title: HepG2 siIGF2BP3 RPF rep1

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed by Cutadapt to remove low-quality bases and adapters then aligned to the human genome (hg38) using STAR.
Reads on each gene were counted using featureCounts.
Assembly: hg38
Supplementary files format and content: Counts
Library strategy: Ribo-seq

source_name: Liver

growth_protocol: HepG2 cell lines were grown in DMEM (Gibco, 11995) media supplemented with 10% FBS and 1% 100X Pen/Strep (Gibco). Cells were cultured at 37 °C under 5.0% CO2.

extract_protocol:
The cell was added with 0.4 mL lysis buffer (20 mM Tris-HCl pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 1 mM DTT, 0.1 mg/mL cycloheximide, 0.1 U/µL Invitrogen Turbo DNase). The cell was scraped and collected into 1.5 mL tubes, and then incubated on ice with periodic inversions for 10 min. The lysate was clarified by centrifugation for 10 minutes at 20,000 xg at 4 °C. 0.3 mL supernatant was transferred to a fresh tube. 300 U of RNAse I was added and the lysate was incubated at room temperature for 45 min. Afterwards, 15 μL Invitrogen SUPERase·In™ RNase Inhibitor (20 U/μL) to stop this reaction. The 0.3 mL of lysate was transferred to a prewashed MicroSpin S-400 column (Sigma: Microspin™ S-400 HR). The column was centrifuged at 600xg for 2 min to collect flow-through. Zymo RNA Clean & Concentrator Kit was used to purify RNA. The 28-30 nt RPFs (Ribosome-protected fragments) were excised from 10% TBU gel and recovered by ZR small-RNA™ PAGE Recovery Kit.
The RPFs were end-repaired to have a 5’-phosphate and 3’-OH by T4 PNK treatment. The rRNA depletion was performed using customed antisense biotin-labeled DNA oligo. The library was prepared by NEB small RNA library preparation kit.

treatment_protocol: Two days after transient knockdown of IGF2BP3 in HepG2 cell in six-well plate, cycloheximide was added with the final concentration of 100 μg/mL. The HepG2 cell was incubated at 37 °C for 4 min. The cells were washed twice with 0.5 mL DPBS with 100 μg/mL cycloheximide.

value: Liver

value: epithelial-like

value: IGF2BP3 knockdown


title: HepG2 siIGF2BP3 RPF rep3

status: Public on Jul 13 2024

type: SRA

city: Shanghai

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: HepG2 siControl RPF rep3

value: control knockdown


title: Hela 3

city: Dalian

first: lingxi

last: tian

state: liaoning

address: lingshui street

institute: Dalian University of Technology

data_processing:
Illumina Casava software used for basecalling
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired_x0002_end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice
Quantification of gene expression level:The raw counts were first normalized using TPM (Zhou et al., 2010 ) Normalized expression level = ( readCount* 1,000,000 ) / libsize (libsize is the sum of circRNA readcount) .
http://circbase.org/
Assembly: GRCh38
Supplementary files format and content: Readcount_TPM text file include TPM values for each sample
Supplementary files format and content: TPM_interval text file include FPKM_Interval for each sample

source_name: Hela 3_1

extract_protocol:
RNA was collected using RNeasy mini plus kit (Qiagen). A total amount of 2 μ g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed and rRNA free residue was cleaned up by ethanol precipitation. the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per µg of RNA, and then used for the construction of sequencing libraries.
The sequencing libraries for RNA-Seq were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’ s recommendations.

value: Hela 3_1

value: Cervical cancer cell


title: HepG2 siIGF2BP3 Input rep1


title: Hela 1

source_name: Hela 1_1

value: Hela 1_1


title: HepG2 siIGF2BP3 RPF rep2


title: T293 1_1

value: normal cell


title: HepG2 siIGF2BP3 Input rep2


title: HepG2 siIGF2BP3 Input rep3


title: NIHOVCAR3 3_1

source_name: NIHOVCAR3 3_1

value: NIHOVCAR3 3_1

value: Ovarian cancer cell


title: HepG2 siControl RPF rep1


title: NIHOVCAR3 2_1

source_name: NIHOVCAR3 2_1

value: NIHOVCAR3 2_1


title: RL95-2 1_1

value: Endometrial cancer cell


title: HepG2 siControl Input rep2


title: HepG2 siControl Input rep3


title: HepG2 siControl Input rep1


title: RV1, USP11-WT, IgG

city: Baltimore

first: Majid

last: Pornour

state: MD

address: 655 W Baltimore street

country: USA

institute: University of Maryland

library_source: genomic

data_processing:
Quality of ChIP-seq read were checked with fastqc
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 28, using trimgalore v0.6.6
ChIP-seq reads were aligned to the UCSC human hg19 reference genome and E. coli K12, MG1655 reference genome using Bowtie2 v2.3.5.1. If one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant (--dovetail)
Samples were normalized compare do total reads counts, and BAM files were processed (remove duplicates, sorting, and indexing) using samtools v1.10 and Picard v2.23.9
Processed Bam files were normalized with spike-in normalization method and formatted in the bigWig and bedgraph file format, using Deeptools v3.5.0
Peaks were called uing MACS2 bdgpeakcall v2.2.6 with the significance cut-off p-value <=0.01 and reproducible peaks were generaged from two replicated peaks using IDR v2.0.4.2
Assembly: hg19, K12 MG1655
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: Cells were maintained in RPMI 1640 media supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were incubated at 37C and 5% CO2.

