title: MNase_CD34plus_PGE2_N128_Rep3

data_processing:
The sequenced paired-end reads were mapped to hg19 using Bowtie aligner v. 0.12.9. Only uniquely mapped reads with no more than two mismatches were retained. The reads with the insert sizes <50 bp or >500 bp were filtered out. Genomic positions with the numbers of mapped tags above the significance threshold of Z-score=7 were identified as anomalous, and the tags mapped to such positions were discarded. Read frequencies were computed in 300bp non-overlapping bins for each titration point independently. The read frequencies were normalized by the corresponding library sizes to represent values per one million of mapped reads. Nucleosome occupancy analysis was carried out as previously described by Mieczkowski et al., 2016
Assembly: hg19
Supplementary files format and content: bed file of called peaks

extract_protocol:
CD34+ HSPC cells were crosslinked by the addition of 1/10 volume 11% fresh formaldehyde for 10 min at room temperature. The crosslinking was quenched by the addition of 1/20 volume 2.5M glycine for 5 minutes. Cells were washed twice with ice-cold PBS. For MNase digestion, the nuclei pellet was resuspended in MNase digestion buffer (50mM Tris, pH 7.4, 25mM KCl, 4mM MgCl2, 1mM CaCl2, 12.5% Glycerol and COMPLETE protease inhibitors (Roche)). Digestion took place with 106 cells per titration point in a volume of 500μl MNase digestion buffer. Either 1, 2, 4, 8, 16, 32, 64, 128 or 256 units of MNase (Worthington Biochemical) were added to pre-warmed nuclei and incubated at 25 °C for 15 min. Digestion was halted with 25mM EDTA/EGTA and 0.5% SDS and 125mM NaCl was added to the samples. Digestions were incubated with RNase (Roche) for 1 hour at 37 °C, with proteinase K (Roche) for 1 hour at 55 °C, and cross-link reversal was performed at 65 °C for 16 hours. DNA was purified by Phenol/Chloroform extraction and ethanol precipitation. MNase digestion was evaluated on a 2% agarose gel and fragments from four MNase concentrations representing 10%, 25%, 50% and 75% mono-nucleosomal fragments were individually prepared for next generation sequencing. Ampure SPRI beads (Beckman Coulter) were used in a double size selection with ratios of 0.7X and 1.7X to obtain a range of fragment sizes from ∼100 to 1,000bp. DNA was eluted from the beads and used as input into the library preparation protocol.
DNA libraries were prepared for each individual titration point using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7370, New England Biolabs) and barcoded using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 & 2; New England Biolabs). Number of PCR cycles was calculated using a real-time qPCR-based approach (Lion et al., 2020). Libraries prepared went through quality control analysis using an Agilent Bioanalyzer. Four barcoded titration libraries were pooled in one sample, and paired-end sequencing on an Illumina Hiseq 2500 instrument was performed. Three biological replicated were sequenced.


title: PLC/PRF/5 cells, NC_SiRNA_1

status: Public on Jun 10 2024

type: SRA

city: shanghai

first: xindong

last: wei

address: 1200 Cailun Road, Shanghai

country: China

institute: shanghai university of Chinese medicine

library_source: transcriptomic

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg38/GRCh38
Supplementary files format and content: Xlsx file includes FPKM for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, Chi

tag: cell line

tag: treatment


title: T3_Nac

city: 郑州市

first: 凯欣

last: 李

state: 河南省

address: 郑州市高新区金梭路

institute: CTQTC

data_processing:
Dr.tom platform for data analysis (https://biosys.bgi.com/#/report/login)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: brain

extract_protocol:
Six brain regions of adult C57 mice at 6-7 weeks were extracted from PFc, VTA, Nac, STR, SN and HP
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

tag: tissue

value: brain

tag: brain region

value: Nac

tag: genotype

value: KI


title: RISP_Het_treatment_PLX3397 Depletion_ageGroup_Adult_02

city: Chicago

first: Rogan

middle: A

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

country: USA

institute: Northwestern University

data_processing:
FASTQ files were generated using bcl2fastq 2.20 (Illumina) for NextSeq500 output or bcl-convert 4.0.3 (Illumina) for NextSeq2000 output using default parameters. To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.9 implemented in Nextflow 22.04.5.5708 using Singularity 3.8.1 with the minimal command nextflow run nf-core/rnaseq \ -r ‘3.9’ \ -profile nu_genomics \--additional_fasta ‘transgenes.fa’ \ --star_index false \ --three_prime_clip_r2 3 \ --genome ‘GRCm38’ for SMARTer-seq samples. For NEBnext samples, 3’ clipping was not performed. Briefly, lane-level reads were trimmed using trimGalore! 0.6.7 and aligned to the hybrid genome described above using STAR 2.6.1d. Gene-level assignment was then performed using salmon 1.5.2.
Assembly: GRCm38
Supplementary files format and content: Gzipped csv of raw counts from STAR/Salmon

source_name: Brain

extract_protocol:
For FACS of microglia for RNAseq and microglial enumeration, single cell suspension from whole brain were initially incubated in 1:50 Anti-mouse CD16/32 (biolegend 101302, clone 93) and, subsequently, stained with the following antibodies: 1:100 Anti-Mouse CD45.2-PacBlue (ebioscience 48-0454-82, clone 104) and 1:200 Anti-mouse CD11b(Mac-1)-APC (ebioscience, 50-0112-80, clone M1/70) in 200µL final volume of FACS Buffer. Viability was assessed with addition of DAPI 3 minutes before collection on flow cytometer (Fisher, D1306 0.1µg/mL final concentration). Immediately after sorting microglia were centrifuged at 500xg for 10 minutes at 4°C then resuspended in 350µL RLT plus buffer (Qiagen) and stored at -80°C until nucleic acid purification with the AllPrep DNA/RNA micro kit (Qiagen) for downstream analysis.
RNA quality and quantity were assessed using TapeStation 4200 High Sensitivity RNA tapes (Agilent), and RNA-seq libraries were prepared from 5-10ng of total RNA using the SMARTer Stranded Total RNA-seq Kit v2 (Takara Bio). For analysis of allele status, libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370L). Library QC was then performed using TapeStation 4200 High Sensitivity DNA tapes (Agilent). Dual-indexed libraries were pooled and sequenced on a NextSeq 500 instrument (Illumina) for untreated RISP-/- and wild-type, age-matched animals, or a NextSeq2000 instrument for all other samples (Illumina) 75 or 100 cycles, respectively, single-end, to an average sequencing depth of 27.5 million reads per sample.

value: Brain

tag: cell type

value: Microglia

value: RISP Het

value: PLX3397 Depletion

tag: age group

value: Adult


title: MNase_CD34plus_PGE2_N32_Rep3

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

library_source: genomic

molecule: genomic DNA

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Human CD34+ hematopoietic stem and progenitor cells (HSPCs), isolated from peripheral blood of granulocyte colony-stimulating factor (G-CSF) mobilized healthy volunteers, were purchased from the Fred Hutchinson Cancer Research Center. The cells were maintained in suspension culture as previously described by Trompouki et al., 2011.

treatment_protocol: 16,16-dimethyl prostaglandin E2 was purchased reconstituted in DMSO from Cayman Chemicals (cat. #14750), aliquoted and stored in -80°C until use. Cells were counted, collected and resuspended in StemSpan medium with 2% PenStrep (CD34+ Cells) or RPMI with 1% Penicillin-Streptomycin, but in the absence of additional cytokines or growth factors. Cells were treated with dmPGE2 (Cayman chemicals) or DMSO (vehicle control) for 2 hours.

value: mobilised peripheral blood CD34+ cells


title: T1_SN

value: SN


title: LN_B2_DSP-1001460000900-C-E02

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

description: Spatial transcriptomic profiling usins DSP GeoMX Nanostring

data_processing:
Raw sequencing data were processed to generate FASTQ files using GeoMx NGS Pipeline.
A gene was called detected if the signal to noise (SNR) was ≥ 4, where the limit of quantitation (LoQ) is defined as GeoMean(NegProbes)*GeoSD(NegProbes)2.
Gene counts were normalized by Q3 normalization after the removal of genes below the detection threshold.
Assembly: GRCh38 / hg38
Supplementary files format and content: Count_matrix_Q3norm.csv: gene expression count table with Q3 normalization in .csv format
Library strategy: GeoMx

source_name: Kidney biopsy

extract_protocol:
4 um AFA-fixed paraffin-embedded human needle kidney biopsies were used.
49 specific ROI were selected for spatial transcriptomic profiling usins DSP GeoMX Nanostring technology. Slides were incubated with GeoMx WTA (Nanostring) assay probe cocktail overnight. The slides were applied with morphology markers incubation before loading onto GeoMx machine.
Library preparations was carried out according to the GeoMx NGS Readout Library Prep Manual (MAN-10117; NanoString). Libraries were sequenced on an Illumina NovaSeq6000 according to the manufacturer’s instructions.

