title: PDX5 biol rep 4, DMSO

city: Gent

first: Lien

last: Provez

address: Corneel Heymanslaan 10 - MRB2

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing: Reads were aligned to GRCh38 using STAR2.7.6a. RNA sequencing counts were analyzed using the DESeq2 packages in R and genes with adjusted P-values <0.05 were considered differentially expressed.

source_name: bone marrow

growth_protocol: Male NOD/SCIDg (NSG) mice were injected with pleural effusion material of human T-LBL patients in the tail vein for PDX development.

extract_protocol:
RNA from full spleen or hCD45+ sorted bone marrow was isolated using the RNeasy Plus Kit (Qiagen).
Library preparation was performed using QuantSeq 3′mRNA-Seq FWD for Illumina (LEXOGEN).

treatment_protocol: Mice were treated via IP with vehicle (1% DMSO in PBS) or decitabine (0.5mg/kg bodyweight) for 5 days once engraftment was over 50%.

value: bone marrow

tag: cell line

tag: cell type

value: leukemic blasts

tag: genotype

value: NSG

tag: treatment

value: DMSO


title: PDX5 biol rep 3, DMSO

status: Public on Mar 02 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: PDX5 biol rep 2, DMSO


title: SD05_D5_RNA

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.3a.
Gene-level read counts were generated using STAR 2.7.3a.
Assembly: hg38
Supplementary files format and content: count_gene.txt: tab-delimited raw gene counts

source_name: Peripheral blood leukocytes

extract_protocol:
Subject's peripheral blood was collected in potassium EDTA tubes (BD Vacutainer, REF 367861) and processed within 4 hours. Briefly, peripheral leukocytes were enriched by centrifugation followed by red blood cells lysis. Cell pellets were resuspended and lysed in Trizol (ThermoFisher Scientific) and stored in -80C until use. We extracted RNA per manufracture's recommended protocol for Trizol.  Precipitated RNA was desolved in RNAse-free ddH2O and treated with DNAse (AM1907, ThermoFisher Scientific) per manufracture's protocol. RNA amount was determined using Nanodrop (ThermoFisher Scientific).
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: Peripheral blood leukocytes

tag: patient id

tag: patient outcome

value: Fatal

tag: timepoint


title: HC6_NA_csRNAinput

library_source: other

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.1a.
Aligned reads were quantified, normalized, and aggregated using HOMER.
Assembly: hg38
Supplementary files format and content: initiation.txt: tab-delimited log-transformed transcription initiation values at specified genomic intervals
Library strategy: csRNA-seq

molecule: other

extract_protocol:
Subject's peripheral blood was collected in potassium EDTA tubes (BD Vacutainer, REF 367861) and processed within 4 hours. Briefly, peripheral leukocytes were enriched by centrifugation followed by red blood cells lysis. Cell pellets were resuspended and lysed in Trizol (ThermoFisher Scientific) and stored in -80C until use. We extracted RNA per manufracture's recommended protocol for Trizol.  Precipitated RNA was desolved in RNAse-free ddH2O. RNA amount was determined using Nanodrop (ThermoFisher Scientific).
Small RNAs of ~20-60 nt were size selected form 2-15 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’ capped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.

value: Healthy control

tag: library type

value: csRNAinput

tag: library strategy

value: small RNA-seq


title: HC6_NA_csRNA

value: csRNA

value: capped short RNA-seq (csRNA-seq)


title: SD05_D3_RNA


title: A079

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
nf-core rnaseq v3.3
Fragment mapping was counted using featureCounts (subread v1.5.1)
Differentially expressed genes (DEGs) were estimated using the SARTools R package (v1.7.3). Significant DEGs were determined when the adjusted p-value (padj) was < 0.05.
Assembly: SSAL_v3.1 (GenBank assembly accession: GCA_905237065.2).
Supplementary files format and content: Count files / Counts for each Sample

organism: Salmo salar

source_name: Distal Intestine

extract_protocol:
Total RNA was extracted from each sample using RNeasy Mini Kit (Qiagen) following the supplier’s instructions. Then, RNA samples were quantified using a NanoDrop™ 8000 spectrophotometer and RNA integrity was measured by Agilent Bioanalyzer 2100. All samples showed an RNA integrity number ≥ 7).
RNA libraries for RNA-seq were prepared by Novogene (UK) Company Limited

value: Distal Intestine

tag: diet

value: MacroGard

tag: water stage

value: Fresh water


title: A081


title: PDX5 biol rep 3, DAC

value: DAC


title: A080


title: PDX5 biol rep 1, DMSO


title: SD05_D11_RNA


title: A045


title: PDX5 biol rep 2, DAC


title: HC1_NA_csRNAinput


title: PDX5 biol rep 1, DAC


title: A044


title: PDX3 biol rep 4, DMSO

source_name: spleen

value: spleen


title: PDX3 biol rep 3, DMSO


title: A043


title: SD05_D1_RNA


title: SD04_DC_RNA

value: Prolonged recovery

value: DC


title: PDX3 biol rep 4, DAC

value: leukemic blasts


title: A009


title: PDX3 biol rep 2, DAC

value: NSG


title: A008


title: PDX3 biol rep 2, DMSO

value: DMSO


title: PDX3 biol rep 1, DAC


title: SD04_D7_RNA

value: Peripheral blood leukocytes


title: SD04_D9_RNA


title: PDX3 biol rep 1, DMSO


title: PDX4 biol rep 3, DAC


title: A007


title: PDX4 biol rep 4, DAC


title: A069

value: HK L-137 Higher inclusion


title: PDX4 biol rep 2, DAC


title: PDX4 biol rep 3, DMSO


title: A068


title: SD04_D5_RNA


title: SD04_D11_RNA


title: SD04_D3_RNA


title: PDX4 biol rep 4, DMSO


title: PDX4 biol rep 2, DMSO


title: PDX4 biol rep 1, DAC


title: A067


title: A027


title: PDX3 biol rep 3, DAC


title: PDX1 biol rep 4, DAC


title: SD02_D7_RNA

value: Fast recovery


title: SD04_D1_RNA


title: PDX1 biol rep 3, DAC


title: A026


title: PDX1 biol rep 2, DAC


title: PDX1 biol rep 1, DAC


title: SD02_D3_RNA


title: PDX1 biol rep 4, DMSO


title: SD02_D1_RNA


title: A015


title: PDX1 biol rep 3, DMSO


title: PDX1 biol rep 2, DMSO


title: SD01_D9_RNA


title: SD01_DC_RNA


title: A014


title: SD01_D7_RNA


title: PDX1 biol rep 1, DMSO


title: A063

value: HK L-137 Medium inclusion


title: HeLa-mCC1a-siRNA-TFEB/TFE3-MHV-1

city: Bethesda

first: Pablo

last: Tapia

state: Maryland

address: 50 South Dr

department: Cell Biology and Physiology Center, National Heart, Lung, and Blood

institute: National Institutes of Health

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for all samples.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

source_name: Uterus, Cervix

growth_protocol: HeLa-mCC1a cells were grown in DMEM, high glucose, GlutaMAX, sodium pyruvate (Gibco, 10569044) supplemented with 10% fetal bovine serum (Invitrogen, 21041-025), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 2114).

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 100 nM of either siRNA-Control or siRNA-TFEB+siRNA-TFE3 for 72h. Then, cells were incubated with MHV for 2h, wash and harvested at 24h.

value: Uterus, Cervix

value: Epithelial cells

value: siRNA, TFEB, TFE3

value: MHV infection for 24h


title: A013

value: Distal Intestine


title: HeLa-mCC1a-siRNA-TFEB/TFE3-MHV-3


title: HeLa-mCC1a-siRNA-Control-MHV-3

value: siRNA, control


title: PDX biol rep 1, DMSO


title: SD01_D5_RNA


title: HeLa-mCC1a-siRNA-TFEB/TFE3-MHV-2


title: HeLa-mCC1a-siRNA-Control-MHV-1


title: SD01_D11_RNA


title: A025

value: Fresh water


title: SD01_D3_RNA


title: A062


title: A039


title: HeLa-mCC1a-siRNA-TFEB/TFE3-1

value: Untreated


title: HeLa-mCC1a-siRNA-TFEB/TFE3-3


title: HeLa-mCC1a-siRNA-Control-2


title: HeLa-mCC1a-siRNA-Control-3


title: SD01_D1_RNA

value: Prolonged recovery


title: A037


title: HeLa-mCC1a-siRNA-Control-1


title: RPNIH_EBSS-4H_TFE3

library_source: genomic

data_processing:
Basecalls performed using Illumina bcl2fastq2 version 2.20
ChIP-seq reads were aligned to the human GRCh38/hg38 genome assembly using Burrows-Wheeler Aligner algorithm with default settings.
Data were filtered as follows: Duplicate reads were removed, and only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7 [2]. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: hg38
Supplementary files format and content: bigWIG files were generated using wigToBigWig version 4 software

molecule: genomic DNA

extract_protocol:
Chromatin was isolated from cells by adding lysis buffer (1% SDS, 10 mM EDTA and 50mM Tris-HCl, pH 8.1 containing protease inhibitors), followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Genomic DNA regions of interest were isolated using monoclonal antibody against TFE3.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara) following the manufacturer's protocol. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end) following the manufacturer's protocols.