extract_protocol:
Cell nuclei were extracted using nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1 % Triton X-100, 20% glycerol, 1X protease cocktail) and incubated with ConA Beads to absorb nuclei to beads for 10 min at RT. The nuclei-beads were placed in magnet and the supernatant was removed. Antibody buffer and 0.5 μg antibody was added to each sample and incubate overnight at 4°C. After washing the nuclei-beads, 2.5 μl of pAG-NMase was added and incubated for 10 min at RT. After washing, 1 μl of Chromatin Digest additive was added and incubate for 2 hrs at 4°C. Then, stop buffer and 0.5 ng of Spike-in DNA were added and incubate for 10 min at 37 °C. We purified DNA from this using DNA purification kit (EpiCypher).
Using 5 ng of purified CUT&RUN-enriched DNA, we prepared sequencing library using library prep kit for illumine sequencing (E7645, NEB). The library was purified with 1.0 X AMPure beads (Beckman) and library fragment size was checked with Agilent Bioanalyzer.

value: Human prostate cancer cell line

tag: chip antibody

value: IgG (Epicypher, #13-0042)


title: RV1, USP11-CS, IgG


title: RV1,  USP11-CS, AR, rep2

value: AR (millipore, #06-680)


title: RV1, USP11-WT, c-Myc,rep1


title: RV1, USP11-CS, AR, rep1


title: RV1, USP1-WT, AR, rep2


title: RV1, USP11-WT, AR, rep1


title: RV1,USP11-WT, c-Myc, rep2


title: Rv1, USP11-WT, HA-USP11, rep2

value: HA (Epicypher, #13-2010)


title: Rv1, pLvx, HA, rep1


title: Rv1, USP11-CS, HA-USP11, rep2


title: Rv1, pLvx, HA, rep2


title: RV1, USP11-CS, c-Myc,rep2


title: RV1, USP11-KD,  IgG


title: Rv1, USP11-WT, HA-USP11, rep1


title: RV1, pLKO.1, c-Myc, rep2


title: RV1, USP11-KD, c-Myc, rep1


title: RV1, pLKO.1,  IgG


title: RV1, USP11-KD, c-Myc, rep2


title: Rv1, USP11-CS, HA-USP11, rep1


title: RV1, USP11-KD, AR, rep2


title: RV1, USP11-KD, AR, rep1


title: HepG2 siControl RPF rep2


title: RV1, USP11-CS, c-Myc, rep1


title: RV1, pLKO.1, AR, rep2


title: RV1, pLKO.1, AR, rep1


title: RV1-USP11KD-rep2

description: RV1, USP11, rep2

data_processing:
the sequenced reads with low quality or adaptor contamination were removed
Clear reads were mapped to the human reference genome (hg19) using Hisat2 v2.0.5 software
To count the reads numbers mapped to each gene, featureCounts v1.5.0-p3 was used.
The fragments per kilobase of transcript per million mapped reads (FPKM) method was used to estimate expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Rv1 cells were transduced with sh-Control, sh-USP11 lentivirus for 48 hours. Total RNAs were extracted using a total RNA miniprep kit (Sigma-Aldrich, St. Louis, MO).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: USP11 knock down


title: RV1-USP11KD-rep3

description: RV1, USP11, rep3


title: RV1-USP11KD-rep1

description: RV1, USP11, rep1


title: RV1-pLKO.1-rep2

description: RV1, rep2

value: WT


title: RV1-pLKO.1-rep3

description: RV1, rep3


title: RV1-pLKO.1-rep1

description: RV1, rep1


title: FOXP4_siRNA2_NCI_N87

city: Hong Kong

first: Bonan

last: Chen

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Trimmed sequence reads were mapped to GrCh38/hg38 using lab server.
Read count extraction and normalization were performed using lab server.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using RNA Extraction Kits (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: gastric cancer cell

value: Knockdown

tag: treatment

value: Lipofectamine™ 2000 Transfection


title: HepG2 WDR4 PARCLIP rep2

data_processing:
Reads were mapped using bowtie with ‘-v 3 -m 10 –best –strata’ parameters. Peaks were called using PARalyzer software.
Assembly: hg38
Supplementary files format and content: peaks
Library strategy: PARCLIP

extract_protocol:
3 volumes of the lysis buffer (50 mM HEPES, pH 7.5; 150 mM KCl; 2 mM EDTA; 0.5% (v/v) NP-40, with 1:100 protease inhibitor (Roche) and 40 U ml-1 RNasin® Ribonuclease Inhibitors (Promega) added freshly) was added to the cell pellet and incubated on ice for 10 min with periodic perturbation. The cell lysate was then centrifuged at 15,000 g for 15 min and the clear supernatant was collected. RNase T1 (1,000 U µL-1, Thermo Fisher Scientific) was added to the clear lysate to a final concentration of 0.1 U µL-1 and an incubation at room temperature was performed for 15 min. The reaction was then quenched on ice. After 5 min, antibodies were added to each sample (5 µg or according to the manufacturer’s protocols). The antibody and the lysate were incubated at 4 °C for 2 hours under periodic rotation. Protein A beads or protein G beads (Thermo Fisher Scientific) were washed (50 µL for each sample, or adjusted to the antibodies amount) with IP wash buffer (50 mM HEPES, pH 7.5, 300 mM KCl, 0.05% (v/v) NP-40, with 1:100 protease inhibitor (Roche) and 40 U ml-1 RNasin® Ribonuclease Inhibitors (Promega) added freshly) for 2 times. The beads were resuspended in 50 µL lysis buffer for each sample and added to the antibody-lysate mixture subsequently. Another two-hour incubation at 4 °C was performed with low-speed rotation. After the incubation, the beads were washed three times with IP wash buffer (50 mM HEPES, pH 7.5, 300 mM KCl, 0.05% (v/v) NP-40, with 1:100 protease inhibitor (Roche) added freshly) and then resuspended with 200 µL IP wash buffer per sample. The beads were treated with a second round of RNase T1 digestion under a final concentration of 10 U µL-1 for 15 min at room temperature. The reaction was then quenched with the addition of 10 µL SUPERase-In followed by a 5-min incubation on ice. The beads were washed three times with high-salt wash buffer (50 mM HEPES, pH 7.5, 500 mM KCl, 0.05% (v/v) NP-40, with 1:100 protease inhibitor (Roche) added freshly) and twice with 1X PNK buffer (NEB) afterward. The beads were resuspended with 200 µL of 1X PNK buffer (NEB) and underwent T4 PNK (Thermo Fisher Scientific) end repair with standard procedures as previously mentioned under 37 °C. After the incubation, the beads were washed once with 1X PNK buffer followed by proteinase K digestion as described before. The RNA was recovered with RNA Clean & Concentrator (Zymo Research) before library construction.
Libraries were constructed followed the commerical protocol for NEBNext Small RNA Library Prep Set for Illumina (NEB).
All libraries were sequenced on Illumina Nova Seq with single-end 100 bp read length.