value: Kidney biopsy

tag: region

value: Glomeruli

tag: disease

value: Lupus Nephritis


title: T2_Nac


title: RISP_WT_treatment_Naïve_ageGroup_Adult_04

value: RISP WT

value: Naive


title: RISP_Het_treatment_PLX3397 Depletion_ageGroup_Adult_01


title: LN_B2_DSP-1001460000900-C-D12


title: T1_Nac


title: MNase_CD34plus_PGE2_N2_Rep3


title: LN_B2_DSP-1001460000900-C-E01


title: RISP_WT_treatment_PLX3397 Depletion_ageGroup_Adult_01


title: MNase_CD34plus_PGE2_N8_Rep3


title: RISP_WT_treatment_Naïve_ageGroup_Adult_02


title: MNase_CD34plus_DMSO_N128_Rep3


title: T3_PFc

value: PFc


title: RISP_WT_treatment_Naïve_ageGroup_Adult_03


title: LN_B2_DSP-1001460000900-C-D10


title: MNase_CD34plus_DMSO_N32_Rep3


title: LN_B2_DSP-1001460000900-C-D11


title: RISP_WT_treatment_Naïve_ageGroup_Adult_01


title: MNase_CD34plus_DMSO_N8_Rep3


title: T1_PFc


title: LN_B2_DSP-1001460000900-C-D09


title: T3_HP

value: HP


title: MNase_CD34plus_PGE2_N128_Rep2


title: T2_HP

value: brain


title: RISP_KO_treatment_Naïve_ageGroup_Adult_03

value: RISP KO


title: LN_B2_DSP-1001460000900-C-D08


title: MNase_CD34plus_PGE2_N32_Rep2


title: RISP_KO_treatment_Naïve_ageGroup_Adult_01


title: RISP_KO_treatment_Naïve_ageGroup_Adult_02


title: MNase_CD34plus_PGE2_N8_Rep2


title: LN_B1_DSP-1001460000900-C-D05


title: N3_STR

value: STR

value: WT


title: LN_B2_DSP-1001460000900-C-D06


title: T1_HP

value: KI


title: Spleen-derived ANKL1 cells of post-treated ANKL1-PDX

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

library_source: transcriptomic single cell

data_processing:
Trimming, mapping, and counting reads were all performed using BD Rhapsody WTA Analysis Pipeline version 1.11 in SevenBridges.
Assembly: GRCh38 (GENCODE v29)
Supplementary files format and content: CSV-formatted includes reads per cell values of all analyzed cells for each sample

source_name: primary ANKL cell

growth_protocol: ANKL cells were inoculated into NOG mice and in vivo cultured.

extract_protocol:
ANKL cells were obtained liver and spleen of treated and untreated ANKL-PDXs by digesting organs with 1 mg/mL of collagenase and 20 U/mL of DNase I and density gradient centrifugation using 35% Percoll. Finally, ANKL cells were stained with biotin-conjugated anti-human CD45 antibody and anti-biotin microbeads, following purification using autoMACS.
Single cell cDNA library was constructed using BD Rhapsody WTA Amplification Kit and BD Hu Single-Cell Sample Multiplexing Kit.

treatment_protocol: 10 mg/kg of PPMX-T003 was intravenously inoculated twice per week for two weeks.

value: primary ANKL cell


title: Liver-derived ANKL1 cells of post-treated ANKL1-PDX


title: N1_STR


title: T2_PFc


title: MNase_CD34plus_PGE2_N2_Rep2


title: PLC/PRF/5 cells, CircUCK2-SiRNA_2


title: MNase_CD34plus_DMSO_N128_Rep2


title: N2_STR


title: N3_VTA

value: VTA


title: MNase_CD34plus_DMSO_N32_Rep2


title: MNase_CD34plus_DMSO_N2_Rep3


title: N2_VTA


title: Liver-derived ANKL1 cells of pre-treated ANKL1-PDX


title: RISP_KO_treatment_Naïve_ageGroup_Adult_04

value: Brain

value: Microglia

value: Adult


title: LN_B1_DSP-1001460000900-C-D02

value: Kidney biopsy


title: LN_B2_DSP-1001460000900-C-D07

value: Glomeruli


title: LN_B1_DSP-1001460000900-C-D01

value: Lupus Nephritis


title: MNase_CD34plus_DMSO_N2_Rep2

value: mobilised peripheral blood CD34+ cells


title: HEK293T cells, wild type, biol rep 2

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description:
FPKM_all_samples.txt
HEK293 IGH minus.bedgraph
HEK293 IGH plus.bedgraph

library_source: other

data_processing:
Original image data file from high-throughput sequencing were transformed into raw reads by CASAVA base recognition (Base Calling) by Novogene.
Clean data were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data by Novogene.
HISAT2 was used to align reads to the human reference genome version GRCh37.87 (hg19) by Novogene.
The mapped reads of each sample were assembled by StringTie. StringTie was run with ‘--library-type’, other parameters were set as default. Then merging transcripts from all samples through cuffmerge.
With the use of usegalaxy.org BAM files provided by Novogene were sliced by genomic region hg19 chr14:106019800-106337000 and filtered by second mate to retrieve information about the strand from which the transcript was derived.
Using Integrated Genome Browser each BAM file was split for reads from plus and minus strand, giving separate tracks. Next, depth graphs were generated for each track. Average from depht graphs representing two biological replicates, separetly for plus and minus strand, was made using "Track operations"/"Mean". Next, BedGraph files were generated.
BedGraph files were visualized in UCSC Genome Browser.
Assembly: hg19, GRCh37.87
Supplementary files format and content: .bedgraph files from average of two biological replicates per each sample, separate files for transcripts from plus and minus strand

molecule: other

growth_protocol: All B-lymphocyte cell lines were grown in RPMI 1640 (Lonza, Basel, Switzerland) supplemented with 2mM L-glutamine, 1% Penicillin-Streptomycin (Biowest, Nuaillé, France) and 10-20% fetal bovine serum (Sigma-Aldrich, Saint Louis, MO, US). HEK293T (DSMZ) cells were cultured in DMEM (Lonza) supplemented as described above. Cell lines were cultured in standard conditions: 37°C and 5% CO2 in humidified incubator. Cells were regularly tested for Mycoplasma contamination by PCR.

extract_protocol:
20 x 106  cells (30 x 106 for SUDHL4) were used for cellular fractionation as described in PMID: 35866590. All steps were performed on ice. Buffers were supplemented with DTT (if noted), 1x EDTA-free protease inhibitors and 40U/ml RNaseOUT (Invitrogen) directly before use and kept on ice. Briefly, cells were washed in ice-cold PBS. Then cell pellet was resuspended in 500 µl Buffer W (300 mM sucrose, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 2 mM MgAc2 0.5 mM DTT), followed by addition of 500 µl Buffer L (Buffer W supplemented with 6 mM CaCl2, 0.2 % IGEPAL CA-630, 0.5 mM DTT). Lysates were centrifuged 1000 x g, 4°C, 10 min. Resulting supernatant was saved as cytoplasmic fraction, while nuclear pellet was processed further. Nuclei were washed in Buffer G (50 mM Tris-HCL pH 8.0, 25% glycerol, 5 mM MgAc2, 0.1 mM EDTA, 5 mM DTT), then lysed with Buffer U (1 M urea, 20 mM HEPER pH 7.5, 7.5 mM MgCl2, 0,1 mM EGTA, 300 mM NaCl, 1 mM DTT), vortexed and centrifuged 20 000 x g, 4°C, 10 min. Resulting supernatant was saved as nuclear fraction, while chromatin pellet was washed twice in Chromatin Wash Buffer (50 mM Tris-HCl pH 8.0 supplemented with 40 U/ml RNaseOUT). Chromatin pellet was then sonicated twice [5 sec on, 30 sec off] (Misonix 3000; Misonix, Farmingdale, NY, USA) on ice in 300 µl Buffer G for RNA isolation. RNA was isolated from each fraction using Trizol method. Additionally, 10 μl 500 mM EDTA was added to chromatin fraction and heated 10 min 65°C with 600 rpm shaking on thermoblock to facillitate RNA release from chromatin. RNA samples were stored in -80°C until analysis. RNA samples were tested on 2% agarose gel for integrity. Prior to sequencing, RNA was treated with TURBO-DNase (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer instructions, followed by purification using RNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) with additional DNase treatment on the column.
EpicentreRibo-zeroTM rRNA Removal Kit (Epicentre, USA) and NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) was used for library preparation.

value: Human embryonic kidney

tag: fraction

value: chromatin-enriched RNA


title: N1_VTA


title: N3_SN

value: SN


title: LN_B1_DSP-1001460000900-C-D04


title: LN_B1_DSP-1001460000900-C-C12


title: LN_B1_DSP-1001460000900-C-C11


title: MNase_CD34plus_PGE2_N128_Rep1


title: Spleen-derived ANKL1 cells of pre-treated ANKL1-PDX


title: LN_B1_DSP-1001460000900-C-D03


title: P493-6 cells, wild type, biol rep 2

description:
FPKM_all_samples.txt
P4936 IGH minus.bedgraph
P4936 IGH plus.bedgraph

value: B lymphoblastoid cells


title: MNase_CD34plus_PGE2_N32_Rep1


title: N2_SN

value: brain


title: P493-6 cells, wild type, biol rep 1


title: SUDHL4 cells, wild type, biol rep 2

description:
FPKM_all_samples.txt
SUDHL4 IGH minus.bedgraph
SUDHL4 IGH plus.bedgraph

