title: CENPA_WT_IP_rep1

city: Beijing

first: Jun

last: Liu

address: Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6), and ribosomal RNAs were removed by Bowtie2 (v2.4.2)
The remaining reads were aligned to the human genome (hg38) using HISAT2 (v2.1.0) with ‘--rna-strandness RF’ parameters. Strand-specific reads were separated using samtools view (v1.9) with flags 99, 147, 83, and 163.
Mapped reads were converted into bigwig format using deeptools (v3.5.0) bamCoverage with parameters ‘--binSize 20 --normalizeUsing RPKM’.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Protein A/G magnetic beads were washed twice with Buffer B (50 mM HEPES, pH 7.5, 10% (V/V) glycerol, 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP40, 0.5 mM DTT, Halt protease, and phosphatase inhibitors) and resuspended in 200 µL Buffer B. Half of the beads were used for immunoprecipitation (IP) by adding the appropriate antibody and rotating at 4°C for 2 h; the other half were used for preclearance of the cell lysate by rotating at 4°C for 30 min. The supernatant was transferred to a fresh tube after magnetic separation of the beads. The antibody-coupled beads were washed three times with IP wash buffer (50 mM HEPES-KOH, pH 7.5, 300 mM KCl, 0.05% (v/v) NP40, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail) and added to the cleared cell lysate. The mixture was rotated overnight at 4°C, and the supernatant was then resuspended in 500 µL TRIzol™ reagent (Invitrogen) and the RNA was extracted. Notably, all consumables and buffers used were guaranteed to be RNA enzyme-free and were supplemented with RNA enzyme inhibitors.
For RIP-seq of non-Rib RNA from total RNA, the library was prepared using the SMARTer® Stranded Total RNA-seq Kit v2 (Takara) following the manufacturer’s instructions.

value: melanoma

value: Control


title: CENPA_WT_Input_rep2

status: Public on Sep 24 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: WT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 1

city: South San Francisco

first: J

middle: Graham

last: Ruby

state: California

address: 1170 Veterans Blvd

country: USA

institute: Calico Life Sciences

description:
RNA-seq
1

data_processing:
FASTQ files were aligned to the human genome (hg38) and sorted by genomic location using STAR (v2.5.3, https://github.com/alexdobin/STAR). Sorted BAM files were counted and mapped to each gene using HTSeq-Count (v.0.11.3, https://github.com/simon-anders/htseq). Differentially expressed genes (DEGs) were identified using DESeq2 (v.1.44.0, https://github.com/thelovelab/DESeq2) in R (v.4.2.2) with a cutoff of P-adjusted < 0.05. Wald test was used to calculate fold change and P values using the model: ~condition, where condition is a variable capturing time point, genotype, and substrate stiffness.
Assembly: hg38
Supplementary files format and content: Raw counts file, each column in a sample

source_name: WI-38 cell line

extract_protocol:
Cells were lysed directly on cell culture plates in Buffer RLT Plus (Qiagen). The lysate was homogenized using Qiashredder columns (Qiagen) and stored at -80°C. Once all samples were collected, RNA was isolated using a RNeasy mini kit (Qiagen).
Quality and concentration of RNA were determined using a 2100 Bioanalyzer Instrument (Agilent). cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina rRNA depletion workflow (New England Biolabs). Samples were sequenced on a NovaSeq 6000 (Illumina).

value: WI-38 cell line

tag: genotype

value: Wild-type


title: CENPA_resWTsh_IP_rep2

value: CENPA knockdown followed by overexpressing wild-type CENPA


title: CENPA_resWTsh_IP_rep1


title: CENPA_resWTsh_Input_rep2


title: CENPA_resWTsh_Input_rep1


title: CENPA_resmutsh_IP_rep2

value: CENPA knockdown followed by overexpressing mutant CENPA


title: CENPA_WT_Input_rep1


title: CENPA_resmutsh_Input_rep1


title: FTOwt_sg_CENPA_IP_rep2

library_source: genomic

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6).
Then trimmed reads were aligned to the human genome (hg38) using Bowtie2 (v2.4.2). PCR duplicates were removed using picard (v2.26.0) MarkDuplicates.
Mapped reads were converted into bigwig format using deeptools (v3.5.0) bamCoverage with parameters ‘--binSize 5 --normalizeUsing RPKM’ or deeptools (v3.5.0) bamCompare with parameters ‘--operation log2 --binSize 5 --normalizeUsing RPKM’.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 15 min at RT, and 0.125 M glycine was added to stop the reaction. Cells were snap-frozen in liquid nitrogen and stored at -80℃. Next, 5 × 106 cells were resuspended in 1 mL ice-cold lysis buffer (50 mM HEPES, pH 7.9, 5 mM MgCl2, 0.2% Triton™ X-100, 20% glycerol, 300 mM NaCl, proteinase inhibitor) and incubated on ice for 10 min. Cells were pelleted by centrifugation at 500 g for 5 min at 4℃, resuspended in 900 µL SDS lysis buffer (50 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% Triton™ X-100, 0.1% sodium deoxycholate, 0.1% SDS, proteinase inhibitor), and incubated on ice for 30 min. The chromatin was sheared with 25 cycles (30 s on/60 s off) of a Bioruptor (Diagenode). Protein A beads were washed twice with 60 µL SDS lysis buffer, and half of the beads were saved for preclearance. The remaining beads were resuspended in 200 µL SDS lysis buffer, to which 7.5 µg antibody was added, and the samples were rotated at 4℃ for at least 2 h. The cell lysate was centrifuged at 15,000 rpm for 10 min at 4℃ and then cleared using 30 µL protein A beads for 1 h at 4℃. The flowthrough was saved, and the precleared lysate was mixed with antibody-coated beads and rotated at 4℃ overnight. The next day, the flowthrough was saved, and the beads were washed twice with 1 mL SDS lysis buffer, twice with 1 mL high-salt wash buffer (50 mM HEPES, pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton™ X-100, 0.1% sodium deoxycholate, 0.1% SDS), twice with 1 mL LiCl buffer (10 mM Tris-HCl, pH 8.0, 250 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.2% Triton™ X-100). During each wash, the sample was rotated for 5 min at 4℃. The beads were then resuspended in 240 µL elution buffer (100 mM NaHCO3, 1% SDS) and shaken at 30℃ for 1 h. The supernatant was collected, 14.4 µL 5 M NaCl was added, and the sample was shaken at 65℃ for 4 h. After the addition of 4 µL RNase A, the sample was shaken at 37℃ for 15 min. Next, 4 µL proteinase K was added, and the sample was shaken at 65℃ for a further 2 h. DNA was then purified by DCC with 5× binding buffer.
Library preparation was performed by using  VAHTS Universal Pro DNA Library Prep Kit for Illumina.

value: dCas13b-wt FTO:cenRNA


title: FTOwt_sg_CENPA_IP_rep1


title: CENPA_resmutsh_IP_rep1


title: FTOwt_ctrl_CENPA_IP_rep2

value: dCas13b-wt FTO:control


title: FTOwt_sg_CENPA_Input_rep1


title: FTOwt_ctrl_CENPA_IP_rep1


title: FTOwt_sg_CENPA_Input_rep2


title: hTERT, 2kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
175

value: hTERT


title: FTOwt_ctrl_CENPA_Input_rep1


title: FTOwt_ctrl_CENPA_Input_rep2


title: FTOmut_sg_CENPA_Input_rep2

value: dCas13b-mu FTO:cenRNA


title: FTOmut_sg_CENPA_IP_rep2


title: CENPA_WT_IP_rep2


title: FTOmut_sg_CENPA_Input_rep1


title: FTOmut_sg_CENPA_IP_rep1


title: FTOwt_sg_H3.3_IP_rep1


title: FTOwt_ctrl_H3.3_IP_rep2


title: FTOwt_ctrl_H3.3_IP_rep1


title: HEK293T_METTL3_Control_MeRIP_rep1

library_source: other

data_processing:
*library strategy: MeRIP-Seq
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6), and ribosomal RNAs were removed by Bowtie2 (v2.4.2)
The remaining reads were aligned to the human genome (hg38) along with spike-in genomes, including two control RNAs (one with m6A modification and one without) (NEB #E1610S), using HISAT2 (v2.1.0) with ‘--rna-strandness RF’ parameters.
Strand-specific reads were separated using samtools view (v1.9) with flags 99, 147, 83, and 163. Mapped reads were converted to bigwig format for Integrative Genomics Viewer (IGV) generated by deeptools (v3.5.0) bamCoverage with the parameters ‘--normalizeUsing RPKM’.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: other

extract_protocol:
Total caRNA was isolated from cells, and 1 μL 1:1000-diluted m6A and non-m6A spike-in from the EpiMark® N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg purified non-Rib caRNA, which was then subjected to fragmentation according to previously published protocols. m6A-IP was performed using the EpiMark N6-Methyladenosine Enrichment Kit according to the manufacturer’s protocol.
RNA library construction was carried out using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocol.

value: human embryonic kidney cells


title: HEK293T_METTL3_Control_MeRIP_rep2


title: FTOmut_sg_H3.3_IP_rep1


title: CENPA_resmutsh_Input_rep2


title: METTL3_KD_MeRIP-2_rep2

value: METTL3 knockdown


title: METTL3_Control-2_MeRIP_rep2


title: FTOmut_sg_H3.3_IP_rep2


title: HEK293T_METTL3_Control_Input_rep1


title: METTL3_KD-2_Input_rep2


title: METTL3_KD_MeRIP-2_rep1


title: METTL3_Control-2_Input_rep2


title: HEK293T_METTL3_Control_Input_rep2


title: FTOwt_sg_IP_rep1


title: METTL3_Control-2_MeRIP_rep1


title: FTOwt_sg_Input_rep1


title: METTL3_Control-2_Input_rep1


title: FTOwt_sg_IP_rep2


title: FTOwt_sg_Input_rep2


title: FTOwt_ctrl_IP_rep1


title: FTOmut_sg_IP_rep1


title: FTOmut_sg_IP_rep2


title: FTOmut_sg_Input_rep2


title: PPPE-257 pre

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The Chromium protocol was followed, including GEM generation and barcoding, followed by GEM-RT cleanup and cDNA amplification, gene expression library construction, and lastly, cell multiplexing library construction and sequencing.
Assembly: GRCh38 2020-A
Supplementary files format and content: tab-separated values files and hierarchical data format version 5

source_name: Blood

extract_protocol:
Blood was diluted with PBS-10%FBS in a 1:1 ratio and added to Sepmate-50 tubes (Stemcell) containing 15mL Lymphoprep density gradient medium (StemCell). Tubes were centrifuged at 1200g for 10 minutes. PBMCs were collected and diluted with PBS for a final volume of 45mL and centrifuged at 300g for 10 mintues. Supernantants were removed and the pellet was resuspended with 10mL of PBS. A 10µl aliquot was taken and combined with 10µl trypan blue solution (Bio-Rad) for cell count on a Bright-Line hemacytometer (Hausser Scientific). The resuspended pellet was centrifuged at 400g for 10 minutes and the supernatant was discarded. Pellets were resuspended with FBS-10%DMSO at a final concentration of 2M cells/mL and aliquoted to be frozen down slowly at -80°C for 24-48 hours and then transferred to liquid nitrogen for long term storage.
Library was constructed according to manufacturer instructions (10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (dual index) with feature barcode technology) for cell multiplexing at the McGill Genome Cente

tag: tissue

value: Blood

tag: condition

value: control

value: PBMC


title: 267607-96 h Blastoids

city: Vienna

first: HEIDAR

last: HEIDARI KHOEI

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

data_processing:
scRNA-seq reads were processed with cellranger v7.2.0 with default settings and using the prebuild 10X GRCh38 reference refdata-gex-GRCh38-2020-A
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: naive hPSCs

extract_protocol:
The structures (human blastoids, rapalink-1 treated blastoids and potimplantation cultures dissociated into single cells. Live cells were enriched using EasySep™ Dead Cell Removal (Annexin V) Kit removal kit (Stem cell technologies). Cells counting was performed using nucleocounter NC-250 (ChemoMetec).
Desired number of cells were used for generation of Gel Beads in Emulsions (GEMs) using 10X Genomics chromium X at VBCF-NGS, Vienna. For 96 HR samples, 1000 cells were targeted using Chromium Next GEM Single Cell 3ʹ LT Kit v3.1 (PN-1000325) on chip L (PN-1000321) and for post implantation samples 10000 cells were targeted using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) on chip G (PN-1000127) according to manufacture’s protocols (CG000399 and CG000315, respectively (10X Genomics, Pleasanton, CA)). cDNA were amplified for 11 cycles. Libraries were purified using Ampure XP bead purification protocol and were analyzed using fragment analyzer and qPCR for distributtion and quantity. Libraries were pooled together and sequenced on NovaSeq instrument series flowcell (Illumina, San Diego, CA) using paired end readmode for a total of 300 cycles.

