIB40, Furfural treated, 0h, rep2

description:
Library name: RNA_S8825Nr9
FF_0h_2


title: bone marrow 230828BM 5


title: bone marrow 230810BM 2

value: Offspring of HFD-fed mother


title: Liver_YOUNG_RM245-15_female_Nx

value: female


title: Heart_OLD_RM237-15_female_Nx

source_name: Heart


title: RIB40, Furfural treated, 0h, rep1

description:
Library name: RNA_S8825Nr8
FF_0h_1

value: Furfural (FF)


title: X8D_KI_MIA_D21_F


title: X7C_KI_SALINE_D21_F

description: Gene expression in L3-5 DRGs from KI mice 21 days after Saline injection

source_name: L3-5 DRGs, KI mouse, Saline injection, 21 days

value: Saline


title: Liver_OLD_RM237-15_female_Nx


title: bone marrow 230810BM 1


title: X8B_KI_MIA_D21_M

value: Male


title: Spleen_OLD_RM237-15_female_Nx


title: RIB40, Ferulic acid treated, 0h, rep3

description:
Library name: RNA_S8825Nr7
FA_0h_3

value: WT

value: Ferulic acid (FA)


title: fat_OLD_RM237-15_female_Nx


title: X7D_KI_SALINE_D21_F


title: RIB40, Ferulic acid treated, 0h, rep2

description:
Library name: RNA_S8825Nr6
FA_0h_2


title: Cerebellum_OLD_RM237-15_female_Nx


title: X6D_WT_MIA_D21_F

description: Gene expression in L3-5 DRGs from WT mice 21 days after MIA injection

source_name: L3-5 DRGs, WT mouse, MIA injection, 21 days


title: bone marrow 230809BM 3


title: Colon_OLD_RM237-15_female_Nx


title: X8A_KI_MIA_D21_M


title: fat_YOUNG_RM243-15_female_Nx


title: RIB40, Ferulic acid treated, 0h, rep1

description:
Library name: RNA_S8825Nr5
FA_0h_1


title: bone marrow 230809BM 4


title: bone marrow 230809BM 2


title: RIB40, Control, 0h, rep4

description:
Library name: RNA_S8825Nr4
CTRL_0h_4


title: X7A_KI_SALINE_D21_M

description: Gene expression in L3-5 DRGs from KI mice 21 Days after Saline injection


title: Heart_YOUNG_RM243-15_female_Nx


title: X6C_WT_MIA_D21_F


title: bone marrow 230809BM 1


title: RIB40, Control, 0h, rep3

description:
Library name: RNA_S8825Nr3
CTRL_0h_3


title: Prostate, CD45-, 22-weeks-old male mice, Castration at 10th week, rep4

first: Zhenpeng

last: Wu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

description: 10x Genomics

data_processing:
Cell Ranger software (version 4.0.0) were used to process reads, barcode and generate count expression matrices.
Assembly: mm10
Supplementary files format and content: cellranger generated barcode, genes and counts matrix files

source_name: prostate

extract_protocol:
tissues were dissociated to single cell  suspension, then stained with fluorescence-labed antibodies. Cells used for library construction were sorted using FACS strategy.
Single cell libraries were prepared using 10x Gemonics 3' or V(D)J kits following manufacturers' protocols.

value: prostate

value: Pb-cre+;PtenLoxP/LoxP

value: Castration at 10th week


title: RIB40, Control, 0h, rep2

description:
Library name: RNA_S8825Nr2
CTRL_0h_2


title: Prostate, CD45-, 22-weeks-old male mice, Castration at 10th week, rep3

description: 10x Genomics


title: Thymus, CD45+, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: thymus

value: thymus


title: Liver_YOUNG_RM243-15_female_Nx


title: X6B_WT_MIA_D21_M


title: Spleen_OLD_RM215-15_female_Nx


title: CTCF_CT_HIP_233848

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: CTCF_CT_HIP_233848
85 year old Female