value: Diffuse Large B-cell Lymphoma


title: Control_B1_DSP-1001460000900-C-C09

value: Control


title: Control_B1_DSP-1001460000900-C-C10


title: N3_Nac

value: Nac

value: WT


title: N1_SN


title: MNase_CD34plus_PGE2_N8_Rep1


title: Control_B1_DSP-1001460000900-C-C08


title: N2_Nac


title: SUDHL4 cells, wild type, biol rep 1


title: Control_B1_DSP-1001460000900-C-C07


title: MNase_CD34plus_DMSO_N128_Rep1


title: HEK293T cells, wild type, biol rep 1


title: DG75 cells, wild type, biol rep 2

description:
FPKM_all_samples.txt
DG75 IGH minus.bedgraph
DG75 IGH plus.bedgraph

value: Burkitt lymphoma


title: N1_Nac


title: N3_PFc

value: PFc


title: MNase_CD34plus_DMSO_N8_Rep1


title: Control_B1_DSP-1001460000900-C-C06


title: Control_B1_DSP-1001460000900-C-C05


title: DG75 cells, wild type, biol rep 1


title: MNase_CD34plus_PGE2_N2_Rep1


title: BL41 cells, wild type, biol rep 2

description:
FPKM_all_samples.txt
BL41 IGH minus.bedgraph
BL41 IGH plus.bedgraph


title: N1_PFc


title: MNase_CD34plus_DMSO_N2_Rep1


title: N2_PFc


title: BL41 cells, wild type, biol rep 1


title: Control_B2_DSP-1001460000900-C-C04


title: N3_HP

value: HP


title: Control_B2_DSP-1001460000900-C-C03


title: RISP_Het_treatment_Cuprizone_ageGroup_Adult_04

value: Brain

value: Microglia

value: RISP Het

value: Cuprizone

value: Adult


title: N2_HP


title: RISP_Het_treatment_Cuprizone_ageGroup_Adult_03


title: Control_B2_DSP-1001460000900-C-C02

value: Kidney biopsy

value: Glomeruli


title: H4_PGE2

data_processing:
All ChIP-Seq datasets were aligned to UCSC build version hg19 of the human genome using Bowtie2 (version 2.2.1; Langmead et al., 2012)with the following parameters: -end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak-finding algorithm to identify regions of ChIP-Seq peaks, with a q-value threshold of enrichment of 0.05 and false discovery rate of < 0.01 for all datasets. The genome-wide occupancy profile figures were generated by deeptools (Ramirez et al., 2016) using the reference-point mode and the scale-regions mode. The genomic distribution of peaks was plotted using the ChIPSeeker R package, annotatePeak to assign peaks to a genomic annotation, which includes whether a peak is in the TSS, Exon, 5’UTR, 3’ UTR, Intronic or Intergenic. The genomeannotation is from the R-bioconductor annotation packages. Heat maps of the ChIP-Seq binding were generated using the input normalized results of the MACS peak calling output. The outputted bedGraph files were converted to BigWig files. Those files were then processed using computeMatrix and plotHeatmap tools within the deeptools 3.0 package. Enhancers were assigned to genes using GREAT to the nearest genes within 15kb of peaks.
Peaks were called using MACS 2.0 with the following setting: q-value 0.05
Assembly: hg19
Supplementary files format and content: bedGraph pileup from MACS 2.0 output

growth_protocol: 16,16-dimethyl prostaglandin E2 was purchased reconstituted in DMSO from Cayman Chemicals (cat. #14750), aliquoted and stored in -80°C until use. Cells were counted, collected and resuspended in StemSpan medium with 2% PenStrep (CD34+ Cells) or RPMI with 1% Penicillin-Streptomycin, but in the absence of additional cytokines or growth factors. Cells were treated with dmPGE2 (Cayman chemicals) or DMSO (vehicle control) for 2 hours.

extract_protocol: ChIP-Seq libraries were prepared using the following protocol. End repair of immunoprecipitated DNA was performed using the End-It End-Repair kit (Epicentre, ER81050) and incubating the samples at 25°C for 45 min. End-repaired DNA was purified using AMPure XP Beads (1.8X of the reaction volume) (Agencourt AMPure XP – PCR purification Beads, BeckmanCoulter, A63881) and separating beads using DynaMag-96 Side Skirted Magnet (Life Technologies, 12027). A-tails were added to the end-repaired DNA using NEB Klenow Fragment Enzyme (3’-5’ exo, M0212L), 1X NEB buffer 2 and 0.2mM dATP (Invitrogen, 18252-015) and by incubating the reaction mix at 37μC for 30 min. A-tailed DNA was cleaned up using AMPure beads (1.8X of reaction volume). Subsequently, cleaned up A-tailed DNA went through Adaptor ligation reaction using Quick Ligation Kit (NEB, M2200L) following manufacturer’s protocol. Adaptor-ligated DNA was first cleaned up using AMPure beads (1.8X of reaction volume), eluted in 100μl and then size-selected using AMPure beads (0.9X of the final supernatant volume, 90μl). Adaptor-ligated DNA fragments of proper size were enriched with PCR reaction using Fusion High-Fidelity PCR Master Mix kit (NEB, M0531S) and specific index primers supplied in NEBNext Multiplex Oligo Kit for Illumina (Index Primer Set 1, NEB, E7335L). Conditions for PCR used are as follows: 98°C, 30 sec; [98°C, 10 sec; 65°C, 30 sec; 72°C, 30 sec] X 15 to 18 cycles; 72°C, 5 min; hold at 4°C. PCR enriched fragments were cleaned up using AMPure beads (1X of reaction volume). Libraries were eluted in 20μl elution buffer. All the libraries went through quality control analysis using an Agilent Bioanalyzer and subjected to next-generation sequencing using Illumina Hiseq 2500 platform.

treatment_protocol: 20 million cells were crosslinked by the addition of 1/10 volume 11% fresh formaldehyde for 10 min at room temperature. The crosslinking was quenched by the addition of 1/20 volume 2.5M glycine for 5 minutes. Cells were washed twice with ice-cold PBS. Cells were lysed in 10mL of Lysis buffer 1 (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, plus protease and phosphatase inhibitors) for 10 min at 4°C. After centrifugation, cells were resuspended in 10 mL of Lysis buffer 2 (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, plus protease and phosphatase inhibitors) for 10 min at room temperature. Cells were pelleted and resuspended in 3mL of sonication buffer (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.05% N-lauroylsarcosine, plus protease and phosphatase Inhibitors) and sonicated in a Bioruptor sonicator for 36 cycles of 30 sec each followed by a 1min resting interval. Samples were centrifuged for 10min at 18,000g and 1% Triton-X was added to the supernatant. Prior to the immunoprecipitation, 50mL of protein G beads (Invitrogen 100-04D) for each reaction were washed twice with PBS, 0.5% BSA twice. Finally, the beads were resuspended in 250μL of PBS, 0.5% BSA and 5μg of each antibody. Beads were rotated for at least 6 hours at 4°C and then washed twice with PBS with 0.5% BSA. Cell lysates were added to the beads and incubated at 4°C overnight. Beads were washed 1x with (20mM Tris-HCl. pH 8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), 1x with (20mM Tris-HCl, pH 8, 500mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100), 1x with (10mM Tris-HCl, pH 8, 250nM LiCl, 2mM EDTA, 1% NP4-0) and 1x with TE and finally resuspended in 200μL elution buffer (50mM Tris-Hcl, pH 8.0, 10mM EDTA, 0.5%–1% SDS). 50μL of cell lysates prior to addition to the beads was kept as input. Crosslinking was reversed by incubating samples at 65C for at least 6 hours. Afterwards the cells were treated with RNase and proteinase K and the DNA was extracted by Phenol/Chloroform extraction.

tag: tag

value: mobilised peripheral blood CD34+ cells


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_06

value: RISP KO


title: Control_B2_DSP-1001460000900-C-C01


title: N1_HP

value: brain


title: H4_DMSO


title: MNase_CD34plus_DMSO_N32_Rep1


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_05


title: WT Th0_4

city: Baltimore

first: Drew

last: Pardoll

state: Maryland

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

data_processing: counts

molecule: polyA RNA

source_name: CD4 Th0 cells

extract_protocol: none provide

value: CD4 Th0 cells


title: Tip60_PGE2


title: Pu.1_PGE2


title: Tip60_DMSO


title: Pu.1_DMSO


title: LN_A2_DSP-1001460000900-C-B11

value: Lupus Nephritis


title: H2B_PGE2


title: WT Th0_3


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_03


title: LN_A2_DSP-1001460000900-C-B10


title: H2B_DMSO


title: RISP_Het_treatment_Cuprizone_ageGroup_Adult_02


title: LN_A2_DSP-1001460000900-C-B12


title: LN_A2_DSP-1001460000900-C-B08


title: LN_A2_DSP-1001460000900-C-B09


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_01


title: WT iTregaCD3_9

source_name: CD4 iTreg cells

value: CD4 iTreg cells

value: iTreg  treat with aCD3+IL2 18hr


title: Nrn1_KO Th0_1


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_02


title: si_4

city: Beijing

first: Danhui

last: Ruan

address: Peking University HSC 38 Xueyuan Road, Haidian District Beijing P.R.China

institute: Peking University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. The UMI (Unique Molecular Identifiers) was extracted by UMI-tools v1.0.0. All the downstream analyses were based on the clean UMI reads with high quality.
Index of the reference genome was built using Hisat2 v2.0.4 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We used UMI-tools v1.0.0 to deduplicate reads based on the mapping co- ordinate and the UMI attached to the read.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw, FPKM values for each Sample

growth_protocol: SMMC-7721 cell lines were cultured in DMEM (Gibco) containing 10% FBS.