value: naive hPSCs

value: Blastoid

value: no


title: PPPE-256 pre

description: 10X Genomics


title: METTL3_KD-2_Input_rep1

value: melanoma


title: PPPE-254 pre

description: 10X Genomics


title: 267608-Blastoids treated with Rapalink-1 for 3 days

value: Rapalink-1 treated blastoid


title: 269045-Rapalink-1 treated blastoids cultured in postimplantation (4 days)


title: 269044-Blastoids cultured in postimplantation (4 days)

value: Postimplantation culture


title: FTOwt_sg_H3.3_IP_rep2


title: PPPE-247 pre

description: 10X Genomics

value: late-onset preeclampsia


title: PPPE-251 pre

description: 10X Genomics


title: PPPE-248 pre

description: 10X Genomics


title: PPPE-243 pre

description: 10X Genomics


title: PPPE-253 pre

description: 10X Genomics


title: FTOwt_ctrl_IP_rep2


title: PPPE-245 pre

description: 10X Genomics

value: early-onset preeclampsia


title: PPPE-246 pre

description: 10X Genomics


title: PPPE-242 pre

description: 10X Genomics


title: FTOwt_ctrl_Input_rep1


title: FTOwt_ctrl_Input_rep2


title: PPPE-244 pre

description: 10X Genomics


title: FTOmut_sg_Input_rep1


title: PPPE-241 pre

description: 10X Genomics


title: PPPE-235 pre

description: 10X Genomics


title: PPPE-236 pre

description: 10X Genomics


title: PPPE-252 pre

description: 10X Genomics


title: PPPE-208 pre

description: 10X Genomics


title: PPPE-226 pre

description: 10X Genomics


title: PPPE-238 pre

description: 10X Genomics


title: PPPE-237 pre

description: 10X Genomics


title: PPPE-232 pre

description: 10X Genomics


title: PPPE-231 pre

description: 10X Genomics


title: PPPE-250 pre

description: 10X Genomics


title: PPPE-234 pre

description: 10X Genomics


title: PPPE-249 pre

description: 10X Genomics


title: PPPE-206 pre

description: 10X Genomics


title: PPPE-207 pre

description: 10X Genomics


title: PPPE-239 pre

description: 10X Genomics


title: PPPE-198 pre

description: 10X Genomics


title: PPPE-230 pre

description: 10X Genomics


title: PPPE-196 pre

description: 10X Genomics


title: PPPE-203 pre

description: 10X Genomics


title: PPPE-215 pre

description: 10X Genomics


title: PPPE.184 pre

description: 10X Genomics


title: PPPE-218 pre

description: 10X Genomics


title: PPPE.183 pre

description: 10X Genomics


title: PPPE-194 pre

description: 10X Genomics


title: PPPE-205 pre

description: 10X Genomics


title: PPPE-240 pre

description: 10X Genomics


title: PPPE-197 pre

description: 10X Genomics


title: PPPE.182 pre

description: 10X Genomics


title: PPPE-213 pre

description: 10X Genomics


title: PPPE-233 pre

description: 10X Genomics


title: PPPE.193 pre

description: 10X Genomics


title: PPPE-195 pre

description: 10X Genomics


title: PPPE.177 pre

description: 10X Genomics


title: PPPE-199 pre

description: 10X Genomics


title: CD4 cells from IBD-3 and IBD-4 at 0 and 6wks and from healthy donor HC-4

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Sequencing libraries for gene expression and BCR/TCR was jointly processed using cellranger multi (v5.0.0) and the GRCh38 genome annotation
Pooled scRNAseq data for FACS-sorted CD3+ CD4+ CD45RA- memory T cells from multiple donors were demultiplexed using Seurat's HTOdemux function combined with SNP-based demultiplexing using cellSNP-lite over common variants from the 1000 Genomes Project and vireo and otherwise processed similarly
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression), contig tables (VDJ), SNP-based donor assignment (donor_ids)

molecule: polyA RNA

source_name: blood

extract_protocol:
To isolate peripheral blood mononuclear cells (PBMCs), peripheral blood was diluted 1:1 in 1x PBS and subjected to density gradient centrifugation using Pancoll human (PAN-Biotech, P06-1391500) at 800g for 20 minutes at room temperature. The resulting PBMC fraction was then resuspended in a freezing medium composed of 90% FCS and 10% DMSO. Subsequently, the PBMCs were frozen using a Cryo-freezing container (Nalgene) and stored in liquid nitrogen for long-term preservation.  Thawed PBMCs underwent sorting using the SONY MA900 sorter, employing a 100-micron nozzle. CD45+ cells were sorted based on CD45 expression while eliminating DAPI-positive cells. The sorted CD45+ cells were stained with the TotalSeq™ Antibody mix following the manufacturer's protocol (Biolegend). Memory CD4 T cells, extracted from the same donors as those utilized for total PBMCs scRNAseq, were sorted on the BD FACSAria II with a 70-micron nozzle. The sorting criteria included CD3, CD4, and CD45RA expression, with the exclusion of non-viable cells through DAPI staining. To distinguish individual donors, memory CD4 T cells were labeled with hashtags post-sorting.
According to the manufacturer's instructions, single-cell RNA-seq libraries were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 by 10x Genomics (CG000330 Rev D). Briefly, a droplet emulsion was generated in a microfluidic chip, followed by barcoded cDNA and surface tag generation inside the droplets. Purified and amplified cDNA and surface tags were then subjected to NGS library preparation. The manufacturer's instructions generated T and B cell receptor sequencing libraries from amplified cDNA. Sequencing was performed on a NovaSeq 6000 instrument (Illumina). The read depth aimed for 30K reads per cell for GEX and ~8K for surface and TCR BCR libraries.

value: blood

tag: donor

tag: timepoint


title: CD4 cells from IBD-10 and IBD-9 at 0 and 6wks and from healthy donor HC-1


title: CD4 cells from IBD-2 and IBD-6 at 0 and 6wks and from healthy donor HC-4


title: CD4 cells from IBD7 and IBD-8 at 0 and 6wks and from healthy donor HC-2


title: PBMCs from IBD-8 at 6wk


title: PBMCs from IBD-7 at 6wk


title: PPPE.185 pre

description: 10X Genomics


title: PBMCs from IBD-6 at 6wk


title: PBMCs from IBD-6 at 0wk


title: PBMCs from IBD-5 at 6wk


title: PBMCs from IBD-7 at 0wk


title: PBMCs from IBD-5at 0wk


title: PBMCs from IBD-3 at 6wk


title: PBMCs from IBD-4 at 0wk


title: PBMCs from IBD-4 at 6wk


title: PBMCs from IBD-10 at 6wk


title: PBMCs from IBD-3 at 0wk


title: PBMCs from IBD-10 at 0wk


title: PBMCs from IBD-9 at 6wk


title: PBMCs from IBD-9 at 0wk


title: PBMCs from IBD-1 at 6wk


title: PBMCs from IBD-1 at 0wk


title: PBMCs from healthy donor HC-4


title: PBMCs from healthy donor HC-3


title: PBMCs from healthy donor HC-1


title: PBMCs from IBD-8 at 0wk


title: PBMCs from healthy donor HC-5


title: siRNA_aCM_2

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing:
Sequenced reads were aligned to the human genome (GRCh38) using STAR (2.7.9a)69. Differential expression analysis was performed with DESeq2 (1.30.1)66
Assembly: hg38
Supplementary files format and content: Processed data table represents raw reads output directly from STAR for each indicated library.

source_name: hESC

growth_protocol: Human embryonic stem cells (hESCs, WiCell) were cultured in feeder-free culture on Geltrex (Invitrogen) coated flasks in a modified. Essential 8 medium containing DMEM/F12 with HEPES (Thermo Fisher, 1133057), 540 mg/L sodium bicarbonate (Thermo Fisher, 25080094), 1% MEM Non-Essential Amino Acids (Invitrogen 11140) and 1x Pen-Strep (ThermoFisher 15140122), 8.5 mM NaCl (Sigma, S5150), 20 μg/mL insulin (Thermo Fisher, 12585014), 200 μM ascorbic acid (Sigma, A8960), 10 μg/mL holo-transferrin (Sigma, T0665), 1 μg/mL heparin (Sigma, H3149), 14 ng/mL sodium selenite (Sigma, S9133), 20 ng/mL bFGF (Thermo Fisher, 13256027), 10 ng/mL activin A (R&D Systems, 338-AC-01M), and 10 ng/mL Neuregulin-beta 1 (R&D Systems, 396-HB-050). Cells were incubated at 5% O2 and 10% CO2 at 37°C. For atrial cardiomyocyte (ACM) differentiation, dissociated single cell PSC suspension was incubated overnight with continuous shaking at 98 RPM to form spheroid clusters (day -1). Spheroids were collected (day 0) and resuspended in Basal Differentiation Media (BDM) containing DMEM/F12 with HEPES, 540 mg/L sodium bicarbonate, 1% non-essential amino acids (Thermo Fisher, 11140), 10 ug/mL holo-transferrin, 200 uM ascorbic acid, 63 ng/mL progesterone (Sigma, P8783), and 14 ng/mL sodium selenite, supplemented with 50 ng/mL activin A, 10 ng/mL BMP4 (R&D Systems, 314-BP-050), 20 ng/mL bFGF (Shenandoah, 100-28-500UG), with 2 μM CHIR-99021 (Selleckchem, S2924). Spheroids were replenished with fresh BDM to remove CHIR-99021 on day 1 and treated with 10 uM XAV-939 (APExBio, A1877), 1 uM IWR1-Endo (APExBio, B2306) and 1 uM IWP-2 (APExBio, A3512) on day 2. To promote atrial induction, 1 nM TTNPB (Tocris, 0761) was applied along with 100 nM retinoic acid, 1 uM SAG (Selleckchem, S7779) and 10 uM XAV-939 on day 3. TTNPB and RA were removed on days 4-5. On day 6 and onward, spheroids were maintained in BDM supplemented with 4 μg/ml insulin. On day 17, spheroids were collected, washed and dissociated with 1 mg/ml collagenase II (Thermo Fisher, 117010015) for one hour at 37 °C. Dissociated cardiomyocytes were seeded in fibronectin-coated plates and cultured in Lactate Media (DMEM without glucose (Thermo Fisher, 11966025), 540 mg/L sodium bicarbonate, 4 mM lactate (Sigma L6402), 200 uM ascorbic acid, and 14 ng/mL sodium selenite) for 4 days to remove non-cardiomyocytes. Cardiomyocytes were then kept in Cardiomyocyte Maintenance Media (DMEM/F12, 10% FBS and 1% Pen/Strep) until day 30.