data_processing:
FASTQ files were processed using cutadapt v5.0 103 and trim galore v0.6.10 104 with -q 20 to remove low quality ends and adaptor sequences, then aligned to hg38 using bowtie2 v2.5.4. Bam files were deduplicated using samtools fixmate -m then samtools markdup -r. RPKM normalized bigwig files were generated using bamCoverage --normalizeUsing RPKM -bs 10.
Assembly: hg38 GRCh38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Human Hippocampus

extract_protocol:
All buffers were prepared as described in Kaya-Okur et al., 2019 (PMID: 31036827) without the addition of digitonin. Human hippocampus tissue (30mg) was dounced in 1mL NE1 Buffer with a loose-fitting pestle (5-10 strokes) followed by a tight-fitting pestle (15-25 strokes). Lysates were filtered through 30µM CellTrics filters (Sysmex, Cat#04-0042-2316). After centrifugation for 4 minutes at 1300g at 4°C, nuclei were resuspended in PBS supplemented with Roche c0mplete EDTA-free protease inhibitor (Roche, Cat# 11873580001).
300K nuclei were crosslinked with formaldehyde (Thermo Scientific, Cat#PI28906) at a final concentration of 0.1% at room temperature for 2 minutes, followed by quenching with 1M glycine. Crosslinked nuclei were centrifuged for 4 minutes at 1300g at 4°C and resuspended in 100-300uL of Wash Buffer. 10uL of ConA beads per sample (Bangs Labs, Cat# BP531) were washed 3x in 1mL Binding Buffer and resuspended in Binding Buffer at the original slurry volume. 10uL of beads were added to the nuclei and tubes were rotated for 5-10 minutes at room temperature before placing on a magnetic stand.  Supernatant was removed and beads were resuspended in 100uL Antibody Buffer. CTCF antibody (CST, Cat#3418S) was added at a 1:100 dilution and samples were rotated overnight at 4°C. The next morning, the supernatant was removed and the nuclei were resuspended in 300uL  Was Buffer with secondary antibody (Novus, Cat#NBP1-72763) at a 1:100 dilution. Samples were rotated for 1 hour at room temperature, then washed 3x in 1mL Wash Buffer. After washing, pA-Tn5 (EpiCypher, Cat#15-1017) was added at a 1:50 dilution in 300uL of Dig-300 Buffer and samples were rotated for 1 hour at room temperature followed by washing 3x in Dig-300 Buffer. After removing the supernatant, 300uL Tagmentation Buffer was added to the nuclei and samples were incubated at 37°C for 1 hour with shaking at 500rpm. Tagmentation was stopped by adding 10 uL 0.5 M EDTA, 3 uL 10% SDS, and 2.5 uL 20 mg/mL Proteinase K. Samples were vortexed and incubated for 1 hour at 55°C with shaking at 500rpm to digest and reverse crosslinks. DNA was extracted using a standard Phenol-Chloroform extraction protocol. PCR  was carried out using Nextera i5 and i7 primers and NEBNext HiFi 2x PCR MM (NEB, Cat#M0541S). PCR products were purified using VAHTS DNA Clean Beads (Vazyme, Cat#N411-01) at 1.3x volume and eluted in 10mM Tris-HCl pH 8. Libraries were sequenced on Element AVITI using 2x150 Sequencing Kit Cloudbreak FS Medium Output (860-00012).

value: Human Hippocampus


title: Spleen_YOUNG_RM243-15_female_Nx


title: Cerebellum_YOUNG_RM243-15_female_Nx


title: Colon_YOUNG_RM243-15_female_Nx


title: Spleen, CD45+, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: spleen

value: spleen


title: X4D_KI_MIA_D5_F

description: Gene expression in L3-5 DRGs from KI mice 5 days after MIA injection

source_name: L3-5 DRGs, KI mouse, MIA injection, 5 days


title: CTCF_CT_HIP_81158

description:
Library name: CTCF_CT_HIP_81158
82 year old Female


title: X5A_WT_SALINE_D21_M

description: Gene expression in L3-5 DRGs from WT mice 21 days after Saline injection