treatment_protocol: Eight 15-cm plates of HepG2 cells were seeded for each replicate and grown to 80% confluency before the addition of 4 µL 1 M 4SU to each plate. After a 14-hour incubation, the media was aspirated; the cells were washed once with 5 ml ice-cold PBS for each plate and crosslinked by 0.15 J cm-2 365 nm UV light twice when on ice. The crosslinked cells were collected with cell lifters.

value: Liver

value: epithelial-like

value: wildtype


title: FOXP4_siRNA1_NCI_N87


title: HepG2 IGF2BP3 PARCLIP bio2 rep1


title: HUVEC, LVCON, H2O2

city: Changsha

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HUVEC

growth_protocol: HUVECs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Oxidative stress was induced by treatment of H2O2 (Sigma) for 24h,

value: HUVEC

value: Human Umbilical Vein Endothelial Cells


title: RV1, pLKO.1, c-Myc, rep1


title: HUVEC, LVZNF667, H2O2

value: ZNF667 overexpression


title: HepG2 METTL1 PARCLIP rep1


title: HUVEC, LVZNF667

value: PBS


title: HUVEC, LVCON


title: flg22 treated plant 24h bio rep 4

city: Girona

first: Luis

middle: Alejandro

last: Moll Dos Santos

state: Catalonia

address: Pic de Peguera 15, Edifici Jaume Casademont

department: Department of Chemical and Agricultural Engineering and Agrifood Technology

country: Spain

institute: University of Girona

description:
flg22-NH treated plant at 24hpt, biological replicate 4
flg22_24h_D

data_processing:
Illumina CASAVA v1.8.2 was used for base-calling
Raw sequence files were subjected to quality control analysisis using FastQC v0.10.1
Raw sequence files were trimmed and adapters were removed with BBDuk (minimum base quality of 25 and a minimum read length of 35 bp)
Reads were mapped against the Prunus dulcis genome with STAR v2.6
Raw expression counts were obtained with FeatureCounts v1.6.1 for each annotated gene using only uniquely mapping reads (MAPQ ≥ 30).
Assembly: PRJDB7547
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Prunus dulcis

source_name: leaf

growth_protocol: All plants were maintained in 0.8 liter pots (sphagnum peat with wood fiber (10%), calcium carbonate (9 g/liter), NPK fertilizer (1 Kg/m3) and microelements) in an environmentally controlled greenhouse at 25±2ºC (day) and 18±2ºC (night), with a minimum relative humidity of 60%, and with a photoperiod of 16 h light and 8 h dark. Prior and during the experiments, plants were watered to saturation every three days, and fertilized with a 200 ppm solution of NPK (20:10:20) once a week.

extract_protocol:
Sampling was carried out 6 and 24 hpt and for each replicate 20 leaves were pooled (4 leaves/plant) and they were immediately frozen in liquid nitrogen. The material was finely grounded and homogenized with a Tissue Lyser II. RNA was extracted from 100 mg of the grounded leaf material coming from each replicate using the PureLink™ Plant RNA Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s instructions. The remaining DNA was digested with the TURBO DNA-freeTM Kit (Invitrogen Life Technologies, Carlsbad, CA, USA).
RNA “TruSeq Stranded mRNA Sample Prep kit” (Illumina, San Diego, CA) was used for library preparation following the manufacturer’s instructions, starting with 1-2 µg of good quality RNA (RIN > 7) as input. The RNA was fragmented 3 min at 94°C and every purification step was performed using 0.81X Agencourt AMPure XP beads. Both RNA samples and final libraries were quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies, Santa Clara, CA, USA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on paired-end (2x150 bp, 30M reads per sample) at the multiplexing level requested on NovaSeq6000 (Illumina, San Diego, CA, USA).

treatment_protocol: The effect of the peptide flg22-NH2 on P. dulcis cv. Avijor transcriptome response was assessed by applying the peptide by two application systems, by spray and microinjection. Each plant was injected with 10 µL of flg22-NH2 at 20 mM , and subsequently sprayed with 2 mL of the peptide at 125 µM using an airbrush. The experimental design consisted of four replicates of five plants per treatment. Plants treated with water were used as untreated controls.

value: leaf

tag: cultivar

value: Avijor

tag: time (hour)

value: Treated with flg22


title: flg22 treated plant 24h bio rep 3

description:
flg22-NH treated plant at 24hpt, biological replicate 3
flg22_24h_C


title: HepG2 IGF2BP3 PARCLIP rep2


title: HepG2 IGF2BP3 PARCLIP rep1


title: flg22 treated plant 24h bio rep 2

description:
flg22-NH treated plant at 24hpt, biological replicate 2
flg22_24h_B


title: HpeG2 IGF2BP2 PARCLIP rep2


title: flg22 treated plant 24h bio rep 1

description:
flg22-NH treated plant at 24hpt, biological replicate 1
flg22_24h_A


title: FOXP4_siScramble_NCI_N87


title: HepG2 IGF2BP1 PARCLIP rep2


title: Non-treated plant 24h bio rep 3

description:
Non-treated control at 24 hpt, biological replicate 3
CNT_24h_C

value: Treated with water


title: HepG2 IGF2BP3 PARCLIP bio2 rep2


title: HpeG2 IGF2BP2 PARCLIP rep1


title: HepG2 IGF2BP1 PARCLIP rep1


title: HepG2 WDR4 PARCLIP rep1


title: Non-treated plant 24h bio rep 2

description:
Non-treated control at 24 hpt, biological replicate 2
CNT_24h_B


title: In Vivo A375 CAR BC Library

city: Cambridge

first: Caleb

middle: R

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

description: CAR library harvested and sequenced from A375 flank tumors on day 10 post-treatment. Tumors from individual mice were stained with different hashing antibodies to allow deconvolution of biological replicates in sequencing space. Tumors were also stained with a panel of CITE-seq antibodies specific for T cell phenotypic markers