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and RNase H. In order to select cDNA fragments of preferentially 100~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Adapter ligation at 25°C for 10min before PCR . Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SMMC-7721  cell lines were transfected with 50 nM si-NC or si-circPTEN-MT (GAGACAAAAAGGTTTTTGG). 48 hours later, cells were collected and subjected to RNA-seq.

value: Hepatocellular carcinoma cell lines

value: transfected with si-circPTEN-MT


title: LN_A2_DSP-1001460000900-C-B06


title: YX6_mRNA_lncRNA

city: Shanghai

first: Qiange

last: Xiao

address: No. 1954 Huashan Road, Xuhui District

institute: Shanghaijiaotong University

data_processing:
For mRNA and lncRNA, high-quality clean data were obtained by removing adapters, poly-N sequences, and low-quality reads from the raw data using in-house Perl scripts. The processed RNA-seq data were then mapped to the Ensembl mouse reference genome (Mus musculus GRCm38) using Hisat2 (version 2.2.1). Transcript assembly was performed with the Ensembl mouse annotation database (GRCm38) using StringTie (version 2.1.5), and the FPKM expression matrix was generated.For miRNA, Cutadapt (version 4.2) was used to remove adapters and sequences smaller than 10 nt. The processed sequencing data were then mapped to the mouse reference genome (GRCm38) using Bowtie (version 1.3.1) and miRDeep2, which provided the final reads of miRNA hairpin precursor and mature miRNA. miRDeep2 was also used for quantifying the processed sequences.For circular RNA, Trimgalore and Fastp were used to remove adapters, poly-N sequences, and low-quality reads from the raw data. Clean data were obtained by removing partial rRNA and E. coli contamination using Bowtie2. Circular RNA quantification and differential expression analysis were performed using CIRI2 software.
Assembly: GRCm38
Supplementary files format and content: Table-delimited text file include reads count of each reads for each sample.

source_name: liver

growth_protocol: Forty-five male C57BL/6 mice were purchased from Shanghai JieSiJie Laboratory Animal Co., Ltd., Shanghai, China. The mice were 6 weeks old and SPF level. Mice were housed at a temperature of 21-22℃ and humidity of about 50-55%, and kept in a 12/12 h light‑dark cycle animal house. Mice ate and drank freely. All experiments on mice have been approved and conducted under the guidance of the Institutional Animal Care and Use Committee, Shanghai Jiao Tong University, China. We confirm that the study is reported in accordance with ARRIVE guidelines.

extract_protocol:
According to manufacturer’s instructions, total RNA was extracted from each liver tissue using TRIzol reagent. The A260/A280 ratio was used to assess RNA purity. There was A260/A280 ratio>1.9 in all liver tissue samples, which meant the RNA purity was high for sequencing.
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations respectively.

treatment_protocol: Forty-five male C57BL/6 mice were randomly divided into three groups of 15 each: the Control group, treated with corn oil and double distilled water; the Cirrhosis group, treated with CCl4 and double distilled water; and the Cirrhosis-PTH group, treated with CCl4 and PTH. The PTH preparation was a 50 mg/ml solution from Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., while the CCl4 mixture was a 10% solution in corn oil. Control group mice received intraperitoneal injections of corn oil and oral double distilled water. Cirrhosis group mice received intraperitoneal injections of 10% CCl4 and oral double distilled water. Cirrhosis-PTH group mice received intraperitoneal injections of 10% CCl4 and oral PTH preparation.

value: liver

tag: strain

tag: Sex

value: male

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: si_NC

value: transfected with si-NC


title: Nrn1_KO iTregaCD3_8


title: RISP_KO_treatment_Naïve_ageGroup_Adult_11

value: Brain

value: Microglia

value: Naive


title: LN_A2_DSP-1001460000900-C-B05

value: Kidney biopsy

value: Glomeruli


title: RISP_KO_treatment_Cuprizone_ageGroup_Adult_04

value: RISP KO

value: Cuprizone

value: Adult


title: Nrn1_KO iTregaCD3_7


title: RISP_KO_treatment_Naïve_ageGroup_Adult_10


title: YX5_mRNA_lncRNA


title: LN_A2_DSP-1001460000900-C-B04

value: Lupus Nephritis


title: YX4_mRNA_lncRNA


title: LN_A1_DSP-1001460000900-C-B03


title: RISP_Het_treatment_Naïve_ageGroup_Adult_11

value: RISP Het


title: WT iTreg_4

value: CD4 iTreg cells

value: WT

value: iTreg resting in IL2 medium


title: RISP_Het_treatment_Naïve_ageGroup_Adult_10


title: LN_A1_DSP-1001460000900-C-B02


title: YX2_mRNA_lncRNA

value: liver


title: Nrn1_KO iTreg_2


title: Nrn1_KO Th0_2

value: CD4 Th0 cells


title: RISP_Het_treatment_Naïve_ageGroup_Adult_09


title: LN_A1_DSP-1001460000900-C-B01


title: Nrn1_KO iTreg_1


title: LN_A2_DSP-1001460000900-C-B07


title: RISP_KO_treatment_Naïve_ageGroup_Adult_09


title: RISP_Het_treatment_Cuprizone_ageGroup_Adult_01


title: WT iTregaCD3_10

value: iTreg  treat with aCD3+IL2 18hr


title: YT6_mRNA_lncRNA

value: male

value: 10% CCl4 mixture injection (10 µl/g, twice a week), double distilled water orally (daily)


title: intestinal organoid, DMSO, rep3

city: Jinan City

first: Yue

last: Wang

address: No. 44, Wenhua West Road

institute: Shandong University

data_processing:
RNA-seq run was performed using the Illumina Novaseq 6000 sequencing platform.
Quantification of mRNA from the RNA-seq FASTQ files was performed using Salmon, v. 1.8.0.
Sample-wise quant.sf files containing raw transcript-level read estimates were read into R, v. 4.1.2 and were combined into a data matrix. Transcripts with very low total counts (< 10) across all samples were filtered out.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Duodenum

growth_protocol: Mouse small intestinal orgnoids were maintained in IntestiCult™ organoid growth medium (STEMCELL) supplemented with 1X penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Organoids cultured for 2 days were incubated with a series of bile acids at 50 mmol/L for 96 hours and lysed for RNA extraction.

value: organoid

value: Duodenum

value: DMSO (Control), 2 days


title: MNase_CD34plus_DMSO_N8_Rep2

value: mobilised peripheral blood CD34+ cells


title: LN_A1_DSP-1001460000900-C-A11

value: Kidney biopsy

value: Glomeruli


title: YX3_mRNA_lncRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: YT5_mRNA_lncRNA


title: RISP_KO_treatment_Naïve_ageGroup_Adult_08

value: Brain

value: Microglia

value: RISP KO

value: Naive

value: Adult


title: intestinal organoid, DMSO, rep2

value: WT


title: WT iTreg_3

value: CD4 iTreg cells

value: iTreg resting in IL2 medium


title: LN_A1_DSP-1001460000900-C-A10

value: Lupus Nephritis


title: intestinal organoid, DMSO, rep1


title: intestinal organoid, DCA, rep3

value: DCA, 2 days


title: RISP_Het_treatment_Naïve_ageGroup_Adult_07

value: RISP Het


title: YT3_mRNA_lncRNA

value: liver

value: male

value: 10% CCl4 mixture injection (10 µl/g, twice a week), double distilled water orally (daily)


title: YX1_mRNA_lncRNA


title: LN_A1_DSP-1001460000900-C-A08

value: Kidney biopsy


title: RISP_Het_treatment_Naïve_ageGroup_Adult_08


title: RISP_KO_treatment_Naïve_ageGroup_Adult_07


title: LN_A1_DSP-1001460000900-C-A12

value: Glomeruli


title: RISP_Het_treatment_Naïve_ageGroup_Adult_06


title: Control_A1_DSP-1001460000900-C-A07

value: Control


title: intestinal organoid, DCA, rep1

value: organoid

value: Duodenum


title: YT1_mRNA_lncRNA


title: YT2_mRNA_lncRNA


title: Control_A1_DSP-1001460000900-C-A05


title: RISP_KO_treatment_Naïve_ageGroup_Adult_06

value: Brain

value: Microglia

value: RISP KO


title: Control_A1_DSP-1001460000900-C-A06


title: YT4_mRNA_lncRNA


title: YC7_mRNA_lncRNA

value: Corn oil injection (10 µl/g, twice a week), double distilled water orally (daily)


title: intestinal organoid, CDCA, rep2

value: WT

value: CDCA, 2 days


title: RISP_Het_treatment_Naïve_ageGroup_Adult_05

value: Naive

value: Adult


title: YC8_mRNA_lncRNA


title: YC6_mRNA_lncRNA


title: intestinal organoid, CDCA, rep1


title: 8_OB_GG

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Partek® Flow® Genomic Analysis Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek® Flow® Genomic Analysis Software
Trimmed sequence reads were mapped to MM10 using Partek® Flow® Genomic Analysis Software
Read count extraction and normalization were performed using Partek® Flow® Genomic Analysis Software
Assembly: MM10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: tissue

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq strandard mRNA Library Prep Kit following manufacturer's protocols.

value: tissue

value: Edited


title: LN_A1_DSP-1001460000900-C-A09

value: Lupus Nephritis


title: Control_A1_DSP-1001460000900-C-A04


title: intestinal organoid, DCA, rep2

value: DCA, 2 days


title: Control_A2_DSP-1001460000900-C-A02

value: Kidney biopsy


title: YC3_mRNA_lncRNA

value: liver

value: male


title: Control_A2_DSP-1001460000900-C-A03

value: Glomeruli

value: Control


title: NK92_treated_withPPMX-T003

data_processing:
Obtained FASTQ-formatted files were trimmed with Trimmomatic version 0.38.
Mapping was performed using HISAT2 version 2.2.0.
Read count was performed with StringTie version 2.1.3b and EdgeR version 3.17.
Assembly: hg38
Supplementary files format and content: CSV-formatted file containig raw count,FKPM value, and TPM value for each sample

growth_protocol: NK92 cells were cultured in 2% human serum-containing Artemis-Medium 1.

extract_protocol:
Total RNA was extracted using Sepasol-RNA I super G.
cDNA library was prepared using TruSeq stranded mRNA Sample Prep Kit.

treatment_protocol: Cells were treated with 10 µg/mL of PPMX-T003 or nothing for 6 hours.

value: 10 µg/mL of PPMX-T003 for 6hrs


title: intestinal organoid, CA, rep1

value: organoid

value: Duodenum

value: CA, 2 days


title: YC2_mRNA_lncRNA

value: Corn oil injection (10 µl/g, twice a week), double distilled water orally (daily)


title: intestinal organoid, CA, rep3

value: WT


title: 5-OB-AA

value: Unedited


title: 6-OB-AA


title: YC1_mRNA_lncRNA


title: intestinal organoid, CA, rep2


title: intestinal organoid, CDCA, rep3

value: CDCA, 2 days


title: YX6_circRNA

data_processing:
For mRNA and lncRNA, high-quality clean data were obtained by removing adapters, poly-N sequences, and low-quality reads from the raw data using in-house Perl scripts. The processed RNA-seq data were then mapped to the Ensembl mouse reference genome (Mus musculus GRCm38) using Hisat2 (version 2.2.1). Transcript assembly was performed with the Ensembl mouse annotation database (GRCm38) using StringTie (version 2.1.5), and the FPKM expression matrix was generated.For miRNA, Cutadapt (version 4.2) was used to remove adapters and sequences smaller than 10 nt. The processed sequencing data were then mapped to the mouse reference genome (GRCm38) using Bowtie (version 1.3.1) and miRDeep2, which provided the final reads of miRNA hairpin precursor and mature miRNA. miRDeep2 was also used for quantifying the processed sequences.For circular RNA, Trimgalore and Fastp were used to remove adapters, poly-N sequences, and low-quality reads from the raw data. Clean data were obtained by removing partial rRNA and E. coli contamination using Bowtie2. Circular RNA quantification and differential expression analysis were performed using CIRI2 software.
Assembly: GRCm38
Supplementary files format and content: Table-delimited text file include cpm value of each reads for each sample.