source_name: L3-5 DRGs, WT mouse, Saline injection, 21 days


title: Liver_OLD_RM215-15_female_Nx

source_name: Liver


title: fat_OLD_RM215-15_female_Nx


title: X6A_WT_MIA_D21_M


title: X5D_WT_SALINE_D21_F


title: CTCF_CT_HIP_6042

description:
Library name: CTCF_CT_HIP_6042
90 year old Male


title: X4C_KI_MIA_D5_F


title: Prostate, CD45+Gr1-, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: RIB40, Control, 0h, rep1

description:
Library name: RNA_S8825Nr1
CTRL_0h_1

value: mycelia


title: X5B_WT_SALINE_D21_M


title: X4A_KI_MIA_D5_M

value: KI


title: CTCF_CT_HIP_4320

description:
Library name: CTCF_CT_HIP_4320
87 year old Male


title: Colon_OLD_RM215-15_female_Nx


title: X3D_KI_SALINE_D5_F

description: Gene expression in L3-5 DRGs from KI mice 5 days after Saline injection

source_name: L3-5 DRGs, KI mouse, Saline injection, 5 days


title: Prostate, CD45-, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: X4B_KI_MIA_D5_M

value: MIA


title: Heart_OLD_RM215-15_female_Nx


title: Prostate, CD45+CD11b+Gr1+, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: CTCF_CT_HIP_5711

description:
Library name: CTCF_CT_HIP_5711
39 year old Male


title: Blood, CD45+, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: blood

value: blood


title: Bone marrow, CD45+, 22-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: bone marrow

value: bone marrow


title: X3C_KI_SALINE_D5_F

value: Female


title: CTCF_CT_HIP_5579

description:
Library name: CTCF_CT_HIP_5579
25 year old Female


title: Thymus, CD45+, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: Cerebellum_OLD_RM215-15_female_Nx

source_name: Cerebellum

value: female


title: Spleen, CD45+, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: X3B_KI_SALINE_D5_M

value: Saline


title: Liver_YOUNG_RM241-15_male_Nx

value: male


title: Small HEK Torin

city: New York

first: Marko

last: Jovanovic

state: New York

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Columbia University

description: Library name: Sample 4

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8
RPM (ATCAGCACTTA) sequence was trimmed using Cutadapt v3.4 from both 5’ and 3’ read ends
The barcodes of trimmed reads were identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline)
RNA read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to the human (hg38) genome using STAR aligner. Only reads that mapped uniquely to the genome were kept for further analysis.
Clusters of barcodes were filtered for repeat UMIs, out-of-order barcodes, and PCR duplicates
Reads from the remaining clusters were split into bam files based on user defined cutoffs for the minimum number of oligos per bead, the maximum number of oligos per bead, and the proportion of oligos with the same ID
Bigwig files were generated from individual antibody DNA alignment files using deeptools v3.5.5
Assembly: hg38
Supplementary files format and content: Bigwig