data_processing:
Reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), and a cell–feature matrix was generated using the CellRanger pipeline (10X Genomics; v6.1.2–7.0.1). Downstream analysis was performed using the Seurat package (v4.3.0.1)
Initial filtering of low-quality cells was done on the basis of mitochondrial gene content and number of unique genes detected, with thresholds set in a dataset-specific manner based on distributions of each metric; ultimately, cells with greater than 5–10% of reads mapped to mitochondrial genes or less than 1000–2500 unique genes were filtered out. For cells stained with a sample-specific hashing antibody, samples were demultiplexed based on antibody hash reads using the HTODemux algorithm, as described previously and implemented in Seurat. Lastly, cells were assigned to specific CAR variants on the basis of CAR BC reads using the MULTIseqDemux algorithm with auto-thresholding, as described previously and implemented in Seurat. For all datasets described in this study, only cells assigned to a single CAR by the MULTIseqDemux algorithm were analyzed, with any cells assigned as negatives or multiplets filtered out. The processed data files available here report cell-feature matrices following this filtering.
Assembly: GRCh38
Supplementary files format and content: Fastq files from both 10X lanes were processed using the CellRanger pipeline to generate cell-feature matrices of UMI counts for GEX, FB, and CARBC libraries. The matrices are provided in sparse matrix format as a single filtered_feature_bc_matrix.tar.gz file.

molecule: polyA RNA

source_name: Lymphocyte

extract_protocol:
Human primary CD3+ T cells were lentivirally transduced to express a library of 35 distinct CAR architectures, then subjected to various tumor perturbations. Live CAR T cells were enriched via FACS prior to scRNA-seq
Cells were encapsulated via Chromium Next GEM Single Cell 5' kit v2. Gene expression (GEX) and feature barcoding (FB) libraries were constructed based on manufacturer's instructions. To generate CAR BC libraries, we used a nested PCR strategy similar to that used for enrichment of TCR transcripts in the generation of scRNA-seq VDJ libraries. In brief, the fraction of cDNA containing full-length transcripts was input into an initial round of PCR, with a universal forward primer that binds upstream of the cell barcode on all transcripts and an “outer” CAR-specific reverse primer. This PCR product was cleaned using a 0.5/1X SPRI selection. This was then input into a second PCR reaction to further enrich for CAR BCs, using the same universal forward primer and an “inner” CAR-specific reverse primer upstream of the original, which also includes Illumina adapters for downstream indexing and sequencing, following the same protocol as the 10X gene expression libraries.
scRNA-seq, CITE-seq

value: Lymphocyte

value: Primary T cell

value: T cell

tag: donor id

value: A375 in vivo tumor challenge


title: Non-treated plant 24h bio rep 1

description:
Non-treated control at 24 hpt, biological replicate 1
CNT_24h_A


title: HepG2 METTL1 PARCLIP rep2


title: In Vivo A375 GEX Library

library_source: transcriptomic single cell


title: flg22 treated plant 6h bio rep 2

description:
flg22-NH treated plant at 6hpt, biological replicate 2
flg22_6h_B


title: Pooled A375 GEX Library

description: CAR library challenged with A375 in vitro in pool on days 0, 3, and 5, then sequenced on day 7.

value: A375 rechallenged (pooled)


title: flg22 treated plant 6h bio rep 1

description:
flg22-NH treated plant at 6hpt, biological replicate 1
flg22_6h_A


title: flg22 treated plant 6h bio rep 3

description:
flg22-NH treated plant at 6hpt, biological replicate 3
flg22_6h_C


title: Pooled NALM6 GEX Library

description: CAR library challenged with NALM6 in vitro in pool on days 0, 3, and 5, then sequenced on day 7.

value: NALM6 rechallenged (pooled)


title: Auricularia auricula-judae 200 Gray treated group

city: Yesan

first: Jeong Heon

last: Kim

address: 54-46 Daehak-ro, Yesan-eup, Yesan-gun, Chungcheongnam-do

country: South Korea

institute: Kongju national university

description: Sample 2-2

data_processing:
Assembly was performed using the Trinity v2.15.1 program
CDS prediction was performed using the TransDecoder v5.7.1 program
To predict the functions of the assembled unigenes and the predicted CDS, NCBI Blast 2.2.28+ with the NCBI Non-redundant (nr) database (2013-07-17) and InterProScan v5 were utilized
Assembly: Trinity v2.15.1 program
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Auricularia auricula-judae

source_name: Fruit body of mushroom

growth_protocol: Auricula auricula-judae is cultured in PDA at 25°C for 14 days, exposed to gamma radiation or not, and then inoculated into a sawdust medium mixed with sawdust and rice bran in an 8:2 (w/w) ratio. After growing the mycelium at 25°C for 30 days, the fruit body is grown by adjusting the temperature to 18°C and humidity to 90%.

extract_protocol:
RNA was extracted from the homogenized fruit bodies using the Ribospin II RNA purification kit (GeneAll Biotechnology, Seoul, Korea). 1,000 ng of total RNA was used of the construction of sequencing libraries.
cDNA was synthesized using the cDNA synthesis kit (BIOFACT, RT PRE-MIX, Daejeon, Korea).