extract_protocol:
For the overexpression of ATRNL1 we packaged the short isoform (ENST00000609571.5) into lentiviral particles via transfection of HEK293T cells according to the manufacturers protocol (Dharmacon lentiviral packaging kit, Horizon Discovery, TLP5913). The overexpression lentiviral vector was obtained from GeneCopoeia (EX-E1118-Lv242). All hESC-aCMs were transduced with lentiviral particles and selected for overexpression with puromycin.  Total RNA was extracted from atrial iPS-CMs using the Direct-zol RNA Miniprep kit (Zymo Research, R2051). RNA-seq libraries were generated with a ribosomal depletion protocol (KAPA RNA HyperPrep with RiboErase, KK8560). All RNA-seq libraries were sequenced on an Illumina NovaSeq.
Total RNA-seq, via ribosomal RNA depletion (KAPA Hyperprep RNA-seq kit with RiboErase)

value: hESC

value: Induced Atrial Cardiomyocyte

value: wt

value: siRNA scramble control


title: PBMCs from healthy donor HC-2


title: lenti_short_10

value: ATRNL1 overexpression Lentivirus


title: ATRNL1_sirna_62


title: lenti_c_78

value: Lentivirus Control


title: siRNA_aCM_3


title: ATRNL1_sirna_41


title: siRNA_aCM_1


title: ATRNL1_sirna_31


title: 1762_1n

description:
AF_snRNA_Processed_Expression_Matrix_barcodes_V1.tsv
AF_snRNA_Processed_Expression_Matrix_genes_final.tsv
AF_snRNA_UMAP_V1.txt
AF_snRNA_Matrix_V1.mtx
AF_snRNA_MetaData.txt

data_processing:
The processing pipeline implemented here followed similar steps than previously described10. The raw files of 36 samples were processed on the TERRA platform (https://app.terra.bio/). The raw base call files (BCLs) were demultiplexed into FASTQ files using the mkfastq workflow from the 10x Genomics Cell Ranger v 4.0.0 tool. Homopolymer repeats (A30, C30, T30 and G30, settings: max_error_rate=0.1; min_overlap=20) and the template-switch oligonucleotide and its reverse complement (AAGCAGTGGTATCAACGCAGAGTACATGGG and CCCATGTACTCTGCGTTGATACCACTGCTT, settings: max_error_rate=0.07 and min_overlap=10) were trimmed using cutadapt v1.18 in Python v3.7.9. Alignment of trimmed reads was performed with Cell Ranger count workflow, to the GRCh38 pre-mRNA human reference (v2020-A), using the parameter expect-cells=5000 and otherwise default values.
Assembly: hg38
Supplementary files format and content: Processed data files output from Scanpy as gene expression matrix (.mtx) with cell barcodes and features (genes) output separately. Further, metadata and published UMAP embedding are attached.

source_name: Cardiac Left Atria

extract_protocol:
In brief, LA tissue was sectioned into 100 um thick slices using a cryostat. Nuclei were liberated by douncing in NIM2 buffer (250 mM sucrose, 25 mM KCl, 0.05% IGEPAL-630, 3 mM MgCl2, 1 μM DTT, 10 mM Tris pH 8.0), and debris was pelleted at 40 xg for 2 mins at 4 degrees C. Nuclei were filtered through 40 and 10 um filters and then washed with PBS wash buffer (0.01% BSA, 5 mM MgCl2, PBS). Nuclei were pelleted by centrifugation at 550 x g for 5 min at 4 degrees C, washed with 6 mL of PBS wash buffer and centrifuged at 550 x g for 5 min at 4 degrees C. Nuclei were resuspended in Nuclei Suspension buffer (Nuclear wash buffer + 0.4 U μl−1 murine RNAse inhibitor) and then counted and 6000 nuclei were loaded into the 10x genomics microfluidic device (10x genomics Single cell 3′ solution v 3). Libraries were constructed using manufacturer's protocol with a few modifications. First, to promote nuclei lysis, GEMS were incubated at 4 °C for 15 min after emulsion generation. Second, the reverse transcription protocol was lengthened to be 42 °C for 20 min then 53 °C for 120 min. Libraries were QCed and quantified using BioAnalyzer and qPCR. Libraries were pooled and sequenced on Illumina Novaseq S1 flow cells, at an average of 16 samples per flow cell.
10x genomics Single cell 3′ solution version 3

value: Cardiac Left Atria


title: lenti_short_910


title: PBMCs from IBD-2 at 6wk


title: PBMCs from IBD-2 at 0wk


title: lenti_short_9


title: lenti_c_8


title: 1623_1n


title: lenti_c_7


title: 1610_1n


title: ATRNL1_sirna_562


title: 1603_1n


title: 1582_1n


title: 1588_1n


title: ATRNL1_sirna_341


title: ATRNL1_sirna_52


title: 1758_1n


title: 1741_1n


title: 1698_3n


title: 1626_1n


title: 1593_1n


title: 1490_3n


title: 1591_1n


title: 1440_1n


title: 1789_1n


title: 1558_1n


title: 1570_1n


title: 1561_1n


title: 1365_1n


title: 1543_1n


title: Non-patterned astrocyte, unsorted, rep1

city: Cardiff

first: Zongze

last: Li

country: United Kingdom

description: UNP

data_processing:
FastQC for as first Quality Control step and MultiQC for summarization
Using the Cogent NGS Analysis Pipeline software v 1.5.1 (Takara), FASTQ files containing all indices for each chip were demultiplexed to FASTQ files containing one index per file.
Adaptor sequences were removed using cutadapt 3.2 with the following settings: -m 15 --trim-n --max-n 0.7 -q 20.
Trimmed FASTQ files were aligned to the Homo sapiens GRCh38.106 primary assembly with the BFP reporter gene attached to the end of the genome, using STAR 2.7.9a with the following settings: --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --outReadsUnmapped Fastx --outSAMstrandField intronMotif --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 –alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30.
Gene-level quantification was performed using featureCounts from subread 2.0.0 (Liao et al. 2013) with the following settings: -t exon --primary -R CORE -F GTF -Q 0 -B -g gene_id.
Assembly: Homo sapiens GRCh38.106
Supplementary files format and content: Gene counts are given as mtx format (matrix.mtx)
Supplementary files format and content: Column names (barcodes.tsv) and row names of count matrix (genes.tsv) are given as tsv format
Supplementary files format and content: Meta data are given as xlsx format(metadata.xlsx)

source_name: cell line

extract_protocol:
Cells were dissociated with Accutase with 10 units/mL of papain (Sigma-Aldrich) for 10 minutes at 37°C and resuspended in 0.5% bovine serum albumin (Sigma Aldrich) with 50 units/mL DNase I in DPBS without calcium or magnesium (Gibco) and passed through a cell strainer with 35 µm mesh. Cells were stained with 1 µM SYTO16 (Invitrogen) and 0.08% (v/v) propidium iodide (part of the Invitrogen ReadyProbes™ Cell Viability Imaging Kit, Blue/Red) for 20 minutes on ice and then dispensed into the nano-well plates of the ICELL8® cx Single-Cell System (Takara). Wells containing single viable cells were automatically selected using the ICELL8 cx CellSelect v2.5 Software (Takara) with the green and not red logic. Manual triage was performed to recover additional candidate wells that contain viable single cells.
The cDNA libraries were generated using the SMART-Seq ICELL8 cx Application Kit protocol provided by the manufacturer

value: cell line

value: KOLF2-C1 human iPSC line

value: iPSC differentiated into astrocytes

value: LMX1A Cre AAVS1 BFP


title: 1540_3n


title: 1513_1n


title: 1498_1n


title: BFP+ astrocyte, unsorted, rep4


title: 1696_1n


title: BFP+ astrocyte, unsorted, rep3


title: 1334_3n


title: 1515_1n


title: 1488_2n


title: BFP+ astrocyte, unsorted, rep2


title: BFP+ astrocyte, unsorted, rep1


title: 1465_1n


title: 1377_3n


title: BFP+ astrocyte, sorted, rep2


title: BFP- astrocyte, sorted, rep1

description: SBN


title: METTL3_KD_ChIRP_IP_rep1

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6)
The trimmed reads were aligned to the human genome (hg38) using Bowtie2 (v2.4.2).
PCR duplicates were removed using picard (v2.26.0) (http://broadinstitute.github.io/picard/) MarkDuplicates.
Peak calling was performed by macs2 (v2.2.7.1) and the mapped reads were converted into bigwig format using Deeptools (v3.5.0) bamCompare with parameters ‘--operation log2 --binSize 5 --normalizeUsing RPKM’.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: ChIRP-seq

extract_protocol:
The cells were treated according to a previously published procedure. In brief, 1 × 107 cells were cross-linked with 1% formaldehyde for 15 min at room temperature, 0.125 M glycine was added, and the samples were incubated for 5 min at RT to stop the reaction. The cells were then snap-frozen using liquid nitrogen and stored at -80 °C. For each sample, the pellet was resuspended in 300 μL of nuclear lysis buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS) with the addition of 1.5 μL protease inhibitor and 1.5 μL PMSF. After centrifugation at 13,000 rpm for 30 seconds, the supernatant was removed. The pellet was resuspended in 200 μL of nuclear lysis buffer and the chromatin was sheared through 25 cycles (30s on/60s of) using a Bioruptor (Diagenode). Next, 1/30 volume (10 μL) of each sample was saved, 90 μL DNA reverse crosslinking buffer (20 mM Tris-Cl, 150 mM NaCl, 10 mM EDTA, 0.5% SDS) with 2 μL protease K was added, the samples were incubated overnight at 56 ℃, and DNA was extracted as the input DNA. The remaining sample was mixed with 1/4 volume of 5× rRIP Hybridization buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS, 1.5 M NaCl, 50% formamide). Next, biotinylated probes (5-30 pmol) were added to each sample, and the mixture was subjected to end-to-end rotation at 39 ℃ for 2-4 h. Subsequently, 20-80 μL well-washed streptavidin M280 beads were added to each sample (20 μL of beads for samples with 5 pmol probes; 40 μL of beads for samples with 20 pmol probes), followed by end-to-end rotation at 39 ℃ for 3 h. Following the pull-down, the beads were washed four times with 0.1× SSC washing buffer (0.1× SSC, 1% SDS) at 39 ℃, with each wash lasting 15-30 min. After the final wash, 100 μL freshly prepared 1× RNase H wash buffer (50 mM Tris-HCl, 75 mM NaCl, 5 mM MgCl2, 0.1% Triton X-100) was added, and the mixture was shaken at 37 ℃ for 5 min. The samples were then transferred to a magnetic stand to remove the supernatant. The DNA was eluted with twice the bead volume of RNase H elution solution (NEB, M0297S) containing 0.2 U/μL RNase H, with shaking at 37 ℃ for 30 min. The elution tube was placed on the magnetic stand, and the elute was transferred into a new tube. The beads were resuspended in twice the bead volume of RNase H wash buffer with 1% SDS at RT and briefly vortexed for 5 s, and the supernatant was transferred and combined with the eluate mentioned above. To the elute, 5 M NaCl and 0.5 M EDTA were added to a final concentration of 100 mM NaCl and 10 mM EDTA, along with 1 μL of 20 mg/mL protease K. Reverse crosslinking was conducted at 56 ℃ overnight. The DNA was then purified using a PCR product purification kit (ZymoDNA Clean & Concentrator-500) following the manufacturer’s instruction. Purified DNA samples were prepared for sequencing using the VAHTS Universal Pro DNA Library Prep Kit for Illumina.
Library preparation was performed using the VAHTS Universal Pro DNA Library Prep Kit.

value: melanoma cells

value: METTL3 knockdown


title: 1369_3n


title: METTL3_Control_ChIRP_IP_rep2

value: control


title: 1360_1n


title: METTL3_KD_ChIRP_IP_rep2


title: 1279_3n


title: 1296_1n


title: BFP+ astrocyte, sorted, rep1


title: BFP+ astrocyte, sorted, rep1_repeat


title: Neuron, unsorted, rep1

description: N

value: iPSC differentiated into neurons

value: CRISPR-Cas9 correction of mutation


title: METTL3_KD_H3.3_rep1

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6).
Then trimmed reads were aligned to the human genome (hg38)  using Bowtie2 (v2.4.2). PCR duplicates were removed using picard (v2.26.0) (http://broadinstitute.github.io/picard/) MarkDuplicates.
Peaks were called using macs2 (v2.2.7.1) callpeak and only peaks overlapped in two biological replicates were used for downstream analysis with ‘bedtools intersect -f 0.5 -F 0.5 -e’ (v2.26.0) parameters.
Mapped reads were converted into bigwig format using Deeptools (v3.5.0) bamCoverage with parameters ‘--binSize 5 --normalizeUsing RPKM’ or Deeptools (v3.5.0) bamCompare with parameters ‘--operation log2 --binSize 5 --normalizeUsing RPKM’.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Supplementary files format and content: bigWig