extract_protocol:
For each experiment, 10 million cells were lysed in 1 mL RIPA buffer (50mM HEPES pH 7.4, 100mM NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS) supplemented with 20 μL Protease Inhibitor Cocktail (Sigma, #P8340-5mL), 10 μL of Turbo DNase (Invitrogen, #AM2238), 1X Manganese/Calcium mix (2.5 mM MnCl2, 0.5 mM CaCl2), and 5 μL of RiboLock RNase Inhibitor (Thermo Fisher, #EO0382)). Samples were incubated on ice for 10 minutes to allow lysis to proceed. After lysis, cells were sonicated at 3-4 W of power for 3 minutes (pulses 0.7 s on, 3.3 s off) using the Branson sonicator and then incubated at 37°C for 10 minutes to allow for DNase digestion. DNase reaction was quenched with addition of 0.25 M EDTA/EGTA mix for a final concentration of 10 mM EDTA/EGTA. RNase If (NEB, #M0243L) was then added at a 1:500 dilution and samples were incubated at 37°C for 10 minutes to allow partial fragmentation of RNA to obtain RNAs of approximately ~300-400 bp in length. RNase reaction was quenched with addition of 500 μL ice cold RIPA buffer supplemented with 20 μL Protease Inhibitor Cocktail and 5 μL of RiboLock RNase Inhibitor, followed by incubation on ice for 3 minutes. Lysates were then cleared by centrifugation at 15000 x g at 4°C for 2 minutes. The supernatant was transferred to new tubes and diluted in additional RIPA buffer such that the final volume corresponded to 1 mL lysate for every 100 μL of Protein G beads used. Lysate was then combined with the labeled antibody-bead pool and 1 M biotin was added to a final concentration of 10 mM as to quench any disassociated streptavidin-coupled oligos. Beads were left rotating overnight at 4°C on a HulaMixer. Following immunoprecipitation, beads were washed twice with RIPA buffer, twice with high salt wash buffer (50 mM HEPES pH 7.4, 1 M NaCl, 1% NP-40, 0.5% Na-Deoxycholate, 0.1% SDS), and twice with Tween buffer (50 mM HEPES pH 7.4, 0.1% Tween-20).
After split-and-pool barcoding, beads were aliquoted into 5% aliquots for library preparation and sequencing. RNA in each aliquot was degraded by incubating with RNase H (NEB, #M0297L) and RNase cocktail (Invitrogen, #AM2286) at 37°C for 20 minutes. 3’ ends of the resulting cDNA were ligated to attach dsDNA oligos containing library amplification sequences using a “splint” ligation as previously described (Quinodoz et al 2021)31. The “splint” ligation reaction was performed with 1X Instant Sticky End Master Mix (NEB #M0370) at 24°C for 1 hour with shaking at 1400 rpm on a ThermoMixer. Barcoded cDNA and biotinylated oligo tags were then eluted from beads by boiling in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsarcosine, 2.5 mM TCEP) for 6 minutes at 91°C, with shaking at 1350 rpm. Biotinylated oligo tags were first captured by diluting the eluant in 1X oligo binding buffer (0.5X PBST, 5 mM Tris pH 8.0, 0.5 mM EDTA, 1M NaCl) and subsequently binding to MyOne Streptavidin C1 Dynabeads (Invitrogen, #65001) at room temperature for 30 minutes. Beads were placed on a magnet and the supernatant, containing cDNA, was moved to a separate tube. Biotinylated oligo tags were amplified on-bead using 2X Q5 Hot-Start Mastermix (NEB #M0494) with primers that add the indexed full Illumina adaptor sequences.

value: Human embryonic kidney cells


title: fat_YOUNG_RM241-15_male_Nx

source_name: fat


title: Colon_YOUNG_RM241-15_male_Nx

source_name: Colon


title: CTCF_CT_HIP_935

description:
Library name: CTCF_CT_HIP_935
38 year old Female


title: X3A_KI_SALINE_D5_M

value: Male


title: 3H11 95 hours of growth biological replicate C

city: Seattle

first: Alex

middle: V

last: Carr

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
FASTQC: default parameters
Trimmomatic: quality score of 20
Kallisto: quant function with default parameters
Assembly: Rhodanobacter sp. FW510-R12 (NCBI BioProject PRJNA255897) and Acidovorax sp. GW101-3H11 (NCBI BioProject PRJNA314893)
Supplementary files format and content: tsv containing transcript counts across both species

organism: Acidovorax sp.

source_name: Acidovorax sp. GW101-3H11

growth_protocol: From freezer stocks, cells were plated on R2A agar and incubated at 30 °C. Following growth of isolated colonies, colonies were picked and used for inoculation of R2A liquid medium cultures. Liquid R2A cultures were incubated at 30°C with shaking at 100 rpm. Following overnight growth, optical density at 600 nm (OD600) was measured and cell density was normalized to using R2A liquid medium if necessary. With starting cultures at ~0.5 OD600 units, 100 uL of Rhodanobacter sp. FW510-R12 (R12) and 100 uL of Acidovorax GW101-3H11 (3H11) were inoculated into a NO3 reduction medium to establish co-cultures. For pure cultures 200 uL of either strain was utilized to normalize starting cell densities. Initial cell densities were normalized to ∼0.01 OD600 units across all experiments and conditions.