treatment_protocol: Cells were incubated with MHV for 2h, wash and harvested at 14h. Also, cells were incubated with EBSS for 4h and harvested.

tag: chip antibody

value: TFE3 Sigma HPA023881-100ui

value: EBSS for 4h


title: RPNIH_MHV-14H_TFE3

value: MHV infection for 14h


title: HeLa-mCC1a-siRNA-Control-MHV-2


title: GX060-TO-DrugCtrl

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

country: China

institute: The University of Hong Kong

data_processing:
The RNAseq reads in FASTA format were aligned to the Genome Reference Consortium human build 37 (hg19) by STAR (version 2.5.2b).
Duplicate reads were removed from the BAM files and the transcript abundances were quantified by RSEM to calculate the transcripts raw mapping reads value for each gene.
Assembly: GRCh37
Supplementary files format and content: no normalized in a tab-delimited text format.

source_name: Control tumor organoid

growth_protocol: Gastric cancer organoids were cultured in a standard gastric organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and FGF10.

extract_protocol:
RNA of organoids were extracted using AllPrep® DNA/RNA/miRNA Universal Kit (Qiagen). following the manufacturers’ protocol.
Four micrograms of total RNA were used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), according to the manufacturer’s protocol. The library was amplified by 6 PCR cycles and sequenced using either the NovaSeq6000/HiSeqX Ten with paired end 151bp reads or the HiSeq1500 with paired end 101bp reads.

treatment_protocol: Gastric cancer organoids were treated with 5-fluorouracil and cisplatin with IC10 and dose increased gradually until reaching IC50 or at dose which organoids remained alive but did not proliferate.

value: Gastric cancer organoids

tag: culture condition

value: Standard gastric organoid medium


title: GX060-TO-CDDP5FU

source_name: Drug treated tumor organoid

value: Standard gastric organoid medium with 5-fluorouracil and cisplatin


title: A061


title: GX055-TO-DrugCtrl


title: RPNIH_HeLa-Pooled_Input


title: HeLa-mCC1a-siRNA-TFEB/TFE3-2


title: A032


title: A033


title: GX055-TO-CDDP5FU


title: GX006-T2O-DrugCtrl


title: A031


title: A038


title: A087

value: HK L-137 Lower inclusion


title: GX006-T2O-CDDP5FU


title: A086


title: Mo1-23-2

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

country: Netherlands

institute: LUMC

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Assembly: hg19
Supplementary files format and content: raw read counts in matrix table
Supplementary files format and content: normalized abundance measurements

source_name: Cardiomyocytes

growth_protocol: hiPSCs were maintained in Essential 8 medium and grown till 80-90% confluency (Day 0). Next, medium was aspirated and the cells were washed once with dPBS (GIBCO, 14190094). Subsequently, cells were fed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES (GIBCO, 72400-021) supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate (Sigma-Aldrich, A8960), and 4 µM CHIR99021 (Sigma-Aldrich, 361559). After 2 days (Day 2), medium was aspirated and cells were washed once with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES, followed by addition of RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate , and 5 µM IWP2 (Sigma-Aldrich, 681671). On day 4 and day 6, cells were refreshed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. From day 8 onwards, cells were maintained in RPMI-1640-Medium-GlutaMAX™-Supplement-HEPES supplemented with B-27™Supplement (50x)-serum free (GIBCO, 17504001). Spontaneous beating cardiomyocytes could be observed between day 8 and day 10. hiPSC-derived cardiomyocytes were subsequently dissociated for downstream applications with TrypLE™ Select Enzyme (10x)-no phenol red (GIBCO, A1217703) for a maximum of 20 minutes at 37oC. Cardiomyocytes were seeded at a density of 100,000 cells/cm2 in Geltrex-coated wells.

extract_protocol:
Qiagen RNeasy mini kit (74104)
Truseq RNA stranded polyA

value: hiPSC-derived cardiomyocytes

value: DSP WT/WT

tag: age

value: 30 days post-differentiation


title: Mo1-23-7


title: Mo1-23-4


title: KI2C3S1

value: DSP p.Tyr1188His/WT


title: Mo1-m2-6


title: KI2C2S1


title: Mo1-23-3


title: A085


title: Propafenone  rep3

city: Shanghai

first: Jinlian

last: Wei

state: Shanghai

address: Meilong Road 130

institute: EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: conjunctival cells

extract_protocol:
CM-AS16 cells were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CM-AS16 cells were cultured in 10 cm dishes, and treated with DMSO or 20 μM Propafenone .

value: Propafenone  20 μM

value: conjunctival


title: Mo1-m2-7


title: Mo1-m2-5


title: KI2C4S1


title: Mo1-m2-2


title: KI2C1S1


title: ATCC4S1


title: A057

value: Distal Intestine


title: Propafenone  rep2


title: DMSO rep3

value: DMSO


title: A056

value: Fresh water


title: ATCC3S1


title: ATCC2S1


title: ATCC1S1


title: A055


title: Propafenone  rep1


title: DMSO rep2


title: A021


title: MM587_D21_snRNA-seq

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger RNA v3.0.2 pipeline
Assembly: hg19
Supplementary files format and content: h5ad object includes raw count matrix (raw.h5ad)
Supplementary files format and content: h5ad object includes cell clustering results (final_cluster.h5ad)

source_name: Islets

growth_protocol: H1 cells were maintained and differentiated as previously described (Geusz RJ, et al., Nature Comm 2021).

extract_protocol:
At D11, D14, D21, D32 and D39 of differentiation, nuclei were isolated from approximately 1,000 aggregates (~1,000 cells per aggregate) using a glass dounce in nuclei permeabilization buffer [0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X Pierce Protease Inhibitor (Fischer, PIA32965), 1 mM DTT (Sigma-Aldrich, D9779), Recombinant RNase inhibitor (0.2 U/μl; Promega, 2% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3). Supernatant was removed and pellet was resuspended in sort buffer [1mM EDTA (Invitrogen, 15575020), 0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV) and stained with DRAQ7 (1:150; Cell Signaling Technology, 7406). 60,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer [1.0U/μL Recombinant RNAsin (Promega, PAN2515), 5% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sorted nuclei were then centrifuged at 1000 g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in reaction buffer [RNase inhibitor (0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV) and counted using a hemocytometer.
16,550 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer specifications. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using TapeStation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp. Libraries were sequenced using a NextSeq 500 or NovaSeq 6000 (Illumina).
Single cell RNA-seq with 10X Next GEM Single Cell 3’ v3.1 kit

tag: day


title: MM588_D32_snRNA-seq


title: MM589_D39_snRNA-seq


title: DMSO rep1


title: MM168_D39

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger ATAC v1.1.0 pipeline
We used ‘clean_barcode_multiplets_1.1.py’ script from 10x to identify barcode multiplets for each donor
We called peaks for each cluster using the MACS2 call peak command using parameters ‘--nomodel --extsize 200 –shift 0 --keep-dup all -q 0.05’
Assembly: hg19
Supplementary files format and content: h5ad object includes raw barcode-by-peak (5kb) count matrix (raw_5kb.h5ad)
Supplementary files format and content: h5ad object includes cell clustering results (final_cluster.h5ad)
Supplementary files format and content: raw barcode-by-peak (500bp) count matrix (all.mtx)
Supplementary files format and content: union accessible peaks (500bp) (all.regions)
Supplementary files format and content: high quality cell barcodes (all.barcodes)

extract_protocol:
At D11, D14, D21, D32 and D39 of differentiation, approximately 1,000 aggregates (~1,500 cells per aggregate) were collected in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water) and homogenized using 1ml glass dounce homogenizer for 15 strokes with a tight-fitting pestle. To extract nuclei, homogenized aggregates were incubated for 10 min at 4°C and filtered with 30 µm filter (CellTrics). Nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and washed twice with Wash buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, and 1% BSA (Proliant 7500804) in molecular biology-grade water). Nuclei were pelleted and resuspended in 30 µL of 1X Nuclei Buffer (10x Genomics). Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation.
Single nucleus ATAC-seq libraries were generated using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.0 (10x Genomics, 1000175), Chromium Next GEM Chip H Single Cell Kit (1000161) and Single Index Kit N Set A (1000212)10x Genomics, 1000084) following manufacturer instructions. Final libraries were quantified using a Qubit fluorimeter (Life Technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500 or NovaSeq 6000 sequencers (Illumina). Reads were trimmed afterwards to fit into corresponding analysis pipeline.
Single nucleus ATAC-seq Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.0.