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and then 0.125 M glycine was added to stop the reaction.
Library preparation was performed using VAHTS Universal Pro DNA Library Prep Kit following the manufacturer’s protocols.

tag: chip antibody

value: rabbit anti-Histone H3.3 (AF1813, Beyotime)


title: METTL3_KD_H3.3_rep2


title: BFP- astrocyte, unsorted, rep1

description: UBN


title: Non-patterned astrocyte, sorted, rep1

description: SNP


title: 1357_2n


title: METTL3_KD_InputH_rep1


title: METTL3_Control_ChIRP_IP_rep1


title: METTL3_Control_InputH_rep1

value: Control


title: METTL3_KD_ChIRP_Input_ep2


title: HA-tagged RUNX1-4A Transduced HEL Cell RNA-seq Rep 2

city: New Haven

first: Evrett

middle: Nathanial

last: Thompson

state: CT

address: 333 Cedar Street

department: Cell Biology

institute: Yale School of Medicine

data_processing:
STAR v2.7.7a was used to align reads to the human reference genome hg38. Set --outFilterMismatchNmax 2, kept all other parameters default.
The htseq-count v0.13.5 from the HTSeq package was used to count reads from the alignments generated using STAR. Set parameters -s reverse -m union -r pos, all other parameters kept default.
Read counts for each sample were input directly into DESeq2, which was used to carry out normalization and differential gene analysis using default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw read counts generated by HTSeq per sample.

source_name: HEL

growth_protocol: The cells were grown in RPMI1640 Medium (Gibco) supplemented with 10% FBS, 1% Pen/Strep and 1% L-Glutamine, with 2μg/ml puromycin to select for transduced cells. The cells were incubated at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using the RNAqueous-Micro kit (Invitrogen) per manufacturer's protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was conducted using standard Illumina protocols.

value: HEL


title: METTL3_Control_InputH_rep2


title: METTL3_Control_H3.3_rep2


title: METTL3_Control_ChIRP_Input_rep1


title: METTL3_Control_ChIRP_Input_rep2


title: METTL3_KD_ChIRP_Input_rep1


title: METTL3_KD_InputH_rep2


title: HA-tagged RUNX1-4D Transduced HEL Cell CUT&RUN Rep 2

data_processing:
Sequencing adapters were trimmed from reads using Cutadapt version 3.4 with default parameters for paired-end input.
Trimmed reads were mapped to the human reference genome hg38 using Bowtie2 version 2.4.2. Set -X 500, -N 1, --very-sensitive, and all other parameters kept default.
Aligned reads were filtered for duplicates using MarkDuplicates from Picard Tools version 2.25.6. Set REMOVE_DUPLICATES = true, all other parameters kept default.
Normalized genomic coverage tracks were generated from each sample using bamCoverage from deepTools version 3.5.1. Set --normalizeUsing BPM and --binSize 10, all other parameters kept default.
Peaks were called using MACS2 version 2.2.7.1 using HEL empty vector as the control file. Set -f BAMPE and all other parameters kept default.
Assembly: hg38
Supplementary files format and content: BigWig files for normalized genomic coverage, normalized to 10 bins per million.
Supplementary files format and content: narrowPeak files called against the HEL empty vector control line.
Library strategy: CUT&RUN

extract_protocol:
500,000 cells for each sample were used to perform CUT&RUN. Cells were bound to magnetic Concanavalin A beads and permeabilized with 0.01% digitonin. The cell/bead mixture was incubated with a 1:100 dilution of anti-HA antibody at 4°C overnight. CUTANA pAG-MNase (EpiCypher) was used to cleave DNA fragments flanking the anti-HA bound sites.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645) per manufacturer's protocol. Illumina TrueSeq single indices are added during library preparation for sample multiplexing and each sequencing library was PCR amplified for 12 cycles. Libraries were size selected using magnetic AMPureXP beads. Sequencing was completed using standard Illumina protocols.

tag: antibody


title: HA-tagged RUNX1-4A Transduced HEL Cell CUT&RUN Rep 1


title: HA-tagged RUNX1-4D Transduced HEL Cell CUT&RUN Rep 1


title: METTL3_Control_H3.3_rep1


title: Empty Vector Transduced HEL Cell RNA-seq Rep 2

value: Empty Vector


title: HA-tagged RUNX1-4A Transduced HEL Cell CUT&RUN Rep 2


title: Empty Vector Transduced HEL Cell CUT&RUN Rep 1


title: shMETTL3_CENPA_rep2

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6).
Then trimmed reads were aligned to the human genome (hg38) and Drosophila melanogaster (dm6) genome using Bowtie2 (v2.4.2). PCR duplicates were removed using picard (v2.26.0) (http://broadinstitute.github.io/picard/) MarkDuplicates.
Peaks were identified by scanning the whole genome using 5000-nt sliding windows. Windows with CPMIP/CPMInput > 4 and a Fishers exact P < 0.05 were retained. Adjacent windows were merged using bedtools merge (v2.26.0), and merged windows were identified as CENPA peaks. Only peaks that overlapped in two biological replicates were used for downstream analysis with bedtools intersect -f 0.5 -F 0.5 -e (v2.26.0) parameters.
Assembly: hg38
Supplementary files format and content: bed (except for Input sample)

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and then 0.125 M glycine was added to stop the reaction.
Library preparation was performed by using VAHTS Universal Pro DNA Library Prep Kit with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.

value: rabbit anti-CENPA(ab45694, Abcam)


title: HA-tagged WT RUNX1 Transduced HEL Cell CUT&RUN Rep 1

value: HA-WT RUNX1


title: HA-tagged RUNX1-4D Transduced HEL Cell RNA-seq Rep 2


title: shMETTL3_CENPA_rep1


title: HA-tagged WT RUNX1 Transduced HEL Cell RNA-seq Rep 2


title: HA-tagged WT RUNX1 Transduced HEL Cell CUT&RUN Rep 2


title: shControl_CENPA_rep1


title: shControl_CENPA_rep2


title: shMETTL3_InputC_rep2


title: shMETTL3_InputC_rep1


title: shControl_InputC_rep2


title: shControl_InputC_rep1


title: shMETTL3_MeRIP_rep1

data_processing:
Basecalls were performed using bcl-convert.
Low-quality bases and adapters were trimmed using Trim Galore (v0.6.6), then trimmed reads mapped to ribosomal RNAs were removed by Bowtie2 (v2.4.2).
The remaining reads were aligned to the human genome along with spike-in genomes, which included two control RNAs (one with m6A modification and one without), using HISAT2 (v2.1.0) with ‘--rna-strandness RF’ parameters.
Strand-specific reads were separated using samtools view (v1.9) with flags 99,147,83,163. m6A peak calling was performed using macs2 (v2.2.7.1) with ‘--keep-dup 5 -q 0.01 --nomodel’ parameters.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: MeRIP-Seq

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of A375 cells. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 following manufacturer's protocols.

tag: m6a antibody


title: shMETTL3_Input_rep2 [MeRIP]


title: shMETTL3_Input_rep1 [MeRIP]


title: shControl_MeRIP_rep1

value: WT

value: EpiMark N6-Methyladenosine Enrichment Kit


title: shMETTL3_MeRIP_rep2


title: shControl_MeRIP_rep2


title: shControl_Input_rep2 [MeRIP]


title: Empty Vector Transduced HEL Cell CUT&RUN Rep 2


title: shControl_Input_rep1 [MeRIP]


title: 488-13_37012_PBMC_TCR

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

data_processing:
CellRanger/Seurat
Assembly: Mmul_10
Supplementary files format and content: Count Matrix / Seurat Object

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
N/A
10x Genomics 5' Chemistry