extract_protocol:
Cell pellets were harvested by centrifugation at 4,000 × g and flash frozen in liquid N2. Total RNA was extracted using the MasterPure™ Complete DNA and RNA Purification Kit from Epicentre. All samples were treated with Invitrogen TURBO DNA-Free kit to remove DNA contamination. The Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina) was used for rRNA depletion and library preparation.
The Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina) was used for rRNA depletion and library preparation.

value: Acidovorax sp. GW101-3H11

value: Anearobic denitrification media:20 mM Acetate, 10 mM Nitrate


title: Prostate, CD45-, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

value: prostate

value: Pb-cre+;PtenLoxP/LoxP

value: Castration at 10th week


title: X2D_WT_MIA_D5_F

description: Gene expression in L3-5 DRGs from WT mice 5 days after MIA injection

source_name: L3-5 DRGs, WT mouse, MIA injection, 5 days

value: WT


title: 3H11 95 hours of growth biological replicate B


title: Prostate, CD45+Gr1-, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: 3H11 95 hours of growth biological replicate A


title: X2B_WT_MIA_D5_M


title: Blood, CD45+, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: 3H11 71 hours of growth biological replicate C


title: fat_OLD_RM23-18_female_Nx

first: Anna


title: X2A_WT_MIA_D5_M


title: X1D_WT_SALINE_D5_F

description: Gene expression in L3-5 DRGs from WT mice 5 days after Saline injection

source_name: L3-5 DRGs, WT mouse, Saline injection, 5 days


title: Heart_YOUNG_RM241-15_male_Nx

source_name: Heart


title: X2C_WT_MIA_D5_F


title: Cerebellum_YOUNG_RM241-15_male_Nx


title: Heart_OLD_RM23-18_female_Nx


title: Spleen_OLD_RM23-18_female_Nx

source_name: Spleen


title: Bone marrow, CD45+, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics


title: X1C_WT_SALINE_D5_F


title: Prostate, CD45+CD11b+Gr1+, 22-weeks-old male mice, Castration at 10th week, rep1

description: 10x Genomics

source_name: prostate


title: 3H11 53 hours of growth biological replicate C


title: 3H11 71 hours of growth biological replicate A


title: X1B_WT_SALINE_D5_M


title: LNCaP-AI_siAR_2

city: Davis

first: Maria

last: Mudryj

address: 1 Shields Ave.

department: Medical Microbiology and Immunology

institute: University of California, Davis

description:
Library name: Sample8
LNCaP-AI_siAR_2_FPKM

data_processing:
Raw sequence data was aligned to the human genome assembly (GRCh37/hg19) using TopHat
Aligned bam files from TopHat were processed with Cufflinks for estimation of transcript abundance.
Assembly: GRCh37/hg19
Supplementary files format and content: Processed data are gene-level FPKM expression values generated from the output of TopHat alignment and subsequent quantification with Cufflinks for each sample.
Supplementary files format and content: Single file in tab-delimited text consisting of a data matrix for all eight samples. The file contains the gene name (column 1), locus (column 2), and gene-level FPKM expression values for each gene for each sample (columns 3-10).

source_name: LNCaP-AI

growth_protocol: Cells were propagated in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) or charcoal stripped FBS (CCS), 2 mmol/L L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin (Invitrogen) at 37 °C and 5% CO2.

extract_protocol:
Total cellular RNA was prepared utilizing RNeasy Mini kit (Qiagen, Inc. CA).
RNA-Sequencing (RNA-Seq) libraries were prepared from total RNA using the Tecan/Nugen Ovation RNA-Seq System V2 (Tecan, Männedorf, Switzerland) according to the manufacturer’s protocol.