title: MM166_D32


title: MM157_D21


title: MM129_D11


title: H1-D32_S6

library_source: transcriptomic single cell

data_processing:
Alignment to the genome and initial processing were performed using the 10x Genomics Cell Ranger RNA v3.0.2 pipeline
Assembly: hg19
Supplementary files format and content: h5ad object includes raw count matrix (raw.h5ad)
Supplementary files format and content: h5ad object includes cell clustering results (final_cluster.h5ad)
Supplementary files format and content: raw barcode-by-gene count matrix (all.mtx)
Supplementary files format and content: all genes (all.genes)
Supplementary files format and content: all cell barcodes (all.barcodes)

extract_protocol:
At D11, D14, D21, D32, D39 of differentiation, cells were collected in microcentrifuge tubes and washed with PBS. Accutase® was used to dissociate aggregates into single cells, which were then stained with propidium iodide (Sigma) in a PBS solution containing 0.2% BSA.  Approximately 200,000 live cells (propidium iodide-negative) were sorted with a FACSAriaTM Fusion Flow Sorter at a sorting speed lower than 3,000 events per second to minimize damage to the cells. Sorted cells were pelleted with 250 x g for 5 minutes at 4°C, and counted with a Scepter™ automated cell counter.
10,000 accurately counted cells per sample were loaded onto a 10X Chromium Controller for GEM formation and cell barcoding using Next GEM Single Cell 3’ v3.1 reagents. Barcoded single cells were subjected to cDNA synthesis and sequencing library construction using 10X Next GEM Single Cell 3’ v3.1 reagents according to manufacturer’s instructions. Final libraries were quantified using a Qubit fluorimeter (Life Technologies) and the fragmented cDNA was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500, HiSeq 4000 or NovaSeq 6000 sequencers (Illumina) and reads were trimmed afterwards to fit into corresponding analysis pipeline.
Single cell RNA-seq with 10X Next GEM Single Cell 3’ v3.1 kit


title: A020


title: H1-D21_S4


title: H1-D39_S8


title: Hs_hESC_D21_CDX2_ChIP_seq_rep2

data_processing:
Two biological replicates were used for ChIP-seq data analysis, and replicates were merged prior to analysis. Bowtie2 v 2.3.4.1 was used for mapping of ChIP-seq data to the human reference genome hg19 with a maximum of 2 mismatches allowed in the seed region, discarding reads aligning to multiple sites. Duplicate reads were removed using SAMtools. Peak calling was performed using MACS2 with ChIP-seq input used as background.
Assembly: hg19
Supplementary files format and content: narrow peaks (cdx2_merge_peakcall_peaks.narrowPeak)
Supplementary files format and content: CDX2 binding sites (cdx2_merge_peakcall_peaks.xls)
Supplementary files format and content: summits of CDX2 binding sites (cdx2_merge_peakcall_summits.bed)

extract_protocol:
Experimentally replicated day 21 human pluripotent stem cell-derived islets were collected in stage 6 differentiation media (MCDB131 with 1.5 g/L NaHCO3, 1X GlutaMAX, 20 mM D-glucose, 2% BSA, 100 nM LDN-193189, 1 µM T3, 100 nm γ-Secretase Inhibitor XX, 10 µM ZnSO4, 10 µg/mL heparin, 1:200 ITS-X) containing 1.11% formaldehyde and fixed on a rocker for 15 minutes. The reaction was quenched for 5 minutes in 0.125 M glycine. Fixed human pluripotent stem cell-derived islets were washed in DPBS containing 0.5% NP-40, then once again in DPBS supplemented with 0.5% NP-40 and 1 mM PMSF, and subjected to ChIP using the ChIP-IT High Sensitivity Kit (Active Motif) with 30 μg of sheared chromatin and 6 μg anti-CDX2 antibody (A300-691A, Bethyl Laboratories).
Libraries were constructed from purified DNA using the KAPA DNA Library Preparation Kit for Illumina (Kapa Biosystems). Input libraries were prepared from each experimental replicate using 10 ng of DNA purified immediately following shearing. Libraries were sequenced using NovaSeq 6000 (Illumina) and reads were trimmed afterwards to fit into corresponding analysis pipeline.

value: CDX2 antibody


title: A074

value: Control Diet


title: WT [MM_844_2_S32]

extract_protocol:
From D21 SC-islets derived from WT and CDX2 KO hESC lines, nuclei were isolated from approximately 1,000 aggregates (~1,000 cells per aggregate) using a glass dounce in nuclei permeabilization buffer [0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X Pierce Protease Inhibitor (Fischer, PIA32965), 1 mM DTT (Sigma-Aldrich, D9779), Recombinant RNase inhibitor (0.2 U/μl; Promega, 2% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV). Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3). Supernatant was removed and pellet was resuspended in sort buffer [1mM EDTA (Invitrogen, 15575020), 0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and stained with DRAQ7 (1:150; Cell Signaling Technology, 7406). 60,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer [1.0U/μL Recombinant RNAsin (Promega, PAN2515), 5% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sorted nuclei were then centrifuged at 1000 g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in reaction buffer [RNase inhibitor (0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and counted using a hemocytometer.
16,550 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer specifications. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using TapeStation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp. Libraries were sequenced using a NextSeq 500 or NovaSeq 6000 (Illumina).
Single cell RNA-seq with 10X Next GEM Single Cell 3’ v3.1 kit

value: WT


title: Hs_hESC_beta_cells_differentiation_D14_scRNAseq


title: A073


title: Hs_hESC_D21_CDX2_ChIP_seq_rep1

value: day 21 human pluripotent stem cell-derived islets


title: MM_466_S15

extract_protocol:
Approximately ~35 mg of frozen pancreas from each donor was resuspended in 500 μl of nuclei permeabilization buffer [0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X Pierce Protease Inhibitor (Fischer, PIA32965), 1 mM DTT (Sigma-Aldrich, D9779), Recombinant RNase inhibitor (0.2 U/μl; Promega, 2% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3). Supernatant was removed and pellet was resuspended in sort buffer [1mM EDTA (Invitrogen, 15575020), 0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)).] and stained with DRAQ7 (1:150; Cell Signaling Technology, 7406). 60,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer [1.0U/μL Recombinant RNAsin (Promega, PAN2515), 5% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sorted nuclei were then centrifuged at 1000 g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in reaction buffer [RNase inhibitor (0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)).] and counted using a hemocytometer.
16,550 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer specifications. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using TapeStation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp. Libraries were sequenced using a NextSeq 500 or NovaSeq 6000 (Illumina).
Single nucleus RNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics)

value: 7 years

tag: gender

value: M

tag: race

value: Caucasian

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: c-peptide level (ng/ml)


title: Hs_hESC_D21_CDX2_ChIP_seq_input2

tag: cell type


title: A051

tag: tissue

tag: treatment


title: Hs_hESC_D21_CDX2_ChIP_seq_input1


title: MM_464_S13

value: 2 years

value: F


title: HZ144_D11_S11


title: MM_434_S39

value: 18 months

value: Hispanic or Latino


title: P7-lymph node-scRNA

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

data_processing:
Quality control
Raw files were demultiplexed and mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v2.0 software (10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix file using RNA raw count

molecule: polyA RNA

source_name: lymph node

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

value: untreated

tag: tnm stage

tag: molecular typing

value: luminal B


title: MM_433_S11

value: 13 months


title: A049

value: Distal Intestine

tag: diet


title: A075

tag: water stage


title: A019

value: HK L-137 Lower inclusion


title: CDX2-KO [MM_845_2_S30]

tag: genotype


title: MM_465_S14

value: 8 years


title: MM290_D14


title: MM_425_S36

value: 9 years


title: A003

value: Control Diet

value: Fresh water


title: MM_458_S2

extract_protocol:
Approximately 25 mg of frozen, ground pancreas from each donor was resuspended in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water) and incubated for 10 min at 4°C. Nuclei were filtered with a 30 µm filter (CellTrics) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were washed  with 1ml Wash buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, and 1% BSA (Proliant 7500804) in molecular biology-grade water). Nuclei were pelleted and resuspended in 30 µL of 1X Nuclei Buffer (10x Genomics). Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation.
Single nucleus ATAC-seq libraries were generated using the Chromium Chip E Single Cell ATAC kit (10x Genomics, 1000086) and indexes (Chromium i7 Multiplex Kit N, Set A, 10x Genomics, 1000084) following manufacturer instructions. Final libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500, HiSeq 4000 or NovaSeq 6000 sequencers (Illumina) and reads were trimmed afterwards to fit into corresponding analysis pipeline.
Single nucleus ATAC-seq with 10X Chromium Chip E Single Cell ATAC kit


title: MM_538_S5

value: not applicable


title: P6-lymph node-scRNA


title: A002


title: MM_459_S3


title: MM_431_S3


title: MM_432_S3


title: A001


title: R5_130

city: Oklahoma City

first: Jason

last: Larabee

state: OK

address: 940 Stanton L. Young Blvd. BMSB 1062

institute: OUHSC

data_processing:
derived sequences were mapped to the human genome (GRCh38) by gSNAP
expression (FPKM) derived by Cufflinks
differential expression determined as a +/-1.5-fold change from control
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include lcounts per million (CPM) values for each sample

source_name: HeLa

growth_protocol: HeLa cells and HeLa R5 cells were cultured under normal growth conditions before RNA was isolated.

extract_protocol:
RNA was isolated from HeLa and HeLa R5 cells using Direct-Zol microprep (Zymogen).
mRNA template libraries that were prepared and sequenced using 2 x 150  bp reads on an Illumina NovaSeq 6000

treatment_protocol: HeLa were either cultured under normal conditions, or cultured under condition to generate C. difficile TcdB2 resistance. TcdB2 resistance was generated  by maintaining  culture in up to 130 pg/ml or 500 pg/ml of TcdB2 for about 1 month.  TcdB2 was removed from culture for a week before isolating RNA.