tag: cdna library_id

tag: subjectid

value: PBMC

value: Primary cells

tag: plateid

tag: hto


title: 488-14_36562_Bone marrow_GEX

source_name: Bone marrow

value: Bone marrow


title: 488-13_36562_PBMC_GEX


title: 488-13_36562_PBMC_HTO


title: 488-14_36562_Bone marrow_ADT


title: 488-13_37012_PBMC_HTO


title: 488-13_36562_PBMC_TCR


title: 488-12_35547_Spleen_HTO

source_name: Spleen

value: Spleen


title: 488-14_36562_Bone marrow_TCR


title: 488-13_37012_PBMC_GEX


title: 488-13_36562_PBMC_ADT


title: 488-14_36562_Bone marrow_HTO


title: 488-13_37012_PBMC_ADT


title: 488-12_35547_Spleen_GEX


title: 488-12_35547_Spleen_ADT


title: 488-12_35547_PLN_HTO

source_name: PLN

value: PLN


title: 488-12_35547_PLN_TCR


title: 488-12_35547_MesLN_TCR

source_name: MesLN

value: MesLN


title: 488-12_35547_PLN_ADT


title: 488-12_35547_MesLN_GEX


title: 488-12_35547_MesLN_HTO


title: 488-12_35547_Spleen_TCR


title: 488-12_35547_MesLN_ADT


title: 488-12_35547_Bone marrow_TCR


title: 488-12_35547_Bone marrow_HTO


title: 488-11_38090_Spleen_TCR


title: 488-12_35547_Bone marrow_ADT


title: 488-11_38090_Spleen_GEX


title: 488-11_38090_Spleen_ADT


title: 488-11_38090_MesLN_HTO


title: 488-11_38090_PLN_GEX


title: 488-11_38090_PLN_ADT


title: 488-11_38090_PLN_TCR


title: 488-11_38090_PLN_HTO


title: 488-11_38090_Spleen_HTO


title: 488-11_38090_MesLN_TCR


title: 488-11_38090_Bone marrow_TCR


title: 488-12_35547_PLN_GEX


title: 488-10_38089_Spleen_GEX


title: 488-10_38089_Spleen_HTO


title: 488-11_38090_Bone marrow_GEX


title: 488-11_38090_MesLN_ADT


title: 488-11_38090_Bone marrow_ADT


title: 488-10_38089_Spleen_ADT


title: 488-10_38089_Spleen_TCR


title: 488-12_35547_Bone marrow_GEX


title: 488-10_38089_PLN_GEX


title: 488-10_38089_PLN_HTO


title: 488-10_38089_PLN_TCR


title: 488-10_38089_MesLN_GEX


title: 488-10_38089_PLN_ADT


title: 488-10_38089_MesLN_HTO


title: 488-10_38089_MesLN_ADT


title: 488-11_38090_Bone marrow_HTO


title: 488-11_38090_MesLN_GEX


title: 488-10_38089_Bone marrow_ADT


title: 488-1_37246_PBMC_TCR


title: 488-1_36131_PBMC_TCR


title: 488-1_37246_PBMC_HTO


title: 488-10_38089_Bone marrow_HTO


title: 488-1_37246_PBMC_GEX


title: 488-10_38089_Bone marrow_GEX


title: 488-1_36131_PBMC_ADT


title: 488-1_36131_PBMC_GEX


title: 488-1_35112_PBMC_TCR


title: 488-1_36131_PBMC_HTO


title: 482-9_38180_PBMC_TCR


title: 488-1_35112_PBMC_GEX


title: 482-9_38180_PBMC_HTO


title: 488-1_35112_PBMC_ADT


title: 482-9_38180_PBMC_ADT


title: 488-1_35112_PBMC_HTO


title: 482-9_38180_PBMC_GEX


title: 482-9_37166_PBMC_GEX


title: 482-9_37166_PBMC_HTO


title: 482-9_37163_PBMC_HTO


title: 482-9_37163_PBMC_TCR


title: 482-9_37163_PBMC_GEX


title: 488-1_37246_PBMC_ADT


title: 482-9_37163_PBMC_ADT


title: 482-8_36622_Spleen_TCR


title: 482-8_36622_Spleen_HTO


title: 482-8_36622_Spleen_GEX


title: 482-8_36622_PLN_GEX


title: 482-8_36622_PLN_TCR


title: 482-8_36622_Spleen_ADT


title: 482-8_36622_PLN_HTO


title: 482-9_37166_PBMC_TCR


title: 482-8_36622_PLN_ADT


title: 482-9_37166_PBMC_ADT


title: 482-7_36135_Spleen_HTO


title: 482-8_36622_MesLN_HTO


title: 482-8_36622_MesLN_TCR


title: 482-7_36135_Spleen_GEX


title: 482-7_36135_PLN_TCR


title: 482-7_36135_Spleen_TCR


title: 482-8_36622_MesLN_GEX


title: 482-7_36135_PLN_HTO


title: 482-7_36135_PLN_GEX


title: 482-8_36622_MesLN_ADT


title: 482-7_36135_Spleen_ADT


title: 482-7_36135_MesLN_HTO


title: 482-7_36135_MesLN_TCR


title: 482-7_36135_MesLN_GEX


title: 482-7_36135_MesLN_ADT


title: 482-7_36135_Bone marrow_TCR


title: 482-7_36135_PLN_ADT


title: 482-7_36135_Bone marrow_HTO


title: 482-7_36135_Bone marrow_GEX


title: 482-7_36135_Bone marrow_ADT


title: 482-6_36497_Spleen_GEX


title: 482-6_36497_PLN_TCR


title: 482-6_36497_Spleen_TCR


title: 482-6_36497_PLN_HTO


title: 482-6_36497_MesLN_HTO


title: 482-6_36497_Spleen_ADT


title: 482-6_36497_PLN_ADT


title: 482-6_36497_Bone marrow_GEX


title: 482-6_36497_Bone marrow_ADT


title: 482-6_36497_MesLN_TCR


title: 482-6_36497_MesLN_ADT


title: 482-6_36497_MesLN_GEX


title: 482-6_36497_Bone marrow_TCR


title: 482-5_36135_PBMC_TCR


title: 482-5_36497_PBMC_GEX


title: 482-6_36497_Bone marrow_HTO


title: 482-5_36497_PBMC_ADT


title: 482-5_36135_PBMC_GEX


title: 482-6_36497_Spleen_HTO


title: 482-5_36622_PBMC_GEX


title: 482-5_36622_PBMC_TCR


title: 482-4_35644_Spleen_TCR


title: 482-5_36497_PBMC_TCR


title: 482-5_36497_PBMC_HTO


title: 482-4_35644_PLN_TCR


title: 482-4_35644_Spleen_HTO


title: 482-5_36622_PBMC_ADT


title: 482-5_36135_PBMC_HTO


title: 482-5_36622_PBMC_HTO


title: 482-4_35644_Spleen_ADT


title: 482-5_36135_PBMC_ADT


title: 482-4_35644_PLN_GEX


title: 482-4_35644_PLN_ADT


title: 482-6_36497_PLN_GEX


title: 482-4_35644_MesLN_GEX


title: 482-4_35644_MesLN_ADT


title: 482-4_35644_Bone marrow_HTO


title: 482-4_35644_Bone marrow_TCR


title: 482-4_35644_Bone marrow_GEX


title: 482-3_37636_Spleen_TCR


title: 482-3_37636_Spleen_HTO


title: 482-3_37636_Spleen_GEX


title: 482-4_35644_Spleen_GEX


title: 482-4_35644_PLN_HTO


title: 482-3_37636_PLN_GEX


title: 482-3_37636_Bone marrow_TCR


title: 482-3_37636_MesLN_GEX


title: 482-3_37636_PLN_ADT


title: 482-3_37636_MesLN_TCR


title: 482-3_37636_Bone marrow_HTO


title: 482-4_35644_MesLN_TCR


title: 482-3_37636_Bone marrow_GEX


title: 482-3_37636_MesLN_ADT


title: 482-4_35644_MesLN_HTO


title: 482-3_37636_Bone marrow_ADT


title: 482-2_37374_Spleen_TCR


title: 482-2_37374_Spleen_HTO


title: 482-3_37636_Spleen_ADT


title: 482-2_37374_PLN_HTO


title: 482-3_37636_PLN_TCR


title: 482-2_37374_PLN_TCR


title: 482-2_37374_Spleen_GEX


title: 482-2_37374_PLN_GEX


title: 482-4_35644_Bone marrow_ADT


title: 482-2_37374_PLN_ADT


title: 482-2_37374_MesLN_HTO


title: 482-2_37374_MesLN_TCR


title: 482-2_37374_Spleen_ADT


title: 482-2_37374_MesLN_ADT


title: 482-3_37636_PLN_HTO


title: 482-3_37636_MesLN_HTO


title: 482-2_37374_MesLN_GEX


title: 482-2_37374_Bone marrow_HTO


title: 482-2_37374_Bone marrow_ADT


title: 482-16_37448_Spleen_HTO


title: 482-16_37448_Spleen_ADT


title: 482-16_37448_PLN_HTO


title: 482-16_37448_Spleen_GEX


title: 482-16_37448_MesLN_GEX


title: 482-16_37448_Bone marrow_TCR


title: 482-16_37448_MesLN_TCR


title: 482-16_37448_MesLN_HTO


title: 482-16_37448_PLN_ADT


title: 482-16_37448_PLN_TCR


title: 482-2_37374_Bone marrow_TCR


title: 482-15_36590_PLN_HTO


title: 482-15_36590_PLN_GEX


title: 482-16_37448_Bone marrow_ADT


title: 482-15_36590_MesLN_TCR


title: 482-16_37448_Bone marrow_GEX


title: 482-16_37448_PLN_GEX


title: 482-16_37448_Spleen_TCR


title: 482-15_36590_MesLN_GEX


title: 482-2_37374_Bone marrow_GEX


title: 482-15_36590_PLN_TCR


title: 482-16_37448_MesLN_ADT


title: 482-15_36590_MesLN_ADT


title: 482-15_36590_Bone marrow_TCR


title: 482-15_36590_PLN_ADT


title: 482-16_37448_Bone marrow_HTO


title: 482-15_36590_MesLN_HTO


title: 482-14_37167_PLN_HTO


title: 482-15_36590_Bone marrow_HTO


title: 482-15_36590_Bone marrow_GEX


title: 482-14_37167_Spleen_ADT


title: 482-14_37167_Spleen_HTO


title: 482-14_37167_PLN_TCR


title: 482-14_37167_MesLN_HTO


title: 482-14_37167_Spleen_GEX


title: 482-14_37167_Bone marrow_TCR


title: 482-14_37167_MesLN_TCR


title: 482-13_37448_PBMC_TCR


title: 482-13_37448_PBMC_GEX


title: 482-13_37448_PBMC_ADT


title: 482-14_37167_PLN_ADT


title: 482-14_37167_MesLN_GEX


title: 482-15_36590_Bone marrow_ADT


title: 482-13_37167_PBMC_TCR


title: 482-14_37167_MesLN_ADT


title: 482-13_37167_PBMC_ADT


title: 482-14_37167_Bone marrow_HTO


title: 482-13_36590_PBMC_TCR


title: 482-14_37167_PLN_GEX


title: 482-14_37167_Bone marrow_GEX


title: 482-13_36590_PBMC_HTO


title: 482-13_36590_PBMC_GEX


title: 482-12_37166_Spleen_HTO


title: 482-13_36590_PBMC_ADT


title: 482-14_37167_Spleen_TCR


title: 482-12_37166_Spleen_ADT


title: 482-13_37448_PBMC_HTO


title: 482-14_37167_Bone marrow_ADT


title: 482-13_37167_PBMC_HTO


title: 482-13_37167_PBMC_GEX


title: 482-12_37166_MesLN_TCR


title: 482-12_37166_PLN_ADT


title: 482-12_37166_Bone marrow_TCR


title: 482-12_37166_MesLN_GEX


title: 482-12_37166_MesLN_ADT


title: 482-12_37166_PLN_TCR


title: 482-12_37166_PLN_HTO


title: 482-12_37166_PLN_GEX


title: 482-12_37166_MesLN_HTO


title: 482-12_37166_Spleen_GEX


title: 482-11_38180_Spleen_GEX


title: 482-11_38180_Spleen_HTO


title: 482-12_37166_Bone marrow_HTO


title: 482-12_37166_Bone marrow_GEX


title: 482-11_38180_MesLN_TCR


title: 482-11_38180_PLN_ADT


title: 482-11_38180_MesLN_GEX


title: 482-12_37166_Bone marrow_ADT


title: 482-11_38180_Bone marrow_HTO


title: 482-11_38180_Bone marrow_ADT


title: 482-11_38180_MesLN_HTO


title: 482-11_38180_PLN_GEX


title: 482-11_38180_PLN_TCR


title: 482-11_38180_Spleen_ADT


title: 482-11_38180_PLN_HTO


title: 482-11_38180_Spleen_TCR


title: 482-12_37166_Spleen_TCR


title: 482-11_38180_MesLN_ADT


title: 482-11_38180_Bone marrow_GEX


title: 482-11_38180_Bone marrow_TCR


title: 482-10_37163_Spleen_GEX


title: 482-10_37163_Spleen_TCR


title: 482-10_37163_Spleen_HTO


title: 482-10_37163_PLN_GEX


title: 482-10_37163_PLN_HTO


title: 482-10_37163_Spleen_ADT


title: 482-10_37163_PLN_TCR


title: 482-10_37163_MesLN_GEX


title: 482-10_37163_MesLN_HTO


title: 482-10_37163_MesLN_ADT


title: 482-10_37163_PLN_ADT


title: 482-10_37163_Bone marrow_TCR


title: 482-10_37163_Bone marrow_ADT


title: 482-10_37163_MesLN_TCR


title: 482-1_37636_PBMC_TCR


title: 482-1_37636_PBMC_ADT


title: 482-10_37163_Bone marrow_GEX


title: 482-1_35644_PBMC_HTO


title: 482-1_35644_PBMC_TCR


title: 482-10_37163_Bone marrow_HTO


title: 482-1_35644_PBMC_ADT


title: 482-1_37636_PBMC_GEX


title: 482-1_37374_PBMC_TCR


title: 482-1_37374_PBMC_HTO


title: 482-1_37374_PBMC_GEX


title: 452-9_37108_MesLN_TCR


title: 452-9_37108_MesLN_HTO


title: 452-9_37108_MesLN_GEX


title: 452-8_37108_Spleen_TCR


title: 482-1_35644_PBMC_GEX


title: 452-8_37108_Spleen_HTO


title: 452-9_37108_MesLN_ADT


title: 452-9_37108_PLN_TCR


title: 452-8_37108_Liver_HTO

source_name: Liver

value: Liver


title: 452-9_37108_PLN_HTO


title: 482-1_37374_PBMC_ADT


title: 452-9_37108_PLN_GEX


title: 452-7_37108_PBMC_TCR


title: 482-1_37636_PBMC_HTO


title: 452-7_37108_PBMC_HTO


title: 452-9_37108_PLN_ADT


title: 452-8_37108_Spleen_GEX


title: 452-8_37108_Liver_GEX


title: 452-8_37108_Spleen_ADT


title: 452-8_37108_Liver_TCR


title: 452-8_37108_Liver_ADT


title: 452-7_37108_PBMC_GEX


title: 452-7_37108_PBMC_ADT


title: 452-6_37877_PLN_HTO


title: 452-6_37877_MesLN_TCR


title: 452-6_37877_PLN_ADT


title: 452-7_37108_Bone marrow_TCR


title: 452-7_37108_Bone marrow_HTO


title: 452-7_37108_Bone marrow_GEX


title: 452-5_37877_Liver_TCR


title: 452-7_37108_Bone marrow_ADT


title: 452-5_37877_Spleen_GEX


title: 452-5_37877_Spleen_HTO


title: 452-5_37877_Spleen_ADT


title: 452-6_37877_MesLN_HTO


title: 452-6_37877_MesLN_ADT


title: 452-6_37877_MesLN_GEX


title: 452-5_37877_Liver_GEX


title: 452-5_37877_Liver_HTO


title: 452-6_37877_PLN_TCR


title: 452-3_35628_PLN_TCR


title: 452-5_37877_Liver_ADT


title: 452-6_37877_PLN_GEX


title: 452-3_35628_PLN_HTO


title: 452-3_35628_MesLN_TCR


title: 452-3_35628_PLN_ADT


title: 452-3_35628_MesLN_HTO


title: 452-24_37190_PLN_TCR


title: 452-3_35628_MesLN_GEX


title: 452-24_37190_PLN_ADT


title: 452-24_37190_PLN_GEX


title: 452-3_35628_MesLN_ADT


title: 452-24_37190_PLN_HTO


title: 452-24_37190_MesLN_TCR


title: 452-24_37190_MesLN_HTO


title: 452-5_37877_Spleen_TCR


title: 452-24_37190_MesLN_ADT


title: 452-23_37190_Spleen_TCR


title: 452-23_37190_Spleen_HTO


title: 452-3_35628_PLN_GEX


title: 452-23_37190_Liver_GEX


title: 452-23_37190_Liver_TCR


title: 452-23_37190_Liver_HTO


title: 452-23_37190_Liver_ADT


title: 452-23_37190_Spleen_GEX


title: 452-22_37190_PBMC_HTO