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: hnRNPK flox/flox Alb-Cre

city: 31上海市

first: Yangjun

last: Luo

address: 岳阳路320号

institute: 中国科学院上海营养与健康研究所

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using , then mapped to mm10 whole genome using Bowtie2 v2.4.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: mm10

source_name: hnRNPK flox/flox Alb-Cre mice liver

extract_protocol:
hnRNPK flox/flox and hnRNPK flox/flox Alb-Cre mice liver were collected.Then mRNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

value: hnRNPK flox/flox Alb-Cre


title: NK92_Control

value: none; Control


title: hMSCs Ti 2

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

source_name: Mesenchymal stem cells

growth_protocol: hMSCs were cultured under media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) supplemented with  1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~2500 cells/cm2. All experiments were completed with cell populations under P4.

extract_protocol:
At the end of 7 days of culture, total RNA was extracted (Zymogen, High Purity RNA Isolation kit), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hMSCs were cultured and treated with/without and the various ion concentrations (29.95 µM Ag, 26.66 µM Cu, 1.48 µM Pt, 41.45 µM Ta, or 10.44 µM Ti) for 7 days with continuous ion exposure (retreatment with ion solutions with media replacement)

value: Bone marrow derived mesenchymal stem cells

value: Ti


title: 7_OB_GG

value: tissue

value: Edited


title: 584ctxDay3

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

description:
Raw_2.csv
Normalized_2.csv

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Homo sapiens (human) genome assembly GRCh38 (hg38)/Mus musculus (house mouse) genome assembly GRCm39 (mm39) according to the corresponding species by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Assembly: hg38 or mm39
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with normalized gene counts

source_name: cortex

growth_protocol: For sample 1-12, mice were breed in cages before collection of tissue. For Sample 13 - 14, the monocyte-derived microglia were maintain in RPMI1640 medium, supplemented with 1 % P/S, 0.1 μg/ml IL-34 and 0.01 μg/ml GM-CSF

extract_protocol:
Total RNA from cultured MDMi and mouse cortex samples was extracted using TRIzol Reagent (Invitrogen, 15596026) according to the instruction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For sample 1-6, they were treated with SM03 (anti-human CD22 antibody) or IgG1 isotype 21 days before sacrifce. Antibodies were intravenously adminstrated once a week. For sample 7-12, mice were intracerebroventricularly injected with PBS or 9 μg mouse soluble CD22. Mouse cortice were collected 3 days after administration. For sample 13-20, cells were treated with 10 μg/mL sCD22 for 24 hours. Cells were then collected for RNA.

value: cortex

value: PBS


title: hMSCs Ti 1


title: hnRNPK flox/flox

institute: 中国科学院上海营养与健康研究所

source_name: hnRNPK flox/flox mice liver

value: liver

value: hnRNPK flox/flox


title: YX5_circRNA

value: male


title: hMSCs Ta 3

value: Ta


title: YX3_circRNA


title: 583ctxDay3

description:
Raw_2.csv
Normalized_2.csv


title: YX2_circRNA


title: hMSCs Ta 1


title: hMSCs Ta 2


title: YX1_circRNA


title: 575ctxDay3

description:
Raw_2.csv
Normalized_2.csv


title: 571ctxDay3

description:
Raw_2.csv
Normalized_2.csv


title: YT5_circRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), double distilled water orally (daily)


title: hMSCs Pt 2

value: Pt


title: 570ctxDay3

description:
Raw_2.csv
Normalized_2.csv


title: hMSCs Cu 3

value: Cu


title: YT6_circRNA


title: hMSCs Cu 2


title: NKL2_delta-LGIIK9het25_MseI-insitu-HiC_rep2

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: processed matrices contain genomic loci in defined bin sizes for the column names

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.5 for all analyses. Briefly, raw fastq files were mapped to the Neurospora genome (version 14 [Rodriguez et al., 2022 [Pubmed ID: 35244156]) using bowtie2 (version 2.3), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with both DpnII [GATC] and MseI [TTAA] restriction sites used for quality control), and resulting images of the contact matrix images were made with hicPlotMatrix; (total) merged matrices were constructed by first merging all replicates using the cat command and processing them in an identical manner. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. Differences between wild type datasets (from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and mutant datasets were performed with hicCompareMatrices in which the experimental (mutant) matrix was listed first and the control (wild type) matrix was listed second; all compare matrices used the --log2diff flag to obtain the log2 difference in contact strength. Wild type matrices with approximately the same number of valid reads as the mutant dataset were generated by selecting the appropriate number of total reads from fastq files of the wild type datasets (Rodriguez et al., 2022) using the sed command, reads were mapped to the nc14 genome, and the contact matrix built with hicBuildMatrix as above.
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156]), or the NKL2 genome generated here (deleted of the LGIIK9het25 constitutiive heterochromatic region).
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts, Knight-Ruiz corrected contact counts, or the calculated log2 difference in contacts between a wild type strain (wild type data from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and the mutant strains presented here.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: To grow WT Neurospora culture, 25 mL cultures containing 1x Vogel’s medium + 1.5% sucrose were inoculated with 1.25x10^8 conidia, (harvested from ~six baby slants by vortexing with water; conidia were washed twice prior to use) and grown at 32 °C with shaking at 200 revolutions per minute (RPM) for ~four hours until ~90% of conidia had germinated, and growth tubes were ~4x the length of the initial conidia.

extract_protocol:
First, the concentration of genomic DNA per spheroplast aliquot was determined by resuspending one aliquot per culture replicate in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 mg proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 mg RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Spheroplasts containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x restriction enzyme buffer (either DpnII, above) and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Spheroplasts were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII or MseI buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII and MseI (double digest) for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used eight and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced on an Illumina HiSeq 2500 at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon as 100 nucleotide (nt) paired-end (PE100) sequencing runs.

treatment_protocol: Methanol-free formaldehyde was added to a final concentration of 1% and cultures were incubated 10 minutes at room temperature (RT; ~25°C) with shaking at 100 RPM for crosslinking; 1 M Tris-HCl [pH 8 at 25°C] (Hoffman et al. 2015) was added to a final concentration of 125 mM and cultures were incubated at RT for 10 minutes, shaking at 100 RPM, to quench the reaction. Conidia were harvested by centrifugation (4000 RPM, 3 min) and resuspended gently in 20 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4 [pH 7.5]) with b-mercaptoethanol added to 30mM. Conidia were pelleted again and resuspended in 20 mL spheroplasting buffer with b-mercaptoethanol added to 1mM. VinoTaste (Novozymes; powder dissolved in water to a stock solution of 50 mg/mL) was added to 50mg and strains were digested at 30°C, shaking at 100 RPM, for 60 min. Spheroplasts were harvested by centrifugation (3500 RPM, 2 min) and pellets were washed twice with 20 mL Spheroplasting buffer, followed by three washes of the buffer of the 1x restriction enzyme to be used for digestion, here DpnII buffer (100 mM NaCl, 50 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL BSA). Washed pellets were resuspended in 3.5 mL of the same restriction enzyme buffer, split into four – 1 mL aliquots in 1.7 mL Eppendorf tubes, pelleted (10,000 rpm, 5 min), whereupon the supernatant was removed, and spheroplast pellets were stored at -80°C.

value: germinated conidia

value: hyphae

value: mat A; {delta}LGIIK9het25::hph


title: YT4_circRNA


title: hMSCs Cu 1


title: YT3_circRNA


title: NKL2_delta-LGIIK9het25_MseI-insitu-HiC_rep1


title: NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep4


title: hMSCs Ag 2

value: Ag


title: YT1_circRNA


title: NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep3


title: hMSCs Ag 1

value: Bone marrow derived mesenchymal stem cells


title: NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep2


title: 576ctxDay3

description:
Raw_2.csv
Normalized_2.csv


title: YX4_circRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: hMSCs Pt 1


title: NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep1


title: hMSCs 2

value: Control


title: YC7_circRNA

value: Corn oil injection (10 µl/g, twice a week), double distilled water orally (daily)


title: YC6_circRNA


title: N4933_delta-K27-region_DpnII-insitu-HiC_rep2

value: mat a; {delta}K27region (delta 47.4kb)::hph


title: hMSCs Ag 3


title: YC3_circRNA


title: ChIP-Seq_RNAPolII_hTERT-RPE1_TPT

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

data_processing:
Illumina HiSeq 4000 and Illumina NovaSeq 6000
Base calling: NovaSeqControl Software v1.8.0, RTA v3 ; HiSeq Control Software v2.2.68, RTA v1.18.66 ; bcl2fastq v2.20.0
Alignment: BWA (v0.7.17) was used to align FASTQ files on GRCh38.p13 reference genome (downloaded from ENCODE) augmented with Gluc_episomal DNA sequence.
Alignment conversion and sorting: the alignment produced by BWA were converted into BAM format and sorted with samtool (v1.10)
Peak calling was done with MACS2 (v2.2.7.1) callpeak using parameters --format BAM --gsize hs --SPMR --keep-dup 1 --qvalue 0.05 --nomodel --extsize 1000.
Smc6 peak filtering: the Smc6 peaks found by MACS were filtered to exclude: 1) peaks whose fold-enrichment is below 2.5; 2) peaks in telomeric region chr5:9277-12488; 3) peaks in centromeric region chr4:49709342-49712626; 3) peaks in episomal promoter regionchr6:73520103-73522066
Smc6 peaks were further annotated with ENCODE v41 genes located within a 10kb distance of them; and manually curated.
Assembly: hg38
Supplementary files format and content: bed.gz format

growth_protocol: ChIP analysis was performed using chromatin extracted from about 5 × 10^6 HA-tagged Smc6-expressing hTERT-RPE1 cells cultured in a 10- cm diameter dish. Cells were treated either with DMSO or with 10 μM of triptolide 24 hours prior fixation.