tag: background strain

value: epithelial cell; cancerous cell

value: wild-type

value: generate C. difficile TcdB2 resistance by maintaining  culture in up to 130 pg/ml TcdB2 for about 1 month


title: MM_393_S25

tag: age

value: M

value: Caucasian


title: HeLa Control


title: HANK1, Ruxo#2

city: Guangzhou

first: jinghong

last: Chen

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Genome_build: GRCh38
Supplementary_files_format_and_content: ChIP-seq samples: bigwig file for each sample
RNA-seq samples: TXT file contain counts for each sample

growth_protocol: HANK1 and SNT8 were cultured in Artemis medium-2 supplemented with 2% human plasma serum and 1% P/S. 100 IU/ml IL-2 was included into HANK1 growth media and 700 IU/ml IL-2 into SNT8, respectively. SNK6 and NK92 were maintained in RPMI1640 medium supplemented with 10% FBS, 10% horse serum, 1% P/S and 100 IU/ml IL-2. KHYG1 was grown in RPMI1640 medium supplemented with 10% FBS, 1% P/S and 100 IU/ml IL-2. MEC04 was cultured in RPMI1640 medium supplemented with 15% FBS, 1% P/S and 50 IU/ml IL-2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: HANK1 was treated with DMSO, 0.25um tofacitinib or 0.125um ruxolitinib for 24h.

value: Natural Killer/T-cell lymphoma

tag: cell line

value: Ruxo


title: Jo006

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

organism: Mus musculus

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: spleen

value: CD8 T cell

tag: sorting markers

value: CD8+ CD44lo CD62Lhi Qa2hi OT-I Nur77-GFPhi

tag: phenotype

tag: mouse genotype

value: Nur77-GFP (Tg(Nr4a1-EGFP)GY139Gsat)


title: hs_islet_R394_2Y_scRNAseq_rep1

extract_protocol:
Upon receipt, human islets were stained with dithizone and positively-staining material was hand-picked using a dissection microscope. Purified human islets were collected in microcentrifuge tubes and washed with PBS. Accutase® was used to dissociate them into single cells, which were then stained with propidium iodide (Sigma) in a PBS solution containing 0.2% BSA.  Approximately 200,000 live cells (propidium iodide-negative) were sorted with a FACSAriaTM Fusion Flow Sorter, at a sorting speed lower than 3,000 events per second, to minimize damage to the cells. Sorted cells were pelleted with 250 x g for 5 minutes at 4°C, and counted with a Scepter™ automated cell counter.
10,000 accurately counted cells were loaded onto a 10X Chromium Controller for GEM formation and cell barcoding using Next GEM Single Cell 3’ v3.1 reagents. Barcoded single cells were subjected to cDNA synthesis and sequencing library construction using 10X Next GEM Single Cell 3’ v3.1 reagents according to manufacturer’s instructions. Final libraries were quantified using a Qubit fluorimeter (Life technologies) and the fragmented cDNA was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500, HiSeq 4000 or NovaSeq 6000 sequencers (Illumina) and reads were trimmed afterwards to fit into corresponding analysis pipeline.
Single cell RNA-seq with 10X Next GEM Single Cell 3’ v3.1 kit

value: 2 years


title: hs_islet_R394_2Y_scRNAseq_rep2


title: Jo005

value: CD8+ CD44lo CD62Lhi Qa2hi OT-I Nur77-GFPlo


title: A050

extract_protocol:
Total RNA was extracted from each sample using RNeasy Mini Kit (Qiagen) following the supplier’s instructions. Then, RNA samples were quantified using a NanoDrop™ 8000 spectrophotometer and RNA integrity was measured by Agilent Bioanalyzer 2100. All samples showed an RNA integrity number ≥ 7).
RNA libraries for RNA-seq were prepared by Novogene (UK) Company Limited

value: Distal Intestine


title: R5_500

value: generate C. difficile TcdB2 resistance by maintaining  culture in up to 500 pg/ml TcdB2 for about 1 month


title: MM_561_2_S11

extract_protocol:
Approximately 35 mg of frozen pulverized pancreas was resuspended in 500 μl of nuclei permeabilization buffer [0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X Pierce Protease Inhibitor (Fischer, PIA32965), 1 mM DTT (Sigma-Aldrich, D9779), Recombinant RNase inhibitor (0.2 U/μl; Promega, 2% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3). Supernatant was removed and pellet was resuspended in sort buffer [1mM EDTA (Invitrogen, 15575020), 0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and stained with DRAQ7 (1:150; Cell Signaling Technology, 7406). 60,000 nuclei were sorted using an SH800 sorter (Sony) into 50 μl of collection buffer [1.0U/μL Recombinant RNAsin (Promega, PAN2515), 5% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)]. Sorted nuclei were then centrifuged at 1000 g for 15 min (Eppendorf, 5920R; 4°C, ramp speed of 3/3), and supernatant was removed. Nuclei were resuspended in reaction buffer [RNase inhibitor (0.2U/μL Recombinant RNAsin (Promega, PAN2515), 1% Fatty-acid-free BSA in PBS (Proliant, 7500804; Corning, 21-040-CV)] and counted using a hemocytometer.
16,550 nuclei were loaded onto a Chromium controller (10x Genomics). Libraries were generated using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3(10x Genomics, PN-1000075) and Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer specifications and date of experiment. Complementary DNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and cleanup steps. Final library concentration was assessed by the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and fragment size was checked using TapeStation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally around 500 bp. Libraries were sequenced using a NextSeq 500 or NovaSeq 6000 (Illumina).
Single nucleus RNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics)

tag: age (year)

tag: gender

value: F

tag: bmi


title: HANK1, Ruxo#1


title: MM_407_2_S34


title: Jo004

tag: cell type


title: MM_404_S8


title: MM_400_S4


title: HANK1, Tofa#2

tag: tissue

value: Tofa


title: MM_457_S1

tag: race

tag: height (cm)

tag: weight (kg)

tag: c-peptide level (ng/ml)


title: Jo003


title: MM_382_S12


title: MM_359_S6


title: HANK1, Tofa#1

tag: treatment


title: MM_356_S3


title: HANK1, DMSO#2

value: DMSO


title: young cells with LMNB1 downregulation – Replicate 1

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

data_processing:
Paired-end sequencing (reads length: 2x150bp) was performed by NovoGene compagny using Illumina sequencer.
Raw RNA-seq reads were trimmed using Trimmomatic. Reads mapping and genome index building were performed using STAR.
Differential expression analysis was performed using DESeq2 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Human fibroblast

growth_protocol: MRC-5 cells were grown in DMEM supplemented with 10% foetal bovine serum, penicillin (100 IU/mL) and streptomycin (100µg/mL). Cells were cultured at 37°C, 5% CO2 and 5% O2

extract_protocol:
RNA extractions were performed accordingly to manufacturer’s instruction of the RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared according to standards Illumina's instructions

treatment_protocol: Young MRC-5 cells were infected with empty (pWPIR-GFP) or TRF2 expressing (pWPIR-GFP-TRF2) virus and were transfected with an siRNA control or LMNB1 and collected for RNA extraction, at PD 30. For senescent cells, MRC-5 cells were passed until they reached a pre-senescent stage and infected with an empty or TRF2 expressing virus. Once they stopped dividing and reached a plateau in their growth curve, they were  transfected with an siRNA control and collected for RNA extraction.


title: young cells with LMNB1 downregulation – Replicate 2


title: Jo001


title: PVN_SEA3 [mRNA]

first: Wei

last: Hu

address: Dongan Road 130

institute: Fudan university

data_processing:
The insert size of the library was examined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and only effective concentrations >2 nM were used for sequencing.
The raw reads were filtered to obtain the clean reads after removing adapter-related reads, reads containing uncertain bases, and low-quality reads with base quality phred score ≤ 20.
The clean reads were then mapped to the human reference genome (GRCh38/HG38) using HISAT2 algorithms and were quantitatively analyzed using the featureCounts software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Total RNA was extracted from tissue samples of the PVN and CEA, and the preparation of the cDNA library and the sequencing were performed by Novo Gene Biotech Co. Ltd. (Beijing, China).
A strand-specific library strategy was used to construct the mRNA and circRNA libraries. Sequencing data for the miRNA library were generated using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA).

value: Brain

value: Hepatectomy + sham electroacupuncture


title: young cells with LMNB1 downregulation – Replicate 3


title: Col7a1 KO mouse 2 scRNAseq

city: Valhalla

first: Morgan

middle: G

last: Anderson-Crannage

state: NY

address: 40 Sunshine Cottage Rd.