title: 452-22_37190_PBMC_TCR


title: 452-22_37190_PBMC_GEX


title: 452-22_37190_Bone marrow_TCR


title: 452-22_37190_Bone marrow_HTO


title: 452-22_37190_Bone marrow_GEX


title: 452-22_37190_PBMC_ADT


title: 452-21_37184_PLN_TCR


title: 452-24_37190_MesLN_GEX


title: 452-21_37184_PLN_GEX


title: 452-22_37190_Bone marrow_ADT


title: 452-21_37184_PLN_HTO


title: 452-21_37184_PLN_ADT


title: 452-21_37184_MesLN_HTO


title: 452-21_37184_MesLN_GEX


title: 452-20_37184_Spleen_HTO


title: 452-20_37184_Spleen_GEX


title: 452-20_37184_Spleen_ADT


title: 452-20_37184_Spleen_TCR


title: 452-21_37184_MesLN_ADT


title: 452-20_37184_Liver_GEX


title: 452-23_37190_Spleen_ADT


title: 452-20_37184_Liver_TCR


title: 452-20_37184_Liver_HTO


title: 452-19_37184_PBMC_HTO


title: 452-20_37184_Liver_ADT


title: 452-19_37184_PBMC_GEX


title: 452-19_37184_PBMC_ADT


title: 452-19_37184_Bone marrow_TCR


title: 452-19_37184_PBMC_TCR


title: 452-21_37184_MesLN_TCR


title: 452-19_37184_Bone marrow_GEX


title: 452-19_37184_Bone marrow_HTO


title: 452-18_36570_PLN_HTO


title: 452-19_37184_Bone marrow_ADT


title: 452-18_36570_PLN_GEX


title: 452-18_36570_PLN_TCR


title: 452-18_36570_PLN_ADT


title: 452-18_36570_MesLN_HTO


title: 452-18_36570_MesLN_GEX


title: 452-18_36570_MesLN_ADT


title: 452-18_36570_MesLN_TCR


title: 452-17_36570_Spleen_GEX


title: 452-17_36570_Liver_TCR


title: 452-16_36570_PBMC_HTO


title: 452-17_36570_Liver_GEX


title: 452-16_36570_PBMC_TCR


title: 452-17_36570_Liver_ADT


title: 452-17_36570_Liver_HTO


title: 452-16_36570_PBMC_GEX


title: 452-16_36570_Bone marrow_HTO


title: 452-17_36570_Spleen_ADT


title: 452-16_36570_Bone marrow_TCR


title: 452-16_36570_PBMC_ADT


title: 452-15_37188_PLN_TCR


title: 452-17_36570_Spleen_TCR


title: 452-16_36570_Bone marrow_GEX


title: 452-15_37188_PLN_GEX


title: 452-16_36570_Bone marrow_ADT


title: 452-15_37188_MesLN_HTO


title: 452-14_37188_Spleen_TCR


title: 452-15_37188_MesLN_TCR


title: 452-15_37188_PLN_HTO


title: 452-15_37188_PLN_ADT


title: 452-15_37188_MesLN_GEX


title: 452-14_37188_Spleen_GEX


title: 452-17_36570_Spleen_HTO


title: 452-14_37188_Spleen_ADT


title: 452-14_37188_Liver_TCR


title: 452-14_37188_Liver_HTO


title: 452-14_37188_Liver_GEX


title: 452-13_37188_PBMC_TCR


title: 452-13_37188_Bone marrow_TCR


title: 452-13_37188_PBMC_HTO


title: 452-13_37188_PBMC_GEX


title: 452-15_37188_MesLN_ADT


title: 452-13_37188_Bone marrow_HTO


title: 452-13_37188_PBMC_ADT


title: 452-13_37188_Bone marrow_GEX


title: 452-12_36569_PLN_TCR


title: 452-14_37188_Spleen_HTO


title: 452-13_37188_Bone marrow_ADT


title: 452-12_36569_MesLN_TCR


title: 452-12_36569_MesLN_HTO


title: 452-12_36569_MesLN_GEX


title: 452-11_36569_Spleen_TCR


title: 452-11_36569_Spleen_HTO


title: 452-12_36569_PLN_GEX


title: 452-12_36569_MesLN_ADT


title: 452-12_36569_PLN_HTO


title: 452-11_36569_Liver_GEX


title: 452-11_36569_Liver_TCR


title: 452-14_37188_Liver_ADT


title: 452-11_36569_Liver_ADT


title: 452-11_36569_Spleen_GEX


title: 452-10_36569_PBMC_GEX


title: 452-10_36569_PBMC_ADT


title: 452-10_36569_PBMC_HTO


title: 452-12_36569_PLN_ADT


title: 452-10_36569_Bone marrow_HTO


title: 452-10_36569_Bone marrow_GEX


title: 452-1_35628_PBMC_GEX


title: 452-1_35628_PBMC_HTO


title: 452-11_36569_Spleen_ADT


title: 452-11_36569_Liver_HTO


title: 452-10_36569_Bone marrow_ADT


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 9

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 9
9v14

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.9.0) was used to map the cleaned reads to the GRCh38.p13 human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release 41). Salmon parameters used: -i ./salmon_index_H41  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport to estimate gene level counts.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table (TxImport.GeneLevel.counts.GEO.txt) with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (txi.counts.annotated.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (txi.lengthScaledTPM.annotated.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: Skeletal muscle biopsy

growth_protocol: In total, 15 overweight and obese males (n = 11) and females (n = 4) were included in the study. Prior to inclusion, all individuals were screened in an overnight fasted state to determine eligibility. Participants were white Western Europeans and aged between 40-75 years, with a BMI of 27-35 kg/m2. Females had to be postmenopausal, which was defined as at least one year post-cessation of menses. Exclusion criteria were: diagnosed with T2DM, cardiovascular disease (as determined by blood pressure measurements, resting ECG, and a medical history questionnaire), cancer, unstable body mass (weight gain or loss >3 kg in the past 3 months), fasting glucose concentration ≥7.0 mmol/L, anaemia, alcohol or drug abuse, engagement in structured exercise >2 hours per week, smoking, medication use regarded as unsafe in the context of the study and/or known to interfere with the primary outcome, and regular exposure to low temperatures such as cold-water baths, cold-water swimming or working in a refrigerated environment in the last one month. Participants started and completed the study between the 6th of November 2020 and the 13th of December 2021, at Maastricht University Medical Centre (Metabolic Research Unit), the Netherlands. The study was conducted in accordance with the declaration of Helsinki and was approved by the Medical Ethical Committee of Maastricht University Medical Centre. The study was registered at ClinicalTrials.gov (NCT-identifier: NCT04516018). All participants provided their written informed consent prior to the start of the screening.

extract_protocol:
Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 100bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: Volunteers participated in a single-arm intervention study. During the study, participants were exposed for 10 days to an individualised cold exposure regimen that involved 1 hour of shivering per day via a cold-water (10°C) perfused suit. Before the intervention, and the day after 10 cold exposures with shivering (i.e. cold acclimation), a muscle biopsy was taken. Biopsies were taken following an overnight fast from the m. vastus lateralis, under local anaesthesia (1% lidocaine without adrenaline) using the Bergström method (PMID: 5584523). All samples were snap-frozen and stored at −80°C until the analyses were performed.

value: muscle

value: m. vastus lateralis biopsy

value: Post

tag: Sex

value: Male

tag: age (years)

tag: bmi (kg/m2)

tag: rna integrity_number_(rin)


title: 452-1_35628_Bone marrow_TCR

tag: cell type


title: 452-1_35628_Bone marrow_HTO


title: 452-1_35628_Bone marrow_ADT


title: muscle biopsy, overweight or obese female, before cold acclimation, subject 5

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese female, before cold acclimation, subject 5
5v2

value: Pre

value: Female


title: 452-1_35628_Bone marrow_GEX


title: muscle biopsy, overweight or obese female, after cold acclimation, subject 4

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese female, after cold acclimation (10 days, 1 hour of shivering per day), subject 4
5v14


title: 438-9_35605_PLN_TCR


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 9

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 9
9v2


title: 438-9_35605_PLN_HTO


title: 452-10_36569_PBMC_TCR


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 2

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, before cold acclimation, subject 2
2v2


title: 452-10_36569_Bone marrow_TCR


title: 452-1_35628_PBMC_TCR


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 2

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, after cold acclimation (10 days, 1 hour of shivering per day), subject 2
2v14


title: 438-9_35605_PLN_GEX


title: 452-1_35628_PBMC_ADT


title: 438-9_35605_PLN_ADT


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 21

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, before cold acclimation, subject 21
21v2


title: 438-9_35605_MesLN_TCR


title: 438-9_35605_MesLN_HTO


title: muscle biopsy, overweight or obese female, before cold acclimation, subject 8

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight female, before cold acclimation, subject 8
8v2


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 1

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, before cold acclimation, subject 1
1v2


title: 438-9_35605_MesLN_GEX


title: muscle biopsy, overweight or obese female, after cold acclimation, subject 8

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight female, after cold acclimation (10 days, 1 hour of shivering per day), subject 8
8v14


title: 438-8_35605_Spleen_TCR


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 21

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, after cold acclimation (10 days, 1 hour of shivering per day), subject 21
21v14


title: 438-8_35605_Spleen_HTO


title: 438-9_35605_MesLN_ADT


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 19

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 19
19v2


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 1

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, after cold acclimation (10 days, 1 hour of shivering per day), subject 1
1v14


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 18

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 18
18v14


title: 438-8_35605_Spleen_GEX


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 17

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 17
17v14


title: 438-8_35605_Spleen_ADT


title: 438-8_35605_Liver_TCR


title: 438-8_35605_Liver_HTO


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 16

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 16
16v2


title: 438-8_35605_Liver_ADT


title: 438-7_35605_PBMC_TCR


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 14

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 14
14v14


title: 438-7_35605_PBMC_HTO


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 19

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 19
19v14


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 16

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 16
16v14


title: 438-7_35605_PBMC_GEX


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 14

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 14
14v2


title: 438-8_35605_Liver_GEX


title: muscle biopsy, overweight or obese female, before cold acclimation, subject 12

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese female, before cold acclimation, subject 12
12v2


title: muscle biopsy, overweight or obese female, before cold acclimation, subject 13

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight female, before cold acclimation, subject 13
13v2


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 18

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 18
18v2


title: 438-7_35605_PBMC_ADT


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 11

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, after cold acclimation (10 days, 1 hour of shivering per day), subject 11
11v14


title: 438-7_35605_Bone marrow_HTO


title: 438-7_35605_Bone marrow_GEX


title: 438-7_35605_Bone marrow_TCR


title: 438-7_35605_Bone marrow_ADT


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 17

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 17
17v2


title: 438-6_34012_PLN_TCR


title: 438-6_34012_PLN_HTO


title: muscle biopsy, overweight or obese male, after cold acclimation, subject 10

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, after cold acclimation (10 days, 1 hour of shivering per day), subject 10
10v14


title: muscle biopsy, overweight or obese female, after cold acclimation, subject 13