treatment_protocol: 200 Gray gamma radation

value: Fruit body of mushroom

value: 200 Gray Gamma radiation treated


title: Pooled A375 CAR BC Library


title: Pooled NALM6 CAR BC Library


title: Non-treated plant 6h bio rep 4

description:
Non-treated control at 6 hpt, biological replicate 4
CNT_6h_D


title: Resting CAR BC Library

description: CAR library sequenced at rest, in the absence of antigen.

value: Unstimulated


title: Non-treated plant 24h bio rep 4

description:
Non-treated control at 24 hpt, biological replicate 4
CNT_24h_D


title: Auricularia auricula-judae Non treated group

description: Sample c-2

value: Non treated


title: Non-treated plant 6h bio rep 3

description:
Non-treated control at 6 hpt, biological replicate 3
CNT_6h_C


title: Arrayed NALM6 D2 CAR BC Library

description: CAR library challenged with NALM6 in vitro in array on days 0, 3, and 5, then combined and sequenced in pool on day 7.

value: NALM6 rechallenged (arrayed)


title: Resting GEX Library


title: Arrayed NALM6 D2 GEX Library


title: Non-treated plant 6h bio rep 2

description:
Non-treated control at 6 hpt, biological replicate 2
CNT_6h_B


title: In Vivo A375 FB Library

library_source: other

molecule: protein


title: B_I593T

city: Cincinnati

first: Stanley

last: DeVore

state: Ohio

address: 3333 Burnett Ave

department: Division of Asthma Research

institute: CCHMC

data_processing:
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
Raw reads were mapped to hg19 version of Human genome
CSBB uses fastqc for quality check, Boiwtie2 for mapping and MACS2 for peak calling
RNA sequencing analysis including count normalization were performed in R using DESeq2.
Assembly: hg19
Supplementary files format and content: Comma-Separated Values file includes raw count data for each sample.

source_name: HaCaT

growth_protocol: CARD14-deficient HaCaT keratinocytes  were grown in DMEM with low glucose, GlutaMAX supplement, and pyruvate supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic at 37 ⁰C at 5% CO2.

extract_protocol:
24 hours after transfection, cells were trypsinized and sorted for positive GFP expression by the Cincinnati Children’s Research Flow Cytometry Facility, and RNA extracted using the mirVana RNA extraction kit.
RNA libraries were prepared using theNEBNext Single Cell/Low Input RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The day after plating into 10 cm dishes, keratinocytes were transfected with the appropriate plasmid (9 ug) and media changed after 2 hours.

value: HaCaT

value: keratinocyte

value: CARD14 KO

value: CARD14-I593T-T2A-eGFP plasmid


title: B_N737H

value: CARD14-N737H-T2A-eGFP plasmid


title: B_R820W

value: CARD14-R820W-T2A-eGFP plasmid


title: CD4 Spike-In CAR BC Library

description: Pilot study to assess CAR BC accuracy at library scale. Antigen-stimulated CD4 cells expressing an alternatively barcoded BBz (AltBBz) were spiked into unstimulated CD8 cells expressing the full library of barcoded CAR variants at ~5%.

value: Lymphocyte

value: CD8s unstimulated, CD4s stimulated


title: Arrayed NALM6 D1 CAR BC Library

value: Primary T cell

value: T cell


title: flg22 treated plant 6h bio rep 4

description:
flg22-NH treated plant at 6hpt, biological replicate 4
flg22_6h_D

value: leaf

value: Avijor

value: Treated with flg22


title: CD4 Spike-In GEX Library


title: Non-treated plant 6h bio rep 1

description:
Non-treated control at 6 hpt, biological replicate 1
CNT_6h_A

value: Treated with water


title: Arrayed NALM6 D1 GEX Library


title: B_WT

value: CARD14-WT-T2A-eGFP plasmid


title: D45_ATAC_Library

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

data_processing:
The  scRCAT-seq2  data  were  processed  using  zUMIs  v2.9.4f  for  UMI  identification,  and  full-length  transcriptome  assembly  and  construction  were  performed.  For  scRNA-seq  and  scATAC-seq  data,the demultiplexing,barcoded processing,gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: hg38
Supplementary files format and content: text file and matrix files

source_name: human retinal organoids

extract_protocol:
hESCs: Digest hESCs cells with Accutase at 37℃ for 15-30 min, remove the culture medium after centrifugation, resuspend the cells in PBS containing 0.04% bovine serum albumin to obtain a single-cell suspension.  Organoids: On day 45, we dissociated these organoids into single-cell suspensions by treating them with Accutase at 37°C for 30 minutes. The suspensions were then filtered through a 35-μm cell strainer, and the cells were resuspended in PBS containing 0.04% bovine serum albumin.
hESCs:  The scRCAT-seq2 method encompasses the following steps: (1) Labeling the ends of individual RNA/cDNA molecules with a tag (barcode); (2) Creating a circular cDNA through end-to-end ligation; (3) Performing circular amplification to generate multiple copies of full-length cDNA, each with an identical tag; (4) Fragmenting the full-length cDNA by randomly inserting Tn5 transposes around the ligated ends; (5) Constructing libraries and conducting paired-end sequencing on the resulting fragments; (6) Integrating short reads with the same molecule tag to identify key features of full-length transcripts, such as transcription start sites (TSS), transcription end sites (TES), and specific exons (Detailed instructions can be found in the Methods section of the article). Organoids:  We used the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit from 10x Genomics, following the manufacturer's protocol to generate cDNA and scATAC library. 10 μL of cDNA is mixed with 1 μL of 10 µM read1 primer, 1 μL of 10 µM TSO-read1 primer, 15 μL of KAPA HiFi HotStart ReadyMix (2x), and the volume is supplemented with Nuclease Free Water to reach 30 μL. The reaction proceeds as follows: 98 ℃ for 3 min, 6-10 cycles of 98 ℃ for 20 s, 60 ℃ for 20 s, and 72 ℃ for 90 s, followed by 72 ℃ for 5 min. After purification using 1x AMPure XP beads, the resulting product is eluted with 10 μL Nuclease Free Water to obtain cDNA suitable for scRCAT-seq2. The TSS and TES library construction can be performed by replacing the corresponding primers in the 10x Genomics Chromium protocol.