treatment_protocol: Three x 10^5 cells were plated in 60 mm dishes and transfected 24 hours later with 100 nM AR siRNA smart pool (L003400-00) or control non-targeting oligonucleotide (D-001210–01) (Dharmacon, currently Horizon) using Lipofectamine 2000 or RNAi Max (Invitrogen). The transfection mix was removed 24 hours later and replaced with normal growth medium. Cells were harvested 72 hours post-transfection.

value: LNCaP-AI

value: prostatic adenocarcinoma

tag: genetic modification

value: AR siRNA

value: siAR


title: 3H11 52 hours of growth biological replicate B


title: Prostate, CD45-, 14-weeks-old male mice, Castration at 10th week, rep3

description: 10x Genomics


title: X1A_WT_SALINE_D5_M


title: Thymus, CD45+, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: thymus

value: thymus


title: 3H11 71 hours of growth biological replicate B


title: 3H11 53 hours of growth biological replicate A


title: LNCaP-AI_siC_2

description:
Library name: Sample7
LNCaP-AI_siC_2_FPKM

value: siControl


title: Cerebellum_OLD_RM23-18_female_Nx

value: female


title: plasmid DNA sequencing, pilot

data_processing:
Adapters were trimmed from raw reads with cutadapt -q 20 -j 25 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA.
Reads were mapped to a custom genome consisting of the expected 3′UTR sequences with 250 nt flanking plasmid sequence using bowtie2 (with parameters -X 1000).
A custom python script was used to identify and count reads containing the barcode region
The barcode 3′UTR linkages were further filtered in R (e.g. to remove lowly detected barcode sequences likely due to PCR or sequencing errors).
Assembly: Custom plasmid genome
Supplementary files format and content: A file containing the final filtered barcode-3′UTR linkages is provided (barcode_3UTR_linkages.tsv).
Library strategy: plasmid-seq

molecule: other

organism: Escherichia coli

source_name: plasmids grown in E. coli

growth_protocol: Plasmids were amplified in E. coli grown in luria broth at 37°C.

extract_protocol:
Plasmid DNA was extracted from E. coli with the Promega PureYield Plasmid Midiprep Kit.
To determine the appropriate ratio of DNA to Tn5 transposase, 50 ng of each plasmid pool was combined with various dilutions of in house purified Tn5 transposase in a 25 µl reaction (reaction conditions 10 mM Tris pH 7.5, 5mM MgCl2, 10% DMF) and incubated at 55°C for 8 minutes. The tagmentation reactions were stopped with 2.5 µl 1% SDS. The optimization reactions were PCR amplified and ran on a 6% PAGE gel. The reaction that yielded the most library in the size range 400 to 1000 bp was selected for full scale amplification. Five µl of the tagmentation reaction was PCR amplified in a 50 µl reaction with Phusion polymerase for 7 cycles, ethanol precipitated and size selected (400 to 1000 bp) on a 6% native PAGE gel.

value: plasmids grown in E. coli


title: PBMC_YOUNG_RM245-15_female_Tp 2

source_name: PBMC


title: Prostate, CD45-, 14-weeks-old male mice, Castration at 10th week, rep4

description: 10x Genomics


title: Spleen, CD45+, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: spleen

value: spleen


title: Liver_OLD_RM23-18_female_Nx

source_name: Liver


title: 3H11 42 hours of growth biological replicate C


title: LNCaP-AI_siAR_1

description:
Library name: Sample6
LNCaP-AI_siAR_1_FPKM

value: Control siRNA


title: Prostate, CD45-, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: 3H11 42 hours of growth biological replicate B


title: PBMC_OLD_RM237-15_female_Tp 2


title: Prostate, CD45+Gr1-, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: Rv1_siAR_2

description:
Library name: Sample4
Rv1_siAR_2_FPKM


title: Colon_OLD_RM23-18_female_Nx


title: 3H11 42 hours of growth biological replicate A


title: Rv1_siC_2

description:
Library name: Sample3
Rv1_siC_2_FPKM


title: Prostate, CD45+CD11b+Gr1+, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics


title: LNCaP-AI_siC_1

description:
Library name: Sample5
LNCaP-AI_siC_1_FPKM


title: Rv1_siAR_1

description:
Library name: Sample2
Rv1_siAR_1_FPKM


title: Primordial Follicles at T16, Replicate 2

city: Lodi

first: Alberto Maria

last: Luciano

state: LO

address: Via dell'Università 6

department: Department of Veterinary Medicine and Animal Sciences

institute: University of Milan

description: Library name: 32PM16

data_processing:
Trimming of the reads was performed to remove artificial constructs like adapters, primers, and overcalled polyG sequences with TrimGalore and Fastp.
Trimmed reads were mapped to the bovine transcriptome assembly, ARS UCD 1.3 using Salmon.
Mapped reads were quantified in TPM (transcripts per million) with Salmon.
Assembly: Bos taurus ARS UCD 1.3
Supplementary files format and content: Tab delimited files contains raw counts and TPM values generated with Salmon

organism: Bos taurus

source_name: Ovarian Follicles (oocyte and pre-granulosa cells)

extract_protocol:
Total RNA was extracted using the miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen) and eluted in RNAse-free water following the manufacturer instructions.
cDNA was generated using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). From the cDNA obtained, libraries were prepared using NEBNext® Ultra DNA Library Prep for Illumina® kit according to the manufacturer's protocol.

value: Isolated primordial follicles retrieved after 16 hours of culture (T16)


title: Blood, CD45+, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: blood

value: blood


title: Primordial Follicles at T16, Replicate 3

description: Library name: 40PM16

value: Ovarian Follicles (oocyte and pre-granulosa cells)


title: Rv1_siC_1

description:
Library name: Sample1
Rv1_siC_1_FPKM


title: Bone marrow, CD45+, 14-weeks-old male mice, Castration at 10th week, rep2

description: 10x Genomics

source_name: bone marrow

value: bone marrow


title: PBMC_YOUNG_RM245-15_female_Tp 1


title: PBMC_YOUNG_RM244-15_female_Tp 4


title: PBMC_OLD_RM237-15_female_Tp 1


title: PBMC_OLD_RM215-15_female_Tp 4


title: sample100: Patient 46, Visit V4

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.8)
Reads were mapped to the human genome hg38 with STAR (version 2.7.9a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
The featureCounts() function from the Bioconductor Rsubread package (version 2.0.1) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model. All subsequent analyses were performed using the R software (version 4.3.1) and Bioconductor 3.18 packages.
Assembly: hg38
Supplementary files format and content: Counts_Table.tsv: TSV file (tab separated values) including read counts for each sample and gene (ENSEMBL ID release 102). Column headers indicate the sample number.
Supplementary files format and content: Gene_Info.tsv: TSV file (tab separated values) including information about each gene used in the file Counts_Table.tsv (ENSEMBL release 102).
Supplementary files format and content: Sample_Info.tsv: TSV file (tab separated values) including information about each sample. Row sample number correspond to columns of the file Counts_Table.tsv.

source_name: Whole blood

extract_protocol:
Blood samples were collected on PAXtubes, and RNA extraction was performed on samples from visit 1, visit 1b, visit 2, visit 3 and visit 4. After quality control the resulting RNA was stored at -80°C for RNA-seq library preparation.
Illumina library preparation and sequencing were performed at the Oxford High-Throughput Genomics Hub. Sequencing was performed for 91 RNA-seq samples across 51 patients on an Illumina Hiseq 2000 instrument to produce paired-end 92 bp-long reads.

tag: donor

value: Whole blood

tag: visit

tag: patient subgroup

value: No diabetes

tag: surgery type

value: gastric bypass


title: Primordial Follicles at T16, Replicate 1

description: Library name: 31PM16


title: PBMC_YOUNG_RM244-15_female_Tp 3


title: Primordial Follicles at T0, Replicate 3

description: Library name: 39PM00

value: Isolated primordial follicles retrieved after collection (T0)