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight female, after cold acclimation (10 days, 1 hour of shivering per day), subject 13
13v14


title: 27_D4 DIM 3

city: Cologne

first: Simon

last: Poepsel

address: Robert-Koch-Str. 21

department: Center for Molecular Medicine Cologne

institute: University of Cologne

data_processing:
Trimming was performed using bbduk1 (k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20)
Alingment with STAR2 v2.7.3a to mm10
Down sampling to 8 million reads with samtools3 v1.13
Reads were counted by HTSeq4 v2.0.1 (-m union -s no -t exon)
Differential expression analysis was performed using DESeq25 v1.42.3
Assembly: mm10
Supplementary files format and content: .txt file contains count matrix per sample

organism: Mus musculus

growth_protocol: mESCs were maintained in GMEM supplemented with 20 % FBS, 2 mM Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium pyruvate, 1x PenStrep, 50 µM 2-mercaptoethanol, 1000 U/mL LIF, 3 µM CHIR99021, and 1 µM PD0325901 on gelatinised plates at 37 °C with 5 % CO2.

extract_protocol:
NucleoSpin RNA Kit (MACHEREY NAGEL, cat. no. 740955) according to manufacturer’s protocol
QuantSeq 3’ mRNA Seq Library Prep Kit FWD with Unique Dual Indices for Illumina (Lexogen, cat. no 115.384)

treatment_protocol: Cells were differentiated with 0.1 µM retinoic acid in culture medium without LIF, CHIR99021, and PD0325901

tag: cell line

value: differentiated cell

tag: genotype

tag: treatment

value: RA, 4 days


title: 438-6_34012_PLN_GEX

tag: tissue


title: 26_D4 DIM 2


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 11

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an overweight male, before cold acclimation, subject 11
11v2


title: 438-6_34012_PLN_ADT


title: 438-6_34012_MesLN_TCR


title: 25_D4 DIM 1


title: 438-6_34012_MesLN_HTO


title: muscle biopsy, overweight or obese female, after cold acclimation, subject 12

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese female, after cold acclimation (10 days, 1 hour of shivering per day), subject 12
12v14


title: 24_D4 WT 3


title: 438-6_34012_MesLN_ADT


title: 23_D4 WT 2


title: 22_D4 WT 1


title: 20_D4 EV 2

source_name: mESC-EV

value: mESC-EV


title: 438-5_34012_Spleen_TCR


title: 438-6_34012_MesLN_GEX


title: 21_D4 EV 3


title: 18_D1 DIM 3

value: RA, 1 day


title: muscle biopsy, overweight or obese male, before cold acclimation, subject 10

description:
Skeletal muscle biopsy, obtained from the m. vastus lateralis, from an obese male, before cold acclimation, subject 10
10v2


title: 438-5_34012_Spleen_ADT


title: 19_D4 EV 1


title: 17_D1 DIM 2


title: 438-5_34012_Spleen_HTO


title: 438-5_34012_Liver_TCR


title: 438-5_34012_Liver_HTO


title: 16_D1 DIM 1


title: 15_D1 WT 3


title: 438-5_34012_Liver_GEX


title: 488-10_38089_Bone marrow_TCR


title: 14_D1 WT 2


title: 438-5_34012_Liver_ADT


title: 13_D1 WT 1


title: 438-4_34012_PBMC_TCR

value: PBMC


title: 438-4_34012_PBMC_HTO

value: Primary cells


title: 12_D1 EV 3


title: 10_D1 EV 1


title: 438-4_34012_PBMC_GEX


title: 11_D1 EV 2


title: 438-5_34012_Spleen_GEX


title: 438-4_34012_Bone marrow_TCR

value: Bone marrow


title: 438-4_34012_PBMC_ADT


title: 438-4_34012_Bone marrow_GEX


title: 438-4_34012_Bone marrow_HTO


title: 7_D0 DIM 1

value: murine embryonic stem cell


title: 8_D0 DIM 2


title: 9_D0 DIM 3


title: 438-4_34012_Bone marrow_ADT


title: 5_D0 WT 2


title: 438-3_34854_PLN_HTO

value: PLN


title: 6_D0 WT 3


title: 3_D0 EV3


title: 438-3_34854_PLN_GEX


title: 438-3_34854_PLN_TCR


title: 4_D0 WT 1


title: 2_D0 EV 2


title: 1_D0 EV 1


title: 438-3_34854_MesLN_TCR

value: MesLN


title: 438-3_34854_PLN_ADT


title: 438-3_34854_MesLN_HTO


title: 438-3_34854_MesLN_GEX


title: WT-71

city: Sanya

first: yan

middle: fang

last: zhi

address: No. 80 Jianglin Road, Haitang District, Sanya City, Hainan Province, CHINA

department: tropical medicine

institute: Chinese Hainan Hospital, General Hospital of the People's Liberation Army

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCm38 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes count values for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: liver tumor

growth_protocol: All animals were maintained under specific pathogen-free conditions and subjected to a 12-hour on/off light cycle. Furthermore, all animal care and experimental procedures were conducted in compliance with the National Institutes of Health Guide for the Care.

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

treatment_protocol: The mice were then administered with DEN-CCl4 through intraperitoneal injection to induce the HCC model.

value: liver tumor

value: WT


title: KO-94


title: KO-93


title: 438-3_34854_MesLN_ADT


title: KO-92


title: 438-24_37114_PLN_TCR


title: WT-66


title: WT-7


title: 438-24_37114_PLN_HTO


title: 438-24_37114_PLN_GEX


title: 438-24_37114_PLN_ADT


title: HIF1aKO-Acetate-96hrs-rep1

city: Birmingham

first: Hongxing

last: Shen

state: AL

address: 1700 6TH AVE S, HSROC 2222N

department: Department of Radiation Oncology

institute: University of Alabama at Birmingham

description:
KO1_NaAc
HIF1aKO1-Acetate-H3K9Ac
Count.txt

data_processing:
Fastq files were quality and adapter trimmed using Trimgalore.
Samples were aligned to the mm10 genome using Bowtie2.
Samples were also aligned to the E.Coli genome for Spike-in calibration
Reads with mapped read pairs were filtered and kept
Spike-in calibration was performed with deepTools based on scaling-factor from the E.Coli alignment.
Peaks were called with Seacr
Peaks for all samples were merged and converted into the SAF format
Merged peak files was used to generate count data for each sample
Assembly: mm10, K-12
Supplementary files format and content: Count matrix, bigWig
Library strategy: Cut&Run

source_name: CD4+ T cells

growth_protocol: All cells were cultured in a humidified 37 °C incubator with 5% CO2. For hypoxic condition, cultures were placed in a hypoxic chamber with oxygen level set at 1% to mimick the O2 tension in the TME of solid tumors.

extract_protocol:
Cut&Run reactions were performed according to manufacturer instructions (Epicypher 14-1048)
Cut&Run library was performedaccording to manufacturer instructions (NEB E7645S)

treatment_protocol: Naïve T cells or Hif1α KO CD4 T cells were activated with plate-bond anti-CD3 plus anti-CD28 in presence of 100U/mL IL-2 for 48h, with or without sodium acetate treatment.

value: CD4+ T cells

value: HIF1a KO

tag: cut&run antibody

value: H3K9Ac(Abcam, AB8898)


title: HIF1aKO-Acetate-96hrs-rep2

description:
KO2_NaAc
HIF1aKO2-Acetate-H3K9Ac
Count.txt


title: 438-24_37114_MesLN_TCR


title: 438-24_37114_MesLN_HTO


title: HIF1aKO-Untreated-96hrs-rep1

description:
KO1_Untx
HIF1aKO1-Untx_H3K9Ac
Count.txt


title: HIF1aKO-Untreated-96hrs-rep2

description:
KO2_Untx
HIF1aKO2-Untx_H3K9Ac
Count.txt


title: 438-24_37114_MesLN_GEX


title: 438-23_37114_Spleen_TCR

value: Spleen


title: WT-Acetate-96hrs-rep2

description:
WT2_NaAc
WT2-Acetate-H3K9Ac
Count.txt

value: Wildtype


title: WT-Untreated-96hrs-rep2

description:
WT2_Untx
WT2-Untx_H3K9Ac
Count.txt


title: 438-23_37114_Spleen_HTO


title: 438-24_37114_MesLN_ADT


title: 438-23_37114_Spleen_GEX


title: WT-Untreated-96hrs-rep1

description:
WT1_Untx
WT1-Untx_H3K9Ac
Count.txt


title: WT-Acetate-96hrs-rep1

description:
WT1_NaAc
WT1-Acetate-H3K9Ac
Count.txt


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane4_Sublib2

city: Durham

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

institute: Duke University

description:
aged_singlecellexpression_sublib2.tar.gz
Ageddiffmethylsites.txt

data_processing:
Adapter sequences were trimmed with Flexbar (3.0.3) and aligned to the mm10 genome using STAR 2.7.5. The STAR aligner was also used to mark PCR duplicates
Bullseye (https://github.com/mflamand/Bullseye) was used to generate a nucleotide representation matrix using parseBAM.pl. Marked PCR duplicates were ignored at this step.
Differential methylation was found by comparing altered %C2U values across RNAs found to be methylated in young mice
The Parse Biosciences split-pipe pipe line was used for barcode correction and assigment, alignment, and gene expression matrix generation
Assembly: mm10
Supplementary files format and content: aged_singlecellexpression_sublib1.tar.gz and aged_singlecellexpression_sublib2.tar.gz (zipped verison of the gene expression matrices).
Supplementary files format and content: Ageddiffmethylsites.txt (txt file with a list of differentially methylated RNAs between young and aged mice).  The sites from the young mouse used for this are contained in GSE266876_youngmousecortex_singlecellsites.bed.gz.

source_name: Cortex

growth_protocol: Mice were 12-14 months old at the start of tamoxifen treatment and house under normal conditions

extract_protocol:
Mice were placed under anesthesia and perfused with ACSF. The brain was removed, cortex isolated and cut into pieces and digested with Neuronal Isolation Enzyme with Papain (Thermo Fisher). Tissue was gently disrupted with 10mL pipettes to release single cells. Debris was removed by centrifuging for 25 min at 250xg in 30% percoll solution. Cells were counted and viablity measured. Cells were fixed with the Whole Cell Fixation Kit (Parse Biosciences). Split pool barcoding and Illumina library preparation was perfomed using the Whole Transcriptome Evercode Kit (Parse Biosciences)
Libraries were prepared using the Parse Biosciences WT Mini Kit. Briefly, reverse transcription added the first barcode within the fixed cells. Then, cells were pooled and redistributed on a 96 well plate where a second barcode was ligated. Cells were again pooled and redistributed on a 96 plate before a 3rd barcode was ligated. Then cells were pooled, lysed, and Illumina libraries were constructed using an indexing PCR followed by purification and size selection with SPRI beads.

treatment_protocol: Mice were treated with 20mg/kg tamoxifen every 24 hours for five days. 7 days after the final treatment, biological material was collected.

value: Cortex

value: Tamoxifen


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane3_Sublib2


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane2_Sublib2


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane1_Sublib2


title: 438-23_37114_Liver_TCR

value: Liver


title: 438-23_37114_Liver_GEX


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane4_Sublib1

description:
aged_singlecellexpression_sublib1.tar.gz
Ageddiffmethylsites.txt


title: 438-23_37114_Liver_ADT


title: 438-22_37114_PBMC_TCR


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane3_Sublib1


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane1_Sublib1


title: 438-22_37114_PBMC_GEX


title: GLORI_Microglia_rep2

description: Illumina NovaSeq X Plus

data_processing:
GLORI-Tools was used for data analysis. This includes making an A-to-G converted STAR index, alignment with STAR, and site calling using the default settings.
Assembly: mm39
Supplementary files format and content: A bed file with the identified m6A sites in each cell type and replicate
Library strategy: GLORI

source_name: Cortex, Microglia

growth_protocol: Mice were 10 weeks old at the start of tamoxifen treatment and housed under normal conditions

extract_protocol:
Mice were placed under anesthesia and perfused with ACSF. The brain was removed, cortex isolated and cut into pieces and digested with Neuronal Isolation Enzyme with Papain (Thermo Fisher). Tissue was gently disrupted with 10mL pipettes to release single cells. Debris was removed by centrifuging for 25 min at 250xg in 30% percoll solution. Cells were counted and viablity measured. Cells were then stained with an anti-ACSA2 antibody conjugated to APC (Miltenyi) (for astrocytes) and an anti-Cd11b antibody conjugated to Alexa 488 (BioLegend) (for microglia) and sorted on a BD FACS Aria A02. Cells were homogenized in Trizol and total RNA extracted. GLORI was then performed as previously described (Liu et al, 2022).
Libraries were prepared with SMARTer Stranded Total RNA-seq Kit v3 - Pico Input Mammalian (Takara).