value: human retinal organoids


title: scRCAT_seq2_D45_1


title: D45_cDNA_Library


title: A_N737H


title: scRCAT_seq2_ES_SIRV_4

source_name: hESCs

value: hESCs


title: scRCAT_seq2_ES_SIRV_5


title: scRCAT_seq2_ES_SIRV_6


title: A_R820W

value: HaCaT


title: scRCAT_seq2_ES_SIRV_2


title: DICER-WT sh22bp replicate 2

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

institute: The Hong Kong University of Science and Technology

data_processing:
The sequencing reads of mRNA were also adapter-trimmed by cutadapt (Martin 2011) (-a AGATCGGAAGAGCACACGTCT for Read 1 and -a GATCGTCGGACTGTAGAACTCTGAAC for Read 2).
Processed pair-end reads were then joined by using fastq-join (Aronesty 2013), and low-quality reads were then discarded by using fastq_quality_filter (-q 30 -p 90) (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
Reads are then mapped to human genome reference (GRCh38) using bowtie2 (bowtie2 --local --score-min L,-4,2 --ma 2 -k 5) (Langmead and Salzberg, 2012).
miRNA genomic coordination file was obtained from miRBase v22 (Kozomara et al., 2019), and annotation of the mapped reads was done by using bedtools intersect (Quinlan A.R. and Hall I. M., 2010).
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

source_name: HCT116 DICER-KO

growth_protocol: The HCT116 DICER-KO cells were cultured in McCoyʼs 5A medium (Gibco, 16600082) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
Transfected cells were harvested 48 h post-transfection and total RNA was extracted using Trizol (Ambion, #15596018). Small RNA fractions were obtained from 10 µg of total RNA by using 12% urea-gel and IPA precipitation. The small RNA sequencing libraries were constructed by using the TruSeq Small RNA Library Prep Kits (Illumina). The DNA libraries of small RNAs were sequenced by Illumina Nextseq 6000. The concentration and size distribution of the DNA libraries were examined by Qubit dsDNA HS Assay Kit (Invitrogen, #Q32854) and Fragment Analyzer system, respectively. Finally, the examined DNA libraries were subjected to the next-generation sequencing (NGS).

treatment_protocol: Cells were transfected with pXG-DICER-WT, pXG-DICER mutant and construct expressing pri-miRNAs or shRNAs using Lipofectamine 3000.

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-WT and pU6-sh22bp plasmid


title: A_WT

value: keratinocyte

value: CARD14 KO


title: scRCAT_seq2_ES_SIRV_1


title: human neutrophils,rtPA+HRG4

city: Tianjin

first: Wei

last: Jiang

address: 154 Anshan Road，Heping District

institute: Tianjin Medical University General Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot  Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)  according to the manufacturer’s instructions. After cluster generation, the library  preparations were sequenced on an Illumina Novaseq platform and 150 bp  paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastp  software. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from  raw data. At the same time, Q20, Q30 and GC content the clean data were  calculated. All the downstream analyses were based on the clean data with  high quality
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to  each gene. And then FPKM of each gene was calculated based on the length  of the gene and reads count mapped to this gene.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: files includes raw counts for each sample
Supplementary files format and content: file include FPKM values for each sample

source_name: Peripheral blood

growth_protocol: It was isolated from human peripheral blood

extract_protocol:
RNA was purified using TRIzol reagent (Ambion, Grand Island, NY, USA) according to the manufacturer’s protocol.Total RNA was uesd for construction of  sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The neutrophils cultured with PBS, rt-PA, and rt-PA+HRG for 2.5 hours

value: Peripheral blood

value: neutrophil

value: rtPA+HRG


title: serum_sedentary_saline-treated_rep6

type: genomic

city: Houston

first: Stan

middle: J

last: Watowich

state: Texas

address: 2450 Holcombe Blvd, Suite J

institute: Ridgeline Therapeutics

description: Biological replicate 6 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)

hyb_protocol: Hybridization was performed following the Illumina protocol.

scan_protocol: The BeadChip was scanned using an iScan to determine DNA methylation following manufacturer directions.

data_processing: SEnsible Step-wise Analysis of Methylation data (SeSAMe) was used to derive beta values for all samples, according to the script at github.com/shorvath/MammalianMethylationConsortium/Manifests and R packages/Archived.RpackagesManifests and R packages/Archived.Rpackages/sesame_1.9.7.tar.gz.

organism: Mus musculus

source_name: sedentary, saline-treated mouse serum (methylated)

label_protocol: AKESOgen then performed bisulfite conversion on at least 150ng of the extracted DNA using a Zymo EZ DNA methylation kit. AKESOgen then used at least 150 nanograms of the total converted DNA and processed it further using Illumina’s Horvath Mammalian Methylation Chip array kit  (a customized Infinium HD iSelect Methyl Custom BeadChip (doi.org/10.1038/s41467-022-28355-z)).

growth_protocol: The left gastrocnemius and serum were collected from approximately 24.5-month-old female C57BL/6N mice. Mice were humanely euthanized via cervical discolacation under deep isoflurane anesthesia.

extract_protocol: DNA was extracted with a Qiagen DNA kit (cat #69504 or 69506) and standard protocols with elution into ultrapure, nuclease-free milliQ water. The Clock Foundation extracted, quantified, and purified the DNA;  purity was assessed via 260/280 absorption ratio.

treatment_protocol: Blood was collected from the heart before cervical dislocation, allowed to clot for ~30 minutes at room temperature, and spun at ~3,000g for 10 minutes and 4oC. The supernatant (serum) was collected and stored -80oC.Muscle was flash-frozen in liquid nitrogen immediately after collection and weighing, and stored -80oC.