extract_protocol:
PBS, cells were resuspended and lysed for 10 min at 4°C in 1 mL Cell Lysis Buffer (20 mM Tris-HCl (pH 8.0), 85 mM KCl, 0.5% NP-40) supplemented with EDTA-free protease inhibitor cocktail (Roche, 4693132001). The nuclei were recovered by centrifugation at 500 g for 5 min at 4°C and washed once in the same buffer. Nuclei were resuspended in 500 μL Nuclei Lysis Buffer (10 mM Tris-HCl (pH 7.5), 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitor cocktail) and incubated for 10 min at 4°C. Chromatin was fragmented by sonication 3 × 10 s at 60% duty cycle, with 30 sec on wet-ice between sonication cycles, using a microtip-equipped SLPe sonifier (Branson Ultrasonics ™ Sonifier™, Brookfield, USA). The sonicated samples were centrifuged at 16,000 g for 10 min. The supernatants were collected and 50 µL (1/10) was set aside as input controls. The rest (450 µL) was diluted with 1500 μl ChIP Dilution Buffer (0.01% SDS, 1.2 mM EDTA, 1.1% Triton X-100, 16.7 mM Tris-HCl (pH 8), 167 mM NaCl) supplemented with protease inhibitors and mixed with 50 μL Dynabeads™ Protein G (Invitrogen, 10009D) coupled either to 3 μg anti-HA antibody (Invitrogen, MA5-27915) in case of HA-Smc6 analysis, 5 μg anti-RPB1 (8WG16) (Covance, MMS-126R) for RNA pol II, 2 μg anti-H3pan  (Diagenode, C15410324) or 4 μg anti-H3.3 (Diagenode, C15210011). After overnight incubation at 4°C on a rotating wheel, the beads were washed twice with 1 mL Cell Lysis Buffer, twice with high-salt buffer (50 mM HEPES-KOH (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), once with LiCl buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute immunoprecipitated chromatin fragments, beads were incubated for 10 min at 65°C in 400 μL freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3). DNA crosslinks were reversed by overnight incubation at 65°C with 0.6M NaCl and 80 μg proteinase K (Eurobio Scientific, GEXPRK01-I5). Samples were extracted once with Phenol – chloroform – isoamyl alcohol (Sigma, 77617), once with chloroform (Reactolab SA, P02410E16), ethanol precipitated and then resuspended in water. The input DNA samples were treated identically.
ChIP-enriched DNA were used to prepare libraries and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Library molarity and quality were assessed with the Qubit (Thermofisher Scientific) and Tapestation (Agilent Technologies - DNA High sensitivity chip). Libraries were sequenced on a HiSeq 4000 and a NovaSeq 6000 Illumina sequencers for SR100 reads.

treatment_protocol: Cells were harvested with trypsin-EDTA and collected by low-speed centrifugation 500 g for 5min. Cells were rinsed once with PBS, resuspended in DMEM and fixed with 1% formaldehyde (Sigma 47608) for 10 min at RT before quenching with 330 mM glycine 5min at RT and then incubated 15min on ice, and washed two further times with ice-cold PBS.

value: immortalized human retina pigment epithelial cells

value: WT HA-Smc6 overexpressing cell

value: Treated with TPT (10µM) 24h prior fixation

tag: chip antibody

value: Anti-RPB1 (Covance, MMS-126R)


title: N4933_delta-K27-region_DpnII-insitu-HiC_rep1


title: PATC50_ICG replicate 3

city: San Antonio

first: Yufan

last: Zhou

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

data_processing:
Raw RNA-seq reads were mapped to human HG19 genome by HISAT2.
The expression counts were computed by htseq-count.
Assembly: HG19
Supplementary files format and content: Headers of count files: gene symbol, counts

growth_protocol: Routine cell media for all cell lines, respectively.

extract_protocol:
Total RNA was extracted from cells with Quick-RNA Miniprep Kit (ZYMO Research) according to manufacturer’s protocols.
The RNA-seq libraries were prepared with Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocols. The prepared RNA-seq libraries were sequenced on Illumina HiSeq 3000 platform.

treatment_protocol: untreated or treated with 10 µM ICG-001 for 48 hours

tag: cell types

value: immortalized pancreatic cell line

value: treated with 10 uM ICG-001 for 48 hours


title: YC2_circRNA

value: liver

value: male


title: ChIP-Seq_RNAPolII_hTERT-RPE1_DMSO


title: YC1_circRNA


title: YT2_circRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), double distilled water orally (daily)


title: Totalinput_RNAPolII_hTERT-RPE1_DMSO


title: YX6_miRNA


title: PATC50_ICG replicate 1


title: hMSCs 1


title: Dermal Fibroblasts

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

institute: Osaka University graduate school of dentistry

data_processing:
Illumina Casava 1.8.2 software was used for base-calling.
Sequenced reads were mapped to the mouse reference genome sequence (mm10) using TopHat v2.0.13 in combination with Bowtie2 (v2.2.3) and SAMtools(v0.1.19).
Differentially expressed genes were identified using the following thresholds: FDR < 0.05 and minimal fold change > 2.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file include

source_name: Skin

extract_protocol:
Total RNA of primary chondrocytes and primary dermal fibroblasts  was isolated using a Nucleo Spin RNA Plus kit
Total RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) in accordance with the manufacturer’s protocol.

value: Skin

value: Primary Dermal Fibloblasts


title: PATC50 replicate 3

value: untreated


title: YX5_miRNA


title: Chondrocytes

source_name: Rib Cartilage

value: Rib Cartilage

value: Primary Chondrocyte


title: ChIP-Seq_HA-Smc6_hTERT-RPE1_TPT

value: Anti-HA (Invitrogen, MA-27915)


title: ChIP-Seq_HA-Smc6_hTERT-RPE1_DMSO


title: PATC50 replicate 2


title: E160/E308_Del_H3K27ac

data_processing:
Quality control and preprocessing of ChIP-seq reads were performed using fastp as default setting
ChIP-seq Reads were mapped to the mm9 reference sequence using Bowtie2 (ver. 2.4.4).
Genomic peaks of ChIP-seq were detected using MACS2 (ver.2.2.4) with the default setting (q-value< 0.05) and input reads were used as control.
Assembly: mm9
Supplementary files format and content: bed(except for Input files)

extract_protocol:
Primary chondrocytes and primary dermal fibroblasts were cross-linked with 1% methanol-free formaldehyde for 5 min. Crosslinking was quenched with 1M glycine for 5min and washed three times with cold PBS. Cells were then lysed with lysis buffer and crosslinked chromatin was sonicated with Covaris M220.
sequencing libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s protocol.

tag: antibody


title: ChIP-Seq_noHA_control_hTERT-RPE1_DMSO

value: WT


title: WT_H3K27ac


title: PATC50 replicate 1


title: PATC50_ICG replicate 2


title: YC8_circRNA

value: Corn oil injection (10 µl/g, twice a week), double distilled water orally (daily)


title: Input


title: HPNE_ICG replicate 3

source_name: HPNE


title: YX2_miRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: HPNE_ICG replicate 2


title: DF_H3K27ac

value: Primary Dermal Fibroblasts


title: Cho_H3k4me2


title: m2591_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS

city: Houston

first: Jia

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. Fastp was used to trim adaptor sequences from fastq data and remove 15 bp from the two ends of the reads based on Swift protocol. MCALL module in MOABS software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig; DNA methylation ratio in single CpG resolution

source_name: Tumor tissue from pediatric medullablastoma patient

extract_protocol:
Total DNA containing cell-free tumor DNA (ctDNA) was isolated from 200-400 µL cerebral spinal fluid (CSF) using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. For MB tumor tissues, up to 20 mg of tumor tissues was snap frozen with liquid nitrogen and grinded. DNA was then isolated using an AllPrep DNA/RNA mini kit according to the manufacturer’s protocol. The isolated DNA concentration was measured by a Qubit 4 Fluorometer with the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific).
The whole genome bisulfite sequencing (WGBS) analysis was used to measure the genome-wide DNA methylation status. The ctDNA WGBS libraries were generated using SWIFT Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences). Briefly, adaptase was applied to the bisulfite-converted DNA, with adaptors as well as a low-complexity tail simultaneously ligated to the 3′ end of the DNA fragments. Following a primer extension, the bottom strand DNA was synthesized and the 3′ end was ligated with adaptor sequences. ctDNA was mixed with 0.1% unmethylated λ-bacteriophage DNA (NEB) .  Constructed libraries were run on 2% agarose gel to assess the size distribution and library concentration was measured by a Qubit 4 Fluorometer with a Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific). Normalized libraries were then pooled in an equimolar ratio and sequenced following the manufacturer’s protocols.   Enriched DNA fragments were purified using the conventional phenol/chloroform/isomyl-alcohol method, and amplified with random primers, followed by adaptor ligation and final amplification with Methyl-Seq Combinatorial Dual Indexing Kit (Swift Biosciences). DNA library sizes and concentrations were verified by Bioanalyzer. The DNA libraries were then sequenced in Novaseq S4 (pair-end reads, 150 Cycles) following the manufacturer’s protocols.