value: Cortex, Microglia

value: Cortical Microglia


title: 438-22_37114_PBMC_HTO

value: PBMC

value: Primary cells


title: GLORI_Astrocytes_rep2

description: Illumina NovaSeq X Plus

source_name: Cortex, Astrocytes

value: Cortex, Astrocytes

value: Cortical Astrocytes


title: GLORI_Microglia_rep1

description: Illumina NovaSeq X Plus


title: 438-22_37114_PBMC_ADT


title: 438-21_34474_PLN_TCR

value: PLN


title: scDART-seq/scRNA-seq in aged mouse cortex_Lane2_Sublib1


title: 438-21_34474_PLN_GEX


title: 438-21_34474_PLN_HTO


title: GLORI_Astrocytes_rep1

description: Illumina NovaSeq X Plus


title: 438-23_37114_Spleen_ADT


title: scDART_Ctx_2_Sublib3

description: APOBEC1YTH_APOBEC1YTHmutpool_scDARTseq_Cortex_Reps1and2_Sublibrary3

data_processing:
Adapter sequences were trimmed with Flexbar (3.0.3) and aligned to the mm10 genome using STAR 2.7.5. The STAR aligner was also used to mark PCR duplicates
Bullseye (https://github.com/mflamand/Bullseye) was used to generate a nucleotide representation matrix using parseBAM.pl. Marked PCR duplicates were ignored at this step.
Bullseye find_edit_sites.pl was used to find editing sites corresponding to m6A methylation using the following criteria. Minimum coverage: 3 reads, 0.5-95% C2U, minimum C2U mutations: 2, called in at least 3 cells, occurs in RAC motif.
The Parse Biosciences split-pipe pipe line was used for barcode correction and assigment, alignment, and gene expression matrix generation
Assembly: mm10
Supplementary files format and content: A bed file with a list of differentially methylated RNAs between young and aged mice
Supplementary files format and content: A zipped verison of the gene expression matrices

source_name: Cortex (Brain)

growth_protocol: Mice were 6-8 weeks old at the start of tamoxifen treatment and housed under normal conditions

extract_protocol:
Mice were placed under anesthesia and perfused with ACSF. The brain was removed, cortex isolated and cut into pieces and digested with Neuronal Isolation Enzyme with Papain (Thermo Fisher). Tissue was gently disrupted with 10mL pipettes to release single cells. Debris was removed by centrifuging for 25 min at 250xg in 30% percoll solution. Cells were counted and viablity measured. Cells were fixed with the Whole Cell Fixation Kit (Parse Biosciences). Split pool barcoding and Illumina library preparation was perfomed using the Whole Transcriptome Evercode Kit (Parse Biosciences)
Libraries were prepared using the Parse Biosciences WT Kit. Briefly, reverse transcription added the first barcode within the fixed cells. Then, cells were pooled and redistributed on a 96 well plate where a second barcode was ligated. Cells were again pooled and redistributed on a 96 plate before a 3rd barcode was ligated. Then cells were pooled, lysed, and Illumina libararies were constructed using an indexing PCR followed by purification and size selection with SPRI beads.

value: Cortex (Brain)

value: APOBEC1-YTH and APOBEC1-YTHmut


title: 438-21_34474_PLN_ADT


title: 438-23_37114_Liver_HTO


title: 438-21_34474_MesLN_HTO

value: MesLN


title: scDART_Ctx_2_Sublib2

description: APOBEC1YTH_APOBEC1YTHmutpool_scDARTseq_Cortex_Reps1and2_Sublibrary2


title: 438-21_34474_MesLN_GEX


title: 438-20_34474_Spleen_TCR


title: 438-21_34474_MesLN_ADT


title: MYO5B induced KO, differentiated enteroids with vehicle, rep-3

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

description:
gene_fpkm.xls
gene_count.xls

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Alignments were parsed using Tophat program.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al. 2008).
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: Excel includes comparisons of differential expression genes by FPKM

source_name: Jejunum organoids

growth_protocol: Isolated crypts of mouse jejunum were embeded in BME-R1 and organoids were grown in Mouse IntestiCult Medium (Stem Cell Technology). Organoids were passaged twice before the tamoxifen induction.

extract_protocol:
Following the differentiation, enteroids were placed in Organoid Harvesting Solution (3700-100-01; Cultrex) for 1 hr at 4˚C. Enteroids were washed with PBS and centrifuged. Enteroid pellets were immersed in TRIzol reagent (15596026; Invitrogen) supplemented with glycogen (G1767; Sigma Aldrich)
Libraries were prepared by Novogene Corporation Inc. (Sacramento, CA). mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified doublestranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: G519R and iKO enteorids were treated with 4-OH-tamoxifen (1 µM) to induce Cre recombinase 24 hours before switching medium to the differentiation medium. Compound-1 (100 nM) or vehicle (PBS) was added into differentiation medium for 2 days.

value: Jejunum organoids

value: Vehicle


title: MYO5B induced KO, differentiated enteroids with vehicle, rep-4

description:
gene_fpkm.xls
gene_count.xls


title: MYO5B induced KO, differentiated enteroids with vehicle, rep-2

description:
gene_fpkm.xls
gene_count.xls


title: 438-20_34474_Spleen_HTO

value: Spleen


title: MYO5B induced KO, differentiated enteroids with Compound-1, rep-4

description:
gene_fpkm.xls
gene_count.xls


title: MYO5B induced KO, differentiated enteroids with vehicle, rep-1

description:
gene_fpkm.xls
gene_count.xls


title: 488-10_38089_MesLN_TCR


title: 438-20_34474_Spleen_GEX


title: 438-20_34474_Spleen_ADT


title: MYO5B induced KO, differentiated enteroids with Compound-1, rep-1

description:
gene_fpkm.xls
gene_count.xls


title: 438-20_34474_Liver_HTO


title: 438-20_34474_Liver_TCR


title: 438-20_34474_Liver_GEX


title: MYO5B(G519R) mutant, differentiated enteroids, rep-4

description:
gene_fpkm.xls
gene_count.xls


title: MYO5B induced KO, differentiated enteroids with Compound-1, rep-3

description:
gene_fpkm.xls
gene_count.xls


title: scDART_Ctx_2_Sublib4

description: APOBEC1YTH_APOBEC1YTHmutpool_scDARTseq_Cortex_Reps1and2_Sublibrary4


title: MYO5B induced KO, differentiated enteroids with Compound-1, rep-2

description:
gene_fpkm.xls
gene_count.xls


title: 438-20_34474_Liver_ADT


title: 438-2_34854_Spleen_HTO


title: 438-21_34474_MesLN_TCR


title: 438-2_34854_Spleen_TCR


title: MYO5B(G519R) mutant, differentiated enteroids, rep-1

description:
gene_fpkm.xls
gene_count.xls


title: scDART_Ctx_2_Sublib1

description: APOBEC1YTH_APOBEC1YTHmutpool_scDARTseq_Cortex_Reps1and2_Sublibrary1


title: 438-2_34854_Spleen_GEX


title: 438-2_34854_Spleen_ADT


title: Control, differentiated enteroids, rep-4

description:
gene_fpkm.xls
gene_count.xls

value: Control


title: 438-2_34854_Liver_TCR


title: Control, differentiated enteroids, rep-2

description:
gene_fpkm.xls
gene_count.xls


title: 438-2_34854_Liver_GEX


title: MYO5B(G519R) mutant, differentiated enteroids, rep-2

description:
gene_fpkm.xls
gene_count.xls


title: 438-2_34854_Liver_HTO


title: Control, differentiated enteroids, rep-3

description:
gene_fpkm.xls
gene_count.xls


title: 438-18_35958_PLN_TCR


title: MYO5B(G519R) mutant, differentiated enteroids, rep-3

description:
gene_fpkm.xls
gene_count.xls


title: 438-2_34854_Liver_ADT


title: 438-18_35958_PLN_GEX


title: C1_male_NASH

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

data_processing:
Sequencing libraries were processed and aligned to the mm10 assembly using Space Ranger 1.2.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: csv file with barcode coordinates
Supplementary files format and content: low- and high-resolution images of tissue
Library strategy: spatial transcriptomics

source_name: liver

extract_protocol:
Five mm liver tissue samples were rinsed with phosphate buffered saline (PBS), embedded in optimal cutting temperature (OCT) medium (Tissue-Tek®), and snap frozen in liquid nitrogen-cooled isopentane. Samples were stored in −80°C prior to use in the spatial transcriptomics workflow.
Spatial transcriptomics libraries were prepared using the Visium Spatial Tissue Optimization slide and reagents from 10x Genomics.

treatment_protocol: Male C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet for 16 weeks.

value: male

value: liver

value: NASH


title: D1_male_NASH


title: Batch3 - HTO

data_processing:
Illumina base call (bcl) files for the samples were converted to fastq files and aligned to the mm10 pre-mRNA assembly using CellRanger 3.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
The top left lobe of the liver was removed and flash-frozen in liquid nitrogen and stored at −80°C until sample processing. Single-nucleus pools from frozen livers were generated with several modifications. Briefly, frozen tissue was dounce homogenized with 10 strokes of the loose pestle followed by 10 strokes with the tight pestle at 4 °C in a low sucrose buffer (0.32 M sucrose, 10 mM HEPES (pH 7.5), 5 mM CaCl2, 0.1 mM EDTA, 3 mM MgAc, 1 mM DTT) with 0.1% Triton X-100 added. The crude nuclei prep was gently mixed with additional low sucrose buffer and was subsequently passed over a pre-wet 30 μm strainer. The filtered crude nuclei prep was centrifuged at 2613 × g for 10 min at 4°C. Supernatant was decanted and the pellet was re-suspended in low sucrose buffer. An additional homogenization step using a TissueRuptor II (Qiagen Inc.) set to the lowest power was completed on each sample for 15 s. High sucrose buffer (1 M sucrose, 10 mM HEPES (pH 7.5), 3 mM MgAc, 1 mM DTT) was then layered underneath the crude prep. The crude prep was centrifuged for 25 min at 2613 × g at 4°C. The supernatant was decanted and re-suspended in resuspension buffer, 1% BSA in PBS with 0.2 U/μL of Ambion RNase Inhibitor (Invitrogen, Cat:AM2684), and transferred to a low-bind conical tube. The nuclei were washed of any residual sucrose by centrifugation at 500 × g for 5 min at 4°C. The pellet was re-suspended in PBS containing 20 μg/mL Fc Block CD16/CD32 (Biolegend, Cat: 101301) and incubated for 5 min at 4 °C. 0.5 μg of a nuclear hashing antibody (10 μg/ml) was added to each sample and incubated for 30 min at 4 °C. Nuclei were washed three times and finally counted using a Countess Automated Cell Counter (ThermoFisher).
Two pools of nuclei were generated each containing 40,000 nuclei from samples of the four experimental groups. Nuclear hashtag antibodies used included anti-Nuclear Pore Complex Proteins Hashtag Antibodies 1–4 (BioLegend, Catalog numbers: TotalSeq-A0451, TotalSeq-A0452, TotalSeq-A0453, TotalSeq-A0454). The 10X Chromium controller (10X Genomics) with v3 chemistry was used to capture, barcode and prepare single-nucleus libraries from each pool of nuclei as per manufacturer’s instructions. The resulting libraries were sequenced on a full lane of an Illumina NovaSeq 6000 S2 flow cell for average depths of 9–10 k reads per nucleus depending on the 10X batch.

treatment_protocol: Male and female C57BL/6J mice were fed fructose-palmitate-cholesterol (FPC-NASH) diet or standard chow (SC) for 16 weeks.

value: pooled male and female

value: multiplexed NASH and Chow


title: 438-18_35958_PLN_HTO


title: Batch2 - HTO


title: 438-18_35958_MesLN_HTO


title: Batch3 - GEX


title: Batch2 - GEX


title: 438-18_35958_PLN_ADT


title: 438-18_35958_MesLN_TCR


title: 438-18_35958_MesLN_GEX