department: Cell Biology & Anatomy

institute: New York Medical College

description:
10x Genomics
KOD12

data_processing:
10X v3 FASTQ files  were processed using loompy module with standard settings (v 3.0.6), kallisto pseudoaligner (v 0.46.0), and genome version GRCm38.v31 from Gencode.
FASTQ files: read files of the experiment. Each FASTQ file is divided into two: one (R1), which contains the read fragments associated with the cell barcode and UMI (28bp), and the second (R2), which contains the read fragments associated with mRNA (91bp).
Dataset processing was performed using scanpy (v 1.7.0rc1), with the following dependencies versions: anndata (0.7.5), h5py (2.10.0), numpy (1.19.5), pandas (1.1.4), scipy (1.6.0), numba (0.52.0), scikit-learn (0.22), umap-learn (0.4.6) .
Each sample was preprocessed independently and then merged using batch effect correction. Firstly, cell QC was performed by removing cells with log1p counts of more than 6.6, and more than 8.0; and cells with more than 10% of mitochondrial counts. Then, samples were normalised and log1p-transformed. PCA with the first 30 was calculated, then k-nearest neighbours with metric cosine and k set to sqrt(n_cells) // 2 were computed. Feature selection was performed using triku package (v 2.1.3).
Once individual samples were processed, they were integrated using harmony (harmonypy, v 0.0.5) with parameters max_iter_harmony=50 and sigma=0.05.
Assembly: mm10
Supplementary files format and content: h5ad files: AnnData files used in scanpy. Each file contains several components: (1) X –count matrix–, (2) obs –table with data associated with the cells, such as cell type or batch–, (3) var –table with data associated with the genes, such as the number of counts, mean counts, of if the gene is highly variable–, (4) uns –dictionaty with unstructured information related to leiden, UMAP, or other processing steps–, (5) obsm –matrices associated to dimensionality reduction methods such as PCA or UMAP–, (6) layers –matrices containing other information, such as the spliced and unspliced counts–, (7) obsp –adjacency matrices related to kNN algorithm–.
Supplementary files format and content: loom files: AnnData files used in scanpy. Each file contains several components: (1) X –count matrix–, (2) obs –table with data associated with the cells, such as cell type or batch–, (3) var –table with data associated with the genes, such as the number of counts or mean counts–.

source_name: Skin (Paw)

extract_protocol:
Paw skin was dissected, dissassociated into a single cell suspension, and washed. Sample KOD11 was passed through a ficoll suspension to remove RBCs.
Single cell library preparation and sequencing were done by Singulomics Corporation (https://singulomics.com/, Bronx, NY). Fresh, viable single cell suspensions were washed and resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 5ʹ Gene Expression library (Chromium Next GEM Single Cell 5' Reagent Kits v2 - Dual Index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).
Libraries were sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA, United States), and reads were subsequently processed using 10x Genomics Cell Ranger analytical pipeline (v6.0.1) and mouse reference genome mm10. Dataset aggregation was performed using the cellranger aggr function normalizing for the total number of confidently mapped reads across libraries.

value: Skin (Paw)

value: All Cells

tag: strain

tag: disease

value: RDEB

tag: genotype

value: Col7a1 KO

value: 2 weeks


title: young cells with TRF2 overexpression – Replicate 3

tag: cell line


title: Col7a1 KO mouse 1 scRNAseq

description:
10x Genomics
KOD11

tag: age


title: WT mouse 2 scRNAseq

description:
10x Genomics
WT2

value: Healthy

value: WT


title: PVN_SEA1 [mRNA]


title: young cells with empty vector – Replicate 1


title: young cells with TRF2 overexpression – Replicate 1


title: PVN_SEA2 [mRNA]


title: senescent cells with TRF2 overexpression (reanalysis) – Replicate 3

description: re-analyzed by GSM4874287


title: young cells with empty vector – Replicate 3


title: WT mouse 1 scRNAseq

description:
10x Genomics
WT1


title: young cells with TRF2 overexpression – Replicate 2


title: senescent cells with TRF2 overexpression (reanalysis) – Replicate 1

description: re-analyzed by GSM4874285


title: PFC-WT-H3K4me3-4

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

data_processing:
Adapator trimming using Trimmomatic
Reads were filtered by samtools and Picard
Reads alignment using Bowtie2 to mm10
Peak calling using MASC2 with q<0.05
Assembly: mm10
Supplementary files format and content: bam file
Library strategy: CUT&RUN

source_name: Adult PFC

extract_protocol:
Nuclei was extracted by Sigma Nuclei EZ Prep kit from mouse brain tissues
CUT&RUN libraries were generated using Roche KAPA HyperPrep Kits

value: Adult PFC

tag: chip antibody

value: H3K4me3 (Active Motif, 39159)


title: PVN_HT3 [mRNA]

value: Hepatectomy


title: senescent cells with TRF2 overexpression (reanalysis) – Replicate 2

description: re-analyzed by GSM4874286


title: HANK1, DMSO#1

value: Natural Killer/T-cell lymphoma


title: senescent cells with empty vector (reanalysis) – Replicate 3

description: re-analyzed by GSM5437005


title: senescent cells with empty vector (reanalysis) – Replicate 2

description: re-analyzed by GSM4874284


title: PVN_HT2 [mRNA]


title: PVN_HT1 [mRNA]


title: Jo002

value: spleen

value: CD8 T cell

tag: sorting markers

value: CD8+ CD44lo CD62Lhi Qa2hi OT-I Nur77-GFPhi

tag: phenotype

tag: mouse genotype

value: Nur77-GFP (Tg(Nr4a1-EGFP)GY139Gsat)


title: PVN_HT+EA3 [mRNA]

value: Brain

value: Hepatectomy + electroacupuncture


title: young cells with empty vector – Replicate 2


title: PFC-WT-H3K4me3-2


title: PFC-WT-H3K4me1-4

value: H3K4me1 (Active Motif, 61633)


title: PVN_HT+EA2 [mRNA]


title: Mouse Tumor, rep6, scRNAseq, CJ_0034

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

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

institute: Dartmouth College

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 2,000 and 5,000) and cells with too many mtRNA (average around 7%), resulting in a total of 8,614 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Twelve distinct cell types were identified, including langerhan cells, IMs, monocytes, DC1, CD301b-.DC2, CD301b+.DC2, inflammatory DC2, pre-DC1, pre-CD301b-.DC2, pre-CD301b+.DC2, lymphocytes, and cycling cells.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 8 samples and different assays of mRNA expression matrixes; The meta data in rds format for every cells, includes the sample source and cell types

source_name: Pulmonary metastases of B16 melanoma

extract_protocol:
Mononuclear phagocytes were isolated from ear skin as previously described. Briefly, the dorsal and ventral sides of the ears were separated before floating dermis-side down on digestion solution. The ear skin was then digested with 500 μg/ml Liberase (Roche/Sigma, Branford, CT/St. Louis, MO) for 30 minutes at 37°C. Single-cell suspensions were obtained by repeated glass pipetting before cells were filtered through a 100-μm nylon filter. Cells were centrifugated at 300g for 5 min at 4°C and stained with fluorescent labeled antibodies. Stained single cell suspensions were enriched by MACS bead purification (Miltenyi, San Diego, CA) using anti-CD11b and anti-CD11c microbeads and then FACS sorted for all mononuclear phagocytes using the FACS Aria Fusion (BD Biosciences). Sorted cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 2 × 105 cells/ml. Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >85%.
Single cells were then processed using the Chromium Next GEM Single Cell 3′ Platform (10X Genomics). Approximately 5,000 cells were loaded on each channel with an average recovery rate of 3,700 cells. Libraries were sequenced on NextSeq 500/550 (Illumina) with an average sequencing depth of 70,000 reads/cell.

value: Mononuclear Phagocytes

value: Pulmonary metastases of B16 melanoma

value: 6-8 weeks old


title: Mouse Tumor, rep8, scRNAseq, CJ_0036

description: 10x Genomics


title: PFC-WT-H3K4me1-3


title: PVN_HT+EA1 [mRNA]


title: Mouse Tumor, rep5, scRNAseq, CJ_0033

description: 10x Genomics


title: Mouse Tumor, rep2, scRNAseq, CJ_0026

description: 10x Genomics


title: Mouse Tumor, rep3, scRNAseq, CJ_0027

description: 10x Genomics


title: Mouse Tumor, rep4, scRNAseq, CJ_0028

description: 10x Genomics


title: PFC-WT-H3K4me3-3


title: Mouse Tumor, rep1, scRNAseq, CJ_0025

description: 10x Genomics


title: PFC-WT-H3K27me3-4

value: H3K27me3 (Active Motif, 29155)


title: PFC-WT-H3K27me3-3


title: PVN_NC3 [mRNA]

value: Normal control


title: PVN_NC2 [mRNA]


title: Mouse Skin, Naive, rep1, scRNAseq, mSK1

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 2,000 and 5,000) and cells with too many mtRNA (average around 7%), resulting in a total of 8,614 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Twelve distinct cell types were identified, including langerhan cells, IMs, monocytes, DC1, CD301b-.DC2, CD301b+.DC2, inflammatory DC2, pre-DC1, pre-CD301b-.DC2, pre-CD301b+.DC2, lymphocytes, and cycling cells.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 3 samples and different assays of mRNA expression matrixes; The meta data in rds format for every cells, includes the sample source and cell types

source_name: Ear skin

value: Ear skin


title: PVN_NC1 [mRNA]


title: Mouse PLF, Naive, rep3, scRNAseq, CJ46

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 2,000 and 5,600) and cells with too many mtRNA (average around 6%), resulting in a total of 43,588 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Fifteen distinct cell types were identified, including large peritoneal macrophages, small peritoneal macrophages, IMs, monocytes, DC1, DC2, inflammatory DC2, neutrophils, B cells, T cells, natural killer cells, natural killer T cells, fibroblasts, epithelial cells, and cycling cells.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 3 samples and different assays of mRNA expression matrixes; The meta data in rds format for every cells, includes the sample source and cell types

source_name: Peritoneal lavage fluid

extract_protocol:
Cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 1 × 106 cells/ml. Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >95%.
Single cells were then processed using the Chromium Next GEM Single Cell 3′ Platform (10X Genomics). Approximately 25,000 cells were loaded on each channel with an average recovery rate of 20,000 cells. Libraries were sequenced on NextSeq 500/550 (Illumina) with an average sequencing depth of 50,000 reads/cell.