tag: patient diagnosis

value: pediatric medullablastoma

tag: sample name


title: HPNE_ICG replicate 1

tag: treatment


title: m2623C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

source_name: cerebrospnial fluid from pediatric medullablastoma patient

tag: tissue

value: CSF


title: YT6_miRNA


title: HPNE replicate 3

value: immortalized pancreatic cell line


title: YX3_miRNA


title: m2585_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: HPNE replicate 2


title: m2591C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Cho_H3K27ac_Rep2


title: E160/E308_Del_ATAC

data_processing:
Quality control and preprocessing of ATAC-seq reads were performed using fastp.
ATAC-seq Reads were mapped to the mm9 reference sequence using Bowtie2 (ver. 2.4.4).
Duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9). Peak calling was performed using MACS2 (ver. 2.2.4) with default parameters.
Assembly: mm9
Supplementary files format and content: narrowPeak

extract_protocol:
approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’sprotocol.
sequencing libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s protocol.


title: m2414C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Cho_H3K27ac_Rep1


title: HPNE replicate 1


title: YT5_miRNA


title: YX1_miRNA


title: m2585C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: YT3_miRNA


title: PATC53_ICG replicate 3

value: treated with 10 uM ICG-001 for 48 hours


title: m2316C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: m2316_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: YT2_miRNA

value: liver


title: Cho_ATAC_Rep2


title: PATC53_ICG replicate 2


title: YT4_miRNA

value: male


title: YT1_miRNA

value: 10% CCl4 mixture injection (10 µl/g, twice a week), double distilled water orally (daily)


title: PATC53_ICG replicate 1


title: YC8_miRNA


title: Cho_ATAC_Rep1


title: m2271C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: m2271_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: Mtissue_37D_Chip_11_08_TS_S29

city: Molndal

first: Fredrik

last: Karlsson

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
RNASeq data was analysed using bcbio (version 1.1.0) and differential analysis was performed with DESeq2 (version 1.18.1).
Assembly: hg38
Supplementary files format and content: Comma separated raw count file.

source_name: Liver spheroids

growth_protocol: We performed co-cultures with islet and liver spheroids on a commercially available multi-organ-chip Chip2 (TissUse) platform. This MPS has two culture compartments for the integration of spatially separated organ models. The culture compartments are interconnected by a microfluidic channel. An on-chip micropump drives a pulsatile flow supporting long-term perfusion and communication between the organ models. Glucose concentration was 5.5 mM in the normoglycemic condition and 11 mM in the hyperglycemic condition.

extract_protocol:
Spheroids were transferred into PCR-clean 1.5 mL microtubes with 100 µL of lysis buffer (LB1 from Macherey-Nagel or 700 µL of Buffer RLT (79216, Qiagen). Lysates were snap-frozen and stored at −80°C. RNA was isolated using the NucleoSpin® RNA Plus XS kit (740990.50, Macherey-Nagel) or RNeasy Mini Kit (74104, Qiagen).
The quantity and quality of RNA samples was assessed using the standard sensitivity RNA fragment analysis kit on Fragment Analyzer (Agilent Technologies). All samples had an RNA integrity number >8 and were deemed of sufficient quantity and quality for RNA-seq analysis. Samples were diluted to a final quantity of 150 ng/sample of total RNA. The KAPA mRNA HyperPrep kit (Roche) was used for reverse transcription, generation of double stranded cDNA and subsequent library preparation and indexing to facilitate multiplexing (Illumina TruSeq).

value: Liver spheroids

tag: cell line

value: HepaRG hepatocytes

value: HepaRG, Primary human hepatic stellate cells

value: Hyperglycemic


title: YC7_miRNA


title: YC6_miRNA


title: MTissue_Exp_3_2_NG_1_12_TS_S14

value: Normoglycemic


title: m2208_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: PATC53 replicate 2

value: untreated


title: WT_ATAC

value: Rib Cartilage

value: Primary Chondrocyte

tag: genotype

value: WT


title: m2208C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: MTissue_Exp_3_1_NG_1_11_TS_S10

tag: cell type


title: YC3_miRNA

value: Corn oil injection (10 µl/g, twice a week), double distilled water orally (daily)


title: m2160_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS

value: pediatric medullablastoma


title: MTissue_Exp_3_2_HG_1_04_TS_S13


title: PATC53 replicate 3


title: PANC1_ICG replicate 3


title: PATC53 replicate 1


title: YC2_miRNA


title: PANC1_ICG replicate 2


title: m2160C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: CSF


title: YC1_miRNA


title: MTissue_Exp_3_1_HG_1_02_TS_S5


title: m2129_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: MTissue_32A_Chip_11_07_TS_S25


title: PANC1_ICG replicate 1

value: immortalized pancreatic cell line


title: m2129C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: RH2_BM_cKit

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

description:
RH2_HSCPs
CountsTable_RH.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
FASTQ files were processed in the AltAnalyze (version 2.1.3)
Transcript per million estimates were calculated in AltAnalyze through a built-in call to Kallisto for read pseudoalignment and transcript quantification (Ensembl 72, mm10)
Assembly: mm10
Supplementary files format and content: raw counts with genes in rows and samples in columns

source_name: Bone marrow

extract_protocol:
Bone marrow cells were harvested from individual mice. HSCPs were purified using EasySep Mice CD117 positive selection kit and mutant clone was FACS sorted. Ly6G+ mutant myeloid BM cells were FACS sorted. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: HSCPs

value: RUNX1 mutant with HMGA2-OE


title: PANC1 replicate 3


title: NK-AF60_D8

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
counts.csv
mrn.csv

data_processing:
quality analysis with FastQC (v0.11.7)
read trimming with Trimmomatic (v0.36)
reference genome indexing with HiSat2 (v2.1.0)
Gene abundance estimation with featureCounts (v1.34.0)
quality control with MultiQC (v1.7)
Assembly: human reference genome (GRCH 38, v109)
Supplementary files format and content: tab delimited raw read counts
Supplementary files format and content: tab delimited MRN normalized read counts

source_name: natural killer cells

growth_protocol: A. fumigatus ATCC 46645 conidia were seeded in 6-well plates (2×10^5 conidia per well in 2 mL of RPMI medium) and incubated for 18 h at 30 °C.

extract_protocol:
Total RNA from purified NK cells was isolated using QIAshredder columns and the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s protocol.
Library preparation was performed with the Illumina TruSeq® Stranded mRNA technology, according to the manufacturer’s protocol.

treatment_protocol: The supernatants were removed, and germ tubes were treated with 2 mL of 10 mM sodium m-periodate (Sigma Aldrich, St. Louis, MO, USA) in RPMI for 10 min and 60 min, respectively, or were left untreated.

value: natural killer cells

value: A. fumigatus germ tubes treated with 60min periodate


title: NK-AF0_D8

description:
counts.csv
mrn.csv

value: A. fumigatus germ tubes untreated


title: m2100_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: HMGA2_BM_cKit

description:
HMGA2_HSCPs
CountsTable_RH.txt


title: m2100C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: NK-AF60_D7

description:
counts.csv
mrn.csv


title: PANC1 replicate 2


title: Brain,miRNA,Hydrogel3

city: Wuhan

first: Huayu

last: Kang

state: Hubei

address: Jiefang Avenue 1095,Qiaokou District

institute: Tongji Medical College, Huazhong University of Science & Technology

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 GRCh38/Rnor_6.0 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
Assembly: GRCh38/Rnor_6.0
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS™ Stranded mRNA-seq Library Prep Kit for Illumina®Library Prep Kit following manufacturer's protocols.

value: Brain

tag: sample group

value: BCCAO rats transplanted with BMSC-loaded hydrogel during EMS treatment

tag: time point

value: 7 days post EMS treatment


title: NK-AF0_D7

description:
counts.csv
mrn.csv


title: Brain,miRNA,Hydrogel2


title: m2091_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: Brain,miRNA,Hydrogel1


title: pancreatic cancer PATC53_ICG replicate 1

data_processing:
The raw reads of Hi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: Headers of validPairs files: read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis (0-0 = first read from genome1 and second read from genome1, 1-0 = first read from genome2 and second read from genome1, 0-1 = first read from genome1 and second read from genome2, 1-1 = first read from genome2 and second read from genome2), please refer to: https://groups.google.com/g/hic-pro/c/qhHNbQVJfYY

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Rao et al. 2014).
Hi-C was performed as described (Rao et al. 2014).

value: treated with 10 µM ICG-001 for 48 hours


title: NK-AF0_D6

description:
counts.csv
mrn.csv


title: NK-AF60_D6

description:
counts.csv
mrn.csv


title: pancreatic cancer PATC53 replicate 2

value: untreated


title: CSF-744_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: m2091C1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS


title: Brain,miRNA,con3

value: bilateral common carotid artery occlusion (BCCAO) rats treated with EMS


title: Brain,miRNA,con2


title: YX4_miRNA

data_processing:
For mRNA and lncRNA, high-quality clean data were obtained by removing adapters, poly-N sequences, and low-quality reads from the raw data using in-house Perl scripts. The processed RNA-seq data were then mapped to the Ensembl mouse reference genome (Mus musculus GRCm38) using Hisat2 (version 2.2.1). Transcript assembly was performed with the Ensembl mouse annotation database (GRCm38) using StringTie (version 2.1.5), and the FPKM expression matrix was generated.For miRNA, Cutadapt (version 4.2) was used to remove adapters and sequences smaller than 10 nt. The processed sequencing data were then mapped to the mouse reference genome (GRCm38) using Bowtie (version 1.3.1) and miRDeep2, which provided the final reads of miRNA hairpin precursor and mature miRNA. miRDeep2 was also used for quantifying the processed sequences.For circular RNA, Trimgalore and Fastp were used to remove adapters, poly-N sequences, and low-quality reads from the raw data. Clean data were obtained by removing partial rRNA and E. coli contamination using Bowtie2. Circular RNA quantification and differential expression analysis were performed using CIRI2 software.
Assembly: GRCm38
Supplementary files format and content: Table-delimited text file include reads count of each reads for each sample.