tag: strain

tag: Sex

value: female

tag: age at tissue collection

value: ~24.5 months

value: serum

tag: animal id

tag: order in batch

source_name: sedentary, saline-treated mouse serum (unmethylated)


title: serum_sedentary_NNMTi-treated_rep7

description: Biological replicate 7 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)

source_name: sedentary, NNMTi-treated mouse serum (methylated)

source_name: sedentary, NNMTi-treated mouse serum (unmethylated)


title: CD11c+ ABCs, mice

first: Fubin

last: Li

state: Shanghai

address: 280 South Chongqing Road, Shanghai, 200025, China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Alignment of the raw sequencing reads to the mouse reference genome (mm10 version) was accomplished using the HISAT2 RNA-sequencing alignment tool
Processed raw bam files were then employed to derive read counts per gene via HISAT and HTSeq tools
Normalization of these read counts was conducted using the DESeq2 package in R, followed by centering and scaling to compute Z-scores for each gene.
To adjust for multiple testing, P-values were corrected using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: .csv file includes raw counts for each sample
Supplementary files format and content: .csv file includes normalized counts for each sample

source_name: Spleen

extract_protocol:
Total RNA extraction was carried out using TRIzol reagent (Invitrogen). 2ng of total RNA was used for the construction of sequencing libraries.
Samples with RIN>7 were selected for cDNA amplification using the SMART-Seq HT kit (Takara, USA). cDNA samples were further tested using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Samples with right size distribution were selected for sequencing library construction using the TruePrep RNA Library Prep Kit V2 for illumina (Vazyme, China).

value: Spleen

value: splenocytes


title: human neutrophils,rtPA+HRG3


title: Mouse brain, microglia,PBS control, replicate8

city: Kunming

first: Yan

last: Wu

state: Yunnan

address: Xichang Road No. 295

institute: First Affiliated Hospital of Kunming Medical University

data_processing:
Raw sequencing files were demultiplexed with bcl2fastq, reads were aligned using hisat2 (v 2.1.0), the count matrix was generated using htseq-count (v 0.11.2), and differential expression analysis was performed using DESeq2 (v 1.22.2) with standard settings.
Assembly: mmu9
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Brain

extract_protocol:
Microglia (CD11b+/CD45int) were purified. Then, total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion). Ribosome RNA was then digested using the TruSeq Stranded. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

treatment_protocol: EAE mice model was induced by treatment of subcutaneous immunization on the back and foot with 200μl of complete Freund's adjuvant and phosphate buffered saline (PBS) at 1:1, containing 200 μg of myelin oligodendrocyte glycoprotein peptide 35–55 (MOG35-55) (SIGMA, USA) and 200 ng of pertussis toxin (SIGMA, USA) intraperitoneally on days 0, 2 and 7.

value: Brain

value: microglia

value: WT

value: PBS


title: serum_sedentary_NNMTi-treated_rep5

description: Biological replicate 5 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: A_I593T

value: HaCaT

value: CARD14-I593T-T2A-eGFP plasmid


title: Mouse brain, microglia,PBS control, replicate7


title: human neutrophils,rtPA+HRG2


title: scRCAT_seq2_ES_SIRV_3

value: hESCs


title: DICER--D1709A sh2122bp replicate 2

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-D1709A and pU6-sh2122bp plasmid


title: Mouse brain, microglia,PBS control, replicate6


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep7

type: RNA

city: Bethesda

first: Narendra

last: Derek

address: 35 Convent Drive, Room 2A215

department: National Institute of Neurological Disorders and Stroke

institute: National Institutes of Health

description: RNA expression from mouse liver

hyb_protocol: Samples were hybridized using Hybridization Control Kit (Applied Biosystems) according to manufacturer's instructions.

scan_protocol: Affymetrix protocol

data_processing: Raw data was processed with Transcriptome Analysis Console (TAC v4.0.3) using the default settings, which uses a one-way ANOVA corrected with the Benjamini-Hochberg procedure for multiple procedures..

label: biotin

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Applied Biosystems) according to manufacturer's instructions.

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow. Mouse livers dissected from adult mice.

extract_protocol: Mice were genotyped beforehand. All samples were snap frozen in liquid N2. Total RNA were extracted from the frozen samples..

treatment_protocol: ASOs were synthesized at Ionis Pharmaceuticals as previously described (Seth et al, 2010; Shammas et al, 2022). Adult C10wt/wt; Oma1+/– mice were given weekly subcutaneous injections of PBS. Adult C10G58R/wt; Oma1+/– mice were given weekly subcutaneous injections of either a nontargeting (control) ASO or an OMA1-targeting ASOs. The mice were between 10.5 months and 13.5 months old. The ASOs were at a concentration of 5 mg/mL, and injections were dosed at 50 mg/kg. A total of 6 injections were administered per mouse over 6 weeks. Then, the mice were anesthetized with isoflurane and transcardially perfused with PBS, and their tissues were collected and flash-frozen in liquid nitrogen.

tag: age

value: adult

tag: agent

value: liver

value: OMA1 ASO


title: serum_sedentary_saline-treated_rep4

description: Biological replicate 4 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months


title: human neutrophils,rtPA+HRG5

value: Peripheral blood

value: neutrophil

value: rtPA+HRG


title: serum_sedentary_NNMTi-treated_rep4

description: Biological replicate 4 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)

value: serum


title: human neutrophils,rtPA+HRG1


title: Mouse brain, microglia,PBS control, replicate5

value: Brain

value: microglia

value: WT


title: serum_sedentary_NNMTi-treated_rep3

description: Biological replicate 3 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: Mouse brain, microglia,PBS control, replicate4

value: PBS


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep5

description: RNA expression from mouse liver


title: human neutrophils,rtPA5

value: rtPA


title: human neutrophils,rtPA4


title: serum_sedentary_saline-treated_rep5

description: Biological replicate 5 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: serum_sedentary_saline-treated_rep3

description: Biological replicate 3 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: serum_sedentary_NNMTi-treated_rep2

description: Biological replicate 2 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: Mouse brain, microglia,PBS control, replicate3