value: PLF cells

value: Peritoneal lavage fluid


title: Mouse Tumor, rep7, scRNAseq, CJ_0035

description: 10x Genomics


title: Mouse Skin, Naive, rep3, scRNAseq, mSK3

description: 10x Genomics


title: senescent cells with empty vector (reanalysis) – Replicate 1

description: re-analyzed by GSM4874283


title: Mouse Skin, Naive, rep2, scRNAseq, mSK2

description: 10x Genomics


title: CEA_SEA3 [mRNA]

value: Hepatectomy + sham electroacupuncture


title: Mouse PLF, Naive, rep2, scRNAseq, CJ44

description: 10x Genomics


title: PFC-WT-H3K27ac-4

value: Adult PFC

value: H3K27ac (Active Motif, 29133)


title: CEA_SEA2 [mRNA]


title: Mouse PLF, Naive, rep1, scRNAseq, CJ42

description: 10x Genomics


title: PFC-WT-H3K4me1-2


title: Mouse Lung MNPs, aGr1-LPS, rep2, scRNAseq, aGr1-LPS-B

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 1,400 and 4,600) and cells with too many mtRNA (average around 4%), resulting in a total of 26,267 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.2 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Ten distinct cell types were identified, including IMs, non-classic IMs, recruited macrophages, non-classic monocytes, DC1, CD301b-.DC2, CD301b+.DC2, inflammatory DC2, migratory DCs, and cycling cells.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 6 samples and different assays of mRNA expression matrixes; The meta data in rds format for every cells, includes the sample source and cell types

source_name: Digested lung

extract_protocol:
IMs were isolated from lung as previously described. Briefly, The lungs were perfused and finely minced with scissors and digested for 30 minutes at 37°C. Single cell suspensions were obtained by repeated glass pipetting and filtration. Cells were centrifugated at 300g for 5 min at 4°C and stained with fluorescent labeled antibodies. Stained single cell suspensions were enriched by MACS bead purification (Miltenyi, San Diego, CA) using anti-CD11b microbeads and then FACS sorted using the FACS Aria Fusion (BD Biosciences; strategy shown in Figure A1). Sorted cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 2.5 × 105 cells/ml. Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >90%.
Single cells were then processed using the Chromium Next GEM Single Cell 3′ Platform (10X Genomics). Approximately 6,000 cells were loaded on each channel with an average recovery rate of 5,000 cells. Libraries were sequenced on NextSeq 500/550 (Illumina) with an average sequencing depth of 30,000 reads/cell.

value: Digested lung


title: CEA_SEA1 [mRNA]


title: Mouse Lung MNPs, aGr1-LPS, rep1, scRNAseq, aGr1-LPS-A

description: 10x Genomics


title: Mouse Lung MNPs, LPS, rep1, scRNAseq, LPS-A

description: 10x Genomics


title: PFC-WT-H3K27ac-3


title: Mouse Lung MNPs, LPS, rep2, scRNAseq, LPS-B

description: 10x Genomics


title: PFC-WT-H3K27me3-2


title: PFC-HT-H3K4me3-4

value: H3K4me3 (Active Motif, 39159)


title: Mouse BALF, Naive, rep3, scRNAseq, CJ45

description: 10x Genomics

data_processing:
Raw sequencing reads were demultiplexed, mapped to the GRCm38 mouse reference genome, and gene expression matrices were generated using CellRanger v6.1 (10X Genomics). The following analyses were conducted in R 4.2 (R Core Team, 2014). Seurat package v4.3 was used for downstream data analyses (Hao et al, 2021), and figures were produced using the package ggplot2. Following a standard workflow, the gene expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than three cells. Samples then underwent quality control to remove cells with either too many or too few expressed genes (average around 2,500 and 5,800) and cells with too many mtRNA (average around 7.5%), resulting in a total of 42,443 cells. Then, “SCTransform” was applied with the “glmGamPoi” method to normalize gene expression data (Stuart et al, 2019; Ahlmann-Eltze & Huber, 2021). After individual preparation, all the samples were merged into a combined Seurat object. Then scaled values of variable genes were then subject to principal component analysis for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (50 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations from different treatment groups.
DEGs were calculated with “FindAllMarkers” function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in different treatment groups (R Core Team, 2014; Hao et al, 2021). The “data” matrices of “SCT” assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant up-regulation when compared against all other clusters and defined by having a Bonferroni-adjusted P-value < 0.05. The DEGs are ranked by the adjusted P-value to select the top DEGs for downstream analysis.
To identify cell types, “FindClusters” function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (Hao et al, 2021). “FindAllMarkers” function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literature and the clusters were then annotated for the most likely identity. For re-clustered IMs subtypes, “FindClusters” was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern. Eight distinct cell types were identified, including AMs, red-blood-cells-phagocytosing AMs, cycling AMs, IMs, resident DCs, migratory DCs, lymphocytes, and epithelial cells.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Integrated SeuratObject in rds format contains all 3 samples and different assays of mRNA expression matrixes; The meta data in rds format for every cells, includes the sample source and cell types

source_name: Bronchoalveolar lavage fluid

extract_protocol:
Cells were centrifugated at 300g for 5 min at 4°C. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 1 × 106 cells/ml. Cell quality and viability were assessed with a Cellometer K2 (Nexcelom Bioscience). All samples had viability >97%.
Single cells were then processed using the Chromium Next GEM Single Cell 3′ Platform (10X Genomics). Approximately 25,000 cells were loaded on each channel with an average recovery rate of 20,000 cells. Libraries were sequenced on NextSeq 500/550 (Illumina) with an average sequencing depth of 55,000 reads/cell.

value: BALF cells

value: Bronchoalveolar lavage fluid


title: CEA_HT2 [mRNA]

value: Brain

value: Hepatectomy


title: PFC-HT-H3K4me3-3


title: Mouse BALF, Naive, rep2, scRNAseq, CJ43

description: 10x Genomics


title: H3K27Me3_SS-Nrf2_KO_ChIP_1

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

institute: Augusta University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
reads were mapped with Bowtie2 and analyzed by MACS2 for the peak calling
Assembly: mm9
Supplementary files format and content: bw

source_name: Bone marrow Ter119+ cells

extract_protocol: Bone marrow Ter119+ erythroid cell was crosslinked with 1% formaldehyde, sonicated, and immunoprecipitated with H3K27Me3 antibody and subjected to library preparation using TruSeq ChIP Sample Preparation kit (Illumina) for the construction of sequencing libraries.

value: Bone marrow Ter119+ cells

tag: background strain

value: mixed B6;129P2 background

value: 2-3 month

value: knockout


title: PFC-HT-H3K4me3-2


title: CEA_HT1 [mRNA]


title: CEA_HT+EA2 [mRNA]

value: Hepatectomy + electroacupuncture


title: PFC-HT-H3K4me1-3

value: H3K4me1 (Active Motif, 61633)


title: H3K27Me3_SS-Nrf2_WT_ChIP_2

tag: cell type

value: wild type


title: H3K27Me3_SS-Nrf2_KO_ChIP_3


title: CEA_HT+EA1 [mRNA]

tag: tissue


title: CEA_HT+EA3 [mRNA]


title: H3K27Me3_SS-Nrf2_WT_ChIP_3


title: Mouse BALF, Naive, rep1, scRNAseq, CJ41

description: 10x Genomics

value: 6-8 weeks old


title: 4wk Mac-1 low rep #4

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
fastq files were processed using the nextflow rnaseq pipeline version 1.4.2
DEG were identified using DESeq2
Supplementary files format and content: raw read counts contain read counts for all samples

source_name: Hematopoietic stem cell

growth_protocol: Mice were housed in ventilated racks with free access to food and water

extract_protocol: Spine, femurs, tibia, and iliac bones were crushed in PBS+2% FBS. Bone marrow was enriched for cKit, followed by FACS sort of live LSK SLAM (CD3e-, B220-, Gr-, NK1.1-, Ter119-, cKit+, Sca1+, CD48-, CD150+) HSCs into sterile PBS+RNAse inhibitor and snap freezed at -80 degrees. cDNA syntesis and amplification were done using SMART-Seq v4 (Takara), followed by library preparation using Nextera XT DNA library prep kit (Illumina).