source_name: liver

extract_protocol:
According to manufacturer’s instructions, total RNA was extracted from each liver tissue using TRIzol reagent. The A260/A280 ratio was used to assess RNA purity. There was A260/A280 ratio>1.9 in all liver tissue samples, which meant the RNA purity was high for sequencing.
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations respectively.

value: liver

value: male

value: 10% CCl4 mixture injection (10 µl/g, twice a week), PTH preparation (0.25 mg/g, daily)


title: NK-AF0_D4

description:
counts.csv
mrn.csv


title: NK-AF60_D4

description:
counts.csv
mrn.csv


title: PANC1 replicate 1


title: RH1_BM_cKit

description:
RH1_HSCPs
CountsTable_RH.txt


title: Brain,miRNA,con1


title: pancreatic cancer PANC1_ICG replicate 2


title: CSF-2381C1-1_cerebrospnial_fluid_from_pediatric_medullablastoma_patient_WGBS

value: CSF

value: pediatric medullablastoma


title: pancreatic cancer PANC1_ICG replicate 1

value: immortalized pancreatic cell line


title: AFF4_KD RNA-seq rep1

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Fragment count were obtained using featureCounts v1.6.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include fragment count values of genes for each sample.

source_name: HEL cell line

growth_protocol: Human cells HEL were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.

value: HEL cell line

value: Human erythroblast

value: AFF4 knockdown


title: sp replicate2

city: Haikou

first: HE

last: Ting

address: Hainan University, Meilan District, Haikou City, Hainan Province, China

institute: Hainan University

data_processing:
1 μg total RNA was firstly treated with Antarctic phosphatase (New England Biolabs) and then with PNK enzyme (New England Biolabs). RNA Library was prepared with treated RNA according to the manufacturer’s instructions of GenSeq® Small RNA Library Prep Kit (GenSeq Inc.). The libraries were size-selected for sRNA fraction (50–500 nt) with TBE polyacrylamide gel. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were sequenced for 150 pair-end cycles on Illumina NovaSeq Sequencer according to the manufacturer’s instructions (Illumina, San Diego, USA).
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
sRNA candidates are predicted using sRNAscanner based on transcriptional signals. sRNA overlapping with known genes are excluded and the rest are added into the gene annotation of the genome.
The clean reads were aligned to the reference genome using Hisat2 software. HTSeq was used to count the read numbers mapped to each gene. edgeR was used to normalizing the read counts for each library and to identifying differentially expressed genes.
Assembly: ASM360622v1
Supplementary files format and content: The processed data is in xlsx format and contains sRNA reads, location and length, etc.

organism: Salmonella enterica subsp. enterica serovar Pullorum

source_name: bacteria

extract_protocol:
1 µg of total RNA was treated sequentially with phosphatase and PNK kinase (New England Biolabs). The treated RNA was subjected to library construction by GenSeq's Small RNA Library Kit. The QC-controlled libraries were subjected to 150bp bipartite sequencing by Illumina NovaSeq High-Throughput Sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacteria

value: WT

value: standard strain


title: pancreatic cancer PANC1 replicate 2


title: pancreatic cancer PANC1 replicate 1


title: Ctrl RNA-seq rep2


title: Normal Colon First_Right

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description: scRNA-seq

data_processing:
Pre-processing of sequencing results to generate transcript matrices was performed using the 10x genomics Cell Ranger pipeline with default settings (version 3.0.2, 10X Genomics) and aligning to the hg38 human reference genome.
Data from the two samples were integrated using Seurat version 3.6.2
Further processing was done with Seurate v3.6.2 (cell and gene filtering, clustering, differential gene expression analysis).
Genome_build: hg38
Supplementary_files_format_and_content: Output of the Cell Ranger pipeline representing tsv and mtx files containing count matrices.

source_name: Colon biopsy

extract_protocol:
Colon biopsies from left and right colon were dissociated into single cell with mechanic and enzymatic dissocation. The single cell solution underwent red blood cell depletion and then were processed as the manufacturer’s instructions (Chromium single cell 3’ reagents, v2 chemistry) and libraries were sequenced on an Illumina Novaseq sequencer.
Chromium Single Cell 3' Reagent Kits (v2)

tag: disease state

value: healthy

value: Right colon biopsy tissue

tag: age

tag: gender

value: female


title: Ctrl RNA-seq rep1


title: Normal Colon Second_Left

description: scRNA-seq

value: Left colon biopsy tissue


title: biol rep 38 liver Male

status: Public on Jun 09 2024

city: Québec

first: Florent

last: Sylvestre

state: Québec

address: 2325, rue de l'Université

country: Canada

institute: Université Laval

description:
Foie_70
Raw_counts_Liver.txt

data_processing:
Read quality: filter low quality read with fastp (v0,15,0), also removes poly-A tail, illumina adapters and first 12bp. Only keep reads >12bp
Read aligment: STAR v2,7,2b two pass mode, followed by quantification using HTSeq v0,11,3 in union mode after discarding multi-mapping reads
Read counts from each samples were merged Per tissus using a custom R script
Assembly: Stickleback reference genome on NCBI, RefSeq assembly GCF_016920845.1. Fisr 0,32Mb were removed from the Y chromosome (pseudo-autosomal region)
Supplementary files format and content: All processed data files contains raw read counts for each gene (row) and each individual (column). Individual are labelled with library lane (Cerveau = Brain, Foie = Liver and Branchie = Gills)

organism: Gasterosteus aculeatus

source_name: Liver

growth_protocol: Natural population

extract_protocol:
Rneasy Mini kit (Qiagen)
Dual indexing  Quant seq 3' mRNAq Seq library prep Kit FWD
Quant-Seq

treatment_protocol: No treatment (Sex was our explanatory variable)

value: Liver


title: sp replicate1


title: biol rep 36 liver Male

description:
Foie_67
Raw_counts_Liver.txt


title: biol rep 39 liver Male

description:
Foie_73
Raw_counts_Liver.txt


title: Normal Colon First_Left

description: scRNA-seq


title: biol rep 37 liver Male

description:
Foie_7
Raw_counts_Liver.txt


title: biol rep 31 liver Male

description:
Foie_54
Raw_counts_Liver.txt


title: biol rep 35 liver Male

description:
Foie_63
Raw_counts_Liver.txt


title: pancreatic cancer PATC53_ICG replicate 2

value: treated with 10 µM ICG-001 for 48 hours


title: biol rep 34 liver Male

description:
Foie_61
Raw_counts_Liver.txt

value: male


title: Normal Colon Second_Right

description: scRNA-seq


title: biol rep 30 liver Male

description:
Foie_53
Raw_counts_Liver.txt


title: biol rep 33 liver Male

description:
Foie_60
Raw_counts_Liver.txt


title: biol rep 29 liver Male

description:
Foie_50
Raw_counts_Liver.txt


title: biol rep 28 liver Male

description:
Foie_43
Raw_counts_Liver.txt


title: sp replicate3


title: biol rep 32 liver Male

description:
Foie_56
Raw_counts_Liver.txt


title: biol rep 26 liver Male

description:
Foie_38
Raw_counts_Liver.txt


title: biol rep 24 liver Male

description:
Foie_279
Raw_counts_Liver.txt


title: pancreatic cancer PATC53 replicate 1

value: untreated


title: biol rep 25 liver Male

description:
Foie_3
Raw_counts_Liver.txt


title: biol rep 19 liver Male

description:
Foie_241
Raw_counts_Liver.txt


title: biol rep 22 liver Male

description:
Foie_270
Raw_counts_Liver.txt


title: biol rep 23 liver Male

description:
Foie_274
Raw_counts_Liver.txt


title: biol rep 17 liver Male

description:
Foie_237
Raw_counts_Liver.txt


title: biol rep 12 liver Male

description:
Foie_223
Raw_counts_Liver.txt


title: biol rep 18 liver Male

description:
Foie_238
Raw_counts_Liver.txt


title: biol rep 20 liver Male

description:
Foie_25
Raw_counts_Liver.txt


title: biol rep 21 liver Male

description:
Foie_269
Raw_counts_Liver.txt


title: biol rep 9 liver Male

description:
Foie_218
Raw_counts_Liver.txt


title: biol rep 8 liver Male

description:
Foie_217
Raw_counts_Liver.txt


title: m2054_T_tumor_tissue_from_pediatric_medullablastoma_patient_WGBS


title: biol rep 10 liver Male

description:
Foie_22
Raw_counts_Liver.txt


title: biol rep 16 liver Male

description:
Foie_235
Raw_counts_Liver.txt


title: biol rep 27 liver Male

description:
Foie_40
Raw_counts_Liver.txt


title: biol rep 15 liver Male

description:
Foie_232
Raw_counts_Liver.txt


title: biol rep 3 liver Male

description:
Foie_204
Raw_counts_Liver.txt


title: biol rep 2 liver Male

description:
Foie_12
Raw_counts_Liver.txt


title: biol rep 11 liver Male

description:
Foie_222
Raw_counts_Liver.txt


title: biol rep 4 liver Male

description:
Foie_205
Raw_counts_Liver.txt