treatment_protocol: Cells isolated from mice transplanted with 8000 LSK (CD3e-, B220-, Gr-NK1.1-, Ter119-, cKit+, Sca1+) 4 weeks earlier into lethally irradiated (900cGy) recipients

value: Hematopoietic stem cell

value: WT

value: 4wk post transplant


title: PFC-WT-H3K27ac-2

value: Adult PFC

value: H3K27ac (Active Motif, 29133)


title: PFC-HT-H3K4me1-4


title: 4wk Mac-1 low rep #3


title: H3K27Me3_SS-Nrf2_WT_ChIP_1


title: PFC-HT-H3K4me1-2


title: 4wk Mac-1 negative rep #3


title: Mouse Lung MNPs, Naive, rep1, scRNAseq, Naive-A

description: 10x Genomics

value: Mononuclear Phagocytes

value: Digested lung


title: CEA_NC3 [mRNA]

value: Brain

value: Normal control


title: PFC-HT-H3K27me3-4

value: H3K27me3 (Active Motif, 29155)


title: Mouse Lung MNPs, Naive, rep2, scRNAseq, Naive-B

description: 10x Genomics


title: H3K27Me3_SS-Nrf2_KO_ChIP_2

value: Bone marrow Ter119+ cells

value: mixed B6;129P2 background


title: CEA_NC2 [mRNA]


title: 4wk Mac-1 positive rep #2


title: PFC-HT-H3K27ac-4


title: 4wk Mac-1 negative rep #1


title: 4wk Mac-1 low rep #1


title: 4wk Mac-1 negative rep #2


title: PFC-HT-H3K27me3-3


title: PVN_SEA1 [miRNA]

value: Hepatectomy + sham electroacupuncture


title: CEA_NC1 [mRNA]


title: 4wk Mac-1 positive rep #3


title: PFC-HT-H3K27ac-2


title: Testis, Ythdc2 cKO, P16, rep 2

city: Stanford

first: Margaret

last: Fuller

state: California

address: 279 Campus Drive, Beckman Center B300

department: Developmental Biology

institute: Stanford University

description:
DE_normalized_counts_P16.txt
Ythdc2_cKO_P16_2.220304_NB551514_0749_AHTGG7BGXK.end1

data_processing:
Libraries were separated by barcode and adapters and low-quality bases were trimmed using trimGalore. Reads were mapped to the mouse genome (GRCm39/mm39) using STAR.
Reads for each transcript were extracted using HTSeq. Differential gene expression was calculated using DESeq2.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include DEseq2 normalized counts

source_name: testes

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
Ribosomal RNAs were depleted from 1 µg of total RNA using TruSeq Stranded Total RNA kit Ribo-Zero components (Illumina) according to the manufacturer’s protocol. Library preparation for high-throughput sequencing was performed on 100 ng of rRNA depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Control and Ythdc2 cKO mice were treated with 10 mg/ml Tamoxifen on P12 and P13.

value: testes

value: Ythdc2 conditional knockout

tag: developmental stage


title: Testis, Ythdc2 cKO, P14, rep 2

description:
DE_normalized_counts_P14.txt
Ythdc2_cKO_P14_2.220304_NB551514_0749_AHTGG7BGXK.end1


title: PVN_SEA2 [miRNA]


title: PFC-HT-H3K27ac-3


title: Testis, control, P16, rep 2

description:
DE_normalized_counts_P16.txt
WT_P16_2.220304_NB551514_0749_AHTGG7BGXK.end1

value: control


title: Steady state Mac-1 negative rep #3

value: untreated


title: 4wk Mac-1 positive rep #1

value: Hematopoietic stem cell


title: PVN_HT2 [miRNA]

value: Hepatectomy


title: Testis, Ythdc2 cKO, P16, rep 1

description:
DE_normalized_counts_P16.txt
Ythdc2_cKO_P16_1.220304_NB551514_0749_AHTGG7BGXK.end1


title: PVN_HT3 [miRNA]


title: 4wk Mac-1 low rep #2

value: WT

value: 4wk post transplant


title: PFC-HT-H3K27me3-2

value: Adult PFC


title: PVN_HT1 [miRNA]


title: PVN_SEA3 [miRNA]


title: Testis, control, P14, rep 2

description:
DE_normalized_counts_P14.txt
WT_P14_2.220304_NB551514_0749_AHTGG7BGXK.end1


title: Testis, control, P14, rep 1

description:
DE_normalized_counts_P14.txt
WT_P14_1.220304_NB551514_0749_AHTGG7BGXK.end1


title: PFC-IgG-KO-3

value: Rb IgG (Jackson Immuno 011-000-002)


title: Steady state Mac-1 low rep #3


title: PFC-IgG-KO-2


title: PVN_HT+EA3 [miRNA]

value: Hepatectomy + electroacupuncture


title: Steady state Mac-1 negative rep #2


title: Steady state Mac-1 low rep #2


title: PFC-MYT1L-KO-4

value: MYT1L (Millipore, ABE2915)


title: PVN_HT+EA2 [miRNA]

value: Brain


title: PFC-MYT1L-KO-3


title: PFC-IgG-KO-4


title: HCT15shNSUN2-2.IP

first: Yu

last: Lin

state: China

address: No. 1838, Guangzhou Dadao North, Baiyun District, Guangzhou

institute: Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital

data_processing:
library strategy: meRIP-seq
Pairing reads were quality controlled using a quality criterion of 1/1000 (Q30) error base call probability in the Illumina HiSeq 4000 sequencer: Q30>80% indicates good sequencing quality. After quality control, trim the 3/adapter using Cutadapt software (v1.9.3) and remove low-quality reads, and harvest high-quality clean reads. Align a clean read of the input library with a reference genome (GRCh38.Geocoding v32) using STAR software (Domin et al., 2013) and identify mRNA peaks using DCC software(Cheng et al., 2016) . Next, align clean reads of all libraries with reference genomes using Hisat2 software (v2.0.4)(Kim et al., 2015). Identify m5C peaks on mRNA using MACS software(Zhang et al., 2008). In addition, different methylation peaks were identified using DiffReps software (Shen et al., 2013): m5C peaks with a fold change of >2 or <0.5 (P<0.00001) in CRC were considered to be up-regulated methylation or down-regulated methylation.(Shen et al., 2013)Peaks that overlap exons of protein-coding genes identified using software and m5C sections were selected using internally developed scripts for further annotation.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colorectum

extract_protocol:
We extracted total RNA using Trizol reagent (Invitrogen, California, USA) following the manufacturer's instructions. Use the Ribo-Zero rRNA Removal Kit (Illumina, Inc., CA, USA) to reduce rRNA content. The quality of RNA is assessed using its OD260/OD280 ratio, which is a measure of nucleotide-to-protein ratio based on optical density measured using spectrophotometry. RNA purity with OD260/OD280 values in the range of 1.8-2.1 is considered acceptable, and RNA extracted from all samples meets this standard.
Total RNA was cleaved into 100 base pair fragments using the GenSeqTM m5C RNA IP Kit (GenSeq Inc, China), followed by m5C immunoprecipitation using the NEBNext® Ultra II Directed RNA Library Preparation Kit (New England Biolaboratories, USA), followed by RNA-seq library generation.The cDNA library was evaluated using the Bioanalyzer 2100 System (Agilent Technologies USA) and the library was sequenced using an Illumina Hiseq instrument with 150 bp pairing readings.

value: colorectum

value: cancer cell

value: NSUN2 knockdown


title: Steady state Mac-1 low rep #1


title: CEA_HT3 [mRNA]


title: HCT15shNSUN2-1.IP


title: PFC-IgG-WT-4


title: input_CM

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

data_processing:
De-multiplexed reads were aligned to mm10 release of the mouse reference genome using bowtie2 (v 2.4.4) MACS2 (v2.2.7.1)(Zhang et al., 2008) was used to perform peak calling procedure (broad peak) using a cutoff FDR q-value of 0.05.
Integrative Genomics Viewer (IGV) was used for the visualization of the results, representing output of bamCompare (deepTools v.3.5.1)(Ramirez et al., 2016)
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

source_name: BM-derived MDSC

extract_protocol:
Cells under the reported conditions were fixed with 1% Formaldehyde (Cat. No. 252549, Sigma) for 5’ RT. Then cells were washed three times with ice cold PBS 1X. Cells were lysed with 900 ul of buffer 1 (50 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 0.1% Nonidet P-40, 10% glycerol and protease and phosphatase inhibitors) for 8 min’ at 4°C. This buffer is needed to extract cytoplasmic proteins. The samples were centrifuged at 3000 rpm for 5’ at 4°C. Then the pellet containing nuclei is lysed with 500 ul of buffer 2 (50 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 1% SDS and protease and phosphatase inhibitors). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 0.5-2 kbp. Lysates were incubated overnight at 4°C shaking with Acetyl-Histone H3K9 antibody (#9649, Cell signaling, 1:50). The day after the immunocomplex were incubated at 4°C rotating with protein A beads (Ge 17-0780-01) for 1.5 h. After incubation, beads were washed thoroughly and then centrifuged. The chromatin was eluted from the beads, and cross-links were removed by incubation at 56°C for 12 hours. DNA was then purified using the DNeasy Blood & Tissue Kit (Cat. No. 69504, Qiagen) according to the manufacturer's instructions
ChIP and input DNA (50 ng) were used for indexed library preparation using NEBNext Ultra II DNA Library Prep kit and subjected to 75 bp single-end sequencing on the Illumina NextSeq500.

value: BM-derived MDSC


title: PVN_HT+EA1 [miRNA]


title: PVN_NC3 [miRNA]

value: Normal control


title: Steady state Mac-1 negative rep #1


title: PFC-MYT1L-KO-2


title: PFC-IgG-WT-3


title: Testis, Ythdc2 cKO, P14, rep 1

description:
DE_normalized_counts_P14.txt
Ythdc2_cKO_P14_1.220304_NB551514_0749_AHTGG7BGXK.end1

value: testes

value: Ythdc2 conditional knockout


title: HCT15shNSUN2-2.Input


title: HCT15shNSUN2-1.Input


title: PVN_NC1 [miRNA]


title: IP_CM

value: Acetyl-Histone H3K9 antibody (#9649, Cell signaling, 1:50).


title: HCT15NC-2.IP


title: CEA_SEA3 [miRNA]

value: Hepatectomy + sham electroacupuncture


title: Testis, control, P16, rep 1

description:
DE_normalized_counts_P16.txt
WT_P16_1.220304_NB551514_0749_AHTGG7BGXK.end1

value: control


title: HCT15NC-1.IP

value: WT


title: input_CM_plus_Romidepsin

value: Romidepsin


title: IP_CM_plus_Romidepsin


title: PFC-IgG-WT-2

value: Adult PFC


title: PFC-MYT1L-WT-4


title: PFC-MYT1L-WT-3


title: CEA_SEA1 [miRNA]


title: HCT15NC-2.Input


title: CEA_SEA2 [miRNA]


title: HCT15NC-1.Input


title: RNA-Seq PHD-fl/fl_CD4cre Acetate Rep4

city: Esch-sur-Alzette

last: Longworth

state: Luxembourg

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: LIH

data_processing:
RNA-seq transcript alignment was performed with Salmon (Patro et al., 2017) against the Mouse Transcriptome from Genecode v.M30
Tximeta (Love et al., 2020) was used to assign transcripts to genes
differential analysis with DESeq2 (Love, Huber and Anders, 2014)
Assembly: Genecode v.M30
Supplementary files format and content: CSV reporting normalized abundance measurements from DESeq

source_name: TH17 cells

growth_protocol: Naïve CD4+ T cells were isolated from PDHfl/fl and PDHfl/fl CD4 Cre+ mouse spleen and lymph nodes by magnetic bead sorting  using the Naïve CD4+ T cell isolation kit according to the manufacturer’s protocol. Sorting was performed using an autoMACS® pro-Separator . Sorted cells were seeded at 2x10e6 cells/mL in complete medium consisting of IMDM supplemented with 10% FBS , 55μM 2-mercaptoethanol and 1% penicillin/streptomycin , and incubated for 3 days in the presence of the appropriate Th subset-specific antibody and cytokine mix (5 μg/mL anti-CD3 (plate-bound), 1 μg/mL anti-CD28, 30 ng/mL IL-6, 5 μg/mL anti-IFNγ, 2 ng/mL TGFβ)

extract_protocol:
RNA was extracted using a NucleoSpin RNA Kit according to the manufacturer’s protocol.
The TruSeq Stranded mRNA Library Prep kit was used for library preparation.

treatment_protocol: For acetate-treated cells, in vitro Th cell differentiation was performed in the presence of 10 mM sodium acetate diluted in culture medium

value: TH17 cells

value: PDH knockout

value: 10 mM Acetate


title: PFC-MYT1L-WT-2

value: MYT1L (Millipore, ABE2915)


title: PVN_NC2 [miRNA]

value: Brain


title: RNA-Seq PHD-fl/fl Acetate Rep4


title: RNA-Seq PHD-fl/fl_CD4cre Untreated Rep4

value: Untretated


title: E14-WT-H3K4me3-2

source_name: E14 CTX

value: E14 CTX

value: H3K4me3 (Active Motif, 39159)


title: CEA_HT2 [miRNA]

value: Hepatectomy


title: s856

city: New York

first: Aya

last: Osman

address: 109 east 102nd street, apartment 3c

department: Neurology

institute: Icahn School of Medicine Mount Sinai

data_processing:
raw sequened data (.bcl filed) generated by illumina were converted to fastq files. One mismatch was allowed for index sequence identification.
raw RNA seq reads for each sample were aligned and read counts generated using BioJupies software package.
non specific filtering required more than 1 million counts per milliom in at least 3 samples
filtered raw counts were then subjected to voom normalisation
voom normalized data were inspected for outlying samples using unsupervised clustering of samples
Assembly: BioJupies
Supplementary files format and content: tab-delimited text files include VOOM normalized values for each Sample

source_name: mPFC

extract_protocol:
Total RNA was isolated from mPFC punches using Rneasy mini kits from Qiagen (74106)
The RNA seq library was generated using NEBNext Ultra II Directional RNAlibrary Prep Kit for Illumina (New England BioLABS, iPSWICH, MS, USA)
Sequencing library was validated on the Aligent TapeStation and quantified by using Qubit 2.0 Flurometer as well as quantitative PCR. Libraries were subsequently multiplexed and sequenced on Illumina HiSeq 4000 using a 2x150bp paired-end configuration.

value: mPFC

value: Bulk tissue

value: KO

tag: Sex

value: f

tag: rin value


title: CEA_HT3 [miRNA]


title: CEA_HT1 [miRNA]


title: s850


title: E14-WT-H3K4me3-1


title: s441


title: RNA-Seq PHD-fl/fl Untreated Rep4


title: CEA_HT+EA3 [miRNA]

value: Hepatectomy + electroacupuncture


title: E14-WT-H3K4me1-2

value: H3K4me1 (Active Motif, 61633)


title: CEA_HT+EA2 [miRNA]


title: RNA-Seq PHD-fl/fl_CD4cre Acetate Rep3


title: s1143

value: WT


title: RNA-Seq PHD-fl/fl Acetate Rep3


title: E14-WT-H3K27me3-2

value: H3K27me3 (Active Motif, 29155)


title: s1185

value: m


title: CEA_HT+EA1 [miRNA]


title: E14-WT-H3K4me1-1


title: E14-WT-H3K27me3-1


title: RNA-Seq PHD-fl/fl Untreated Rep3

value: TH17 cells


title: E14-WT-H3K27ac-2

value: H3K27ac (Active Motif, 29133)


title: s381


title: RNA-Seq PHD-fl/fl_CD4cre Untreated Rep3

value: PDH knockout


title: CEA_NC2 [miRNA]

value: Brain

value: Normal control


title: RNA-Seq PHD-fl/fl_CD4cre Acetate Rep2

value: 10 mM Acetate


title: E14-WT-H3K27ac-1

value: E14 CTX


title: E14-KO-H3K4me3-2

value: H3K4me3 (Active Motif, 39159)


title: PVN_SEA3 [circRNA]

extract_protocol:
Total RNA was extracted from tissue samples of the PVN and CEA, and the preparation of the cDNA library and the sequencing were performed by Novo Gene Biotech Co. Ltd. (Beijing, China).
A strand-specific library strategy was used to construct the mRNA and circRNA libraries. Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA).

value: Hepatectomy + sham electroacupuncture


title: s382

value: mPFC

value: Bulk tissue


title: CEA_NC1 [miRNA]


title: RNA-Seq PHD-fl/fl_CD4cre Untreated Rep2

value: Untretated


title: s1094

value: KO

value: abx


title: PVN_SEA2 [circRNA]


title: E14-KO-H3K4me3-1


title: E14-KO-H3K4me1-2

value: H3K4me1 (Active Motif, 61633)


title: RNA-Seq PHD-fl/fl Untreated Rep2

value: WT


title: s844

value: m


title: PVN_SEA1 [circRNA]


title: CEA_NC3 [miRNA]


title: RNA-Seq PHD-fl/fl_CD4cre Acetate Rep1

value: TH17 cells


title: RNA-Seq PHD-fl/fl Acetate Rep1


title: PVN_HT3 [circRNA]

value: Hepatectomy


title: E14-KO-H3K4me1-1


title: E14-KO-H3K27me3-2

value: H3K27me3 (Active Motif, 29155)


title: s1052

value: f


title: s1166


title: PVN_HT2 [circRNA]

value: Brain


title: s324


title: s358


title: RNA-Seq PHD-fl/fl Untreated Rep1


title: s1199


title: PVN_HT1 [circRNA]


title: RNA-Seq PHD-fl/fl Acetate Rep2

value: 10 mM Acetate


title: s395


title: E14-KO-H3K27ac-2

value: E14 CTX

value: H3K27ac (Active Motif, 29133)


title: s1203

value: acetate


title: RNA-Seq PHD-fl/fl_CD4cre  Rep3

value: PDH knockout


title: E14-KO-H3K27ac-1


title: RNA-Seq PHD-fl/fl  Rep3


title: PVN_HT+EA2 [circRNA]

value: Hepatectomy + electroacupuncture


title: s1084

value: mPFC

value: Bulk tissue


title: PVN_HT+EA1 [circRNA]


title: RNA-Seq PHD-fl/fl_CD4cre  Rep2


title: E14-IgG-KO-3

value: Rb IgG (Jackson Immuno 011-000-002)


title: RNA-Seq PHD-fl/fl_CD4cre Untreated Rep1

value: Untretated


title: E14-IgG-KO-2


title: PVN_NC3 [circRNA]

value: Normal control


title: RNA-Seq PHD-fl/fl  Rep2

value: WT


title: RNA-Seq PHD-fl/fl_CD4cre  Rep1

value: TH17 cells


title: E14-MYT1L-KO-3

value: MYT1L (Millipore, ABE2915)


title: PVN_NC2 [circRNA]


title: E14-IgG-KO-1


title: PVN_NC1 [circRNA]


title: s1074

value: KO

value: m


title: s339


title: E14-KO-H3K27me3-1

value: H3K27me3 (Active Motif, 29155)


title: s1190

value: f


title: s1139


title: RNA-Seq PHD-fl/fl  Rep1