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep6

description: RNA expression from mouse liver


title: human neutrophils,rtPA3


title: Mouse brain, microglia,PBS control, replicate2


title: Mouse brain, microglia,PBS control, replicate1


title: G58R OMA1+/- liver, treated with control ASO, biological rep5

description: RNA expression from mouse liver

value: control ASO


title: human neutrophils,rtPA1


title: human neutrophils,rtPA2


title: serum_sedentary_saline-treated_rep2

description: Biological replicate 2 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: G58R OMA1+/- liver, treated with control ASO, biological rep4

description: RNA expression from mouse liver


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep4

description: RNA expression from mouse liver


title: human neutrophils,control5


title: serum_sedentary_NNMTi-treated_rep1

description: Biological replicate 1 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: serum_sedentary_saline-treated_rep1

description: Biological replicate 1 of 6. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: Mouse brain, microglia,EAE, replicate7

value: MOG (35-61) and pertussis toxin


title: G58R OMA1+/- liver, treated with control ASO, biological rep3

description: RNA expression from mouse liver


title: muscle_sedentary_NNMTi-treated_rep9

description: Biological replicate 9 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)

source_name: sedentary, NNMTi-treated mouse muscle (methylated)

value: gastrocnemius muscle

source_name: sedentary, NNMTi-treated mouse muscle (unmethylated)


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep3

description: RNA expression from mouse liver

value: adult


title: human neutrophils,control4


title: Mouse brain, microglia,EAE, replicate6

value: MOG (35-60) and pertussis toxin


title: human neutrophils,control3


title: Mouse brain, microglia,EAE, replicate5

value: MOG (35-59) and pertussis toxin


title: muscle_sedentary_saline-treated_rep9

description: Biological replicate 9 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)

source_name: sedentary, saline-treated mouse muscle (methylated)

value: female

source_name: sedentary, saline-treated mouse muscle (unmethylated)


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep2

description: RNA expression from mouse liver

value: liver

value: OMA1 ASO


title: SclSOr_seq_ES_SIRV

value: hESCs


title: G58R OMA1+/- liver, treated with OMA1 ASO, biological rep1

description: RNA expression from mouse liver


title: Mouse brain, microglia,EAE, replicate8

value: MOG (35-62) and pertussis toxin


title: Mouse brain, microglia,EAE, replicate4

value: MOG (35-58) and pertussis toxin


title: human neutrophils,control2

value: Peripheral blood

value: neutrophil


title: human neutrophils,control1


title: KO_NT_c

data_processing:
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
Raw reads were mapped to hg19 version of Human genome
CSBB uses fastqc for quality check, Boiwtie2 for mapping and MACS2 for peak calling
RNA sequencing analysis including count normalization were performed in R using DESeq2.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet file (.xlsx format) includes raw count data for each sample.

growth_protocol: HaCaT keratinocytes of each genotype were grown in DMEM with low glucose, GlutaMAX supplement, and pyruvate supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic at 37 ⁰C at 5% CO2.

extract_protocol:
RNA was harvested and purified using the ReliaPrepr RNA Miniprep System. 1.5 ug of total RNA was provided for the construction of sequencing libraries.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit following manufacturer's protocols.

treatment_protocol: The day after plating, keratinocytes were treated for 24 hours with either mepazine (MALT1 inhibitor; 10 uM) or vehicle (DMSO)

value: HaCaT

value: keratinocyte

value: CARD14 KO

value: Vehicle (DMSO)


title: Mouse brain, microglia,EAE, replicate3

value: Brain

value: microglia

value: WT

value: MOG (35-57) and pertussis toxin


title: G58R OMA1+/- liver, treated with control ASO, biological rep2

description: RNA expression from mouse liver

value: adult

value: control ASO


title: muscle_exercised_saline-treated_rep9

description: Biological replicate 9 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)

source_name: exercised, saline-treated mouse muscle (methylated)

value: female

value: ~24.5 months

value: gastrocnemius muscle

source_name: exercised, saline-treated mouse muscle (unmethylated)


title: muscle_sedentary_saline-treated_rep8

description: Biological replicate 8 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: R820W_M_c

source_name: HaCaT

value: Mepazine


title: HepG2 m6A-IP rep2

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters.
Mapped reads were separated by strands with samtools (version 1.9)
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: MeRIP-Seq

source_name: Liver

extract_protocol:
Total RNA was isolated from HeLa cells with TRIzol reagent. Poly(A)+RNA was further enriched from total RNA by using Dynabeads™ mRNA Purification Kit (Invitrogen).m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
All libraries were sequenced on Illumina Nova Seq with single-end 100 bp read length.

value: Liver

value: epithelial-like

value: wildtype

tag: fraction


title: Mouse brain, microglia,EAE, replicate2

tag: tissue

value: MOG (35-56) and pertussis toxin


title: HepG2 m6A-IP rep1

tag: cell line


title: R820W_NT_c

value: HaCaT

tag: cell type

value: keratinocyte


title: Mouse brain, microglia,EAE, replicate1

tag: genotype

value: MOG (35-55) and pertussis toxin


title: WT_M_c

value: CARD14 WT/WT


title: muscle_exercised_saline-treated_rep10

description: Biological replicate 10 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)


title: muscle_sedentary_NNMTi-treated_rep8

description: Biological replicate 8 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: muscle_sedentary_saline-treated_rep7

description: Biological replicate 7 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: WT_NT_c

value: Vehicle (DMSO)


title: HepG2 Input rep2

value: Input


title: HepG2 Input rep1


title: KO_NT_b

value: CARD14 KO


title: HepG2 siIGF2BP3 6h rep2

data_processing:
Raw reads were trimmed by Trimmomatic-0.39 to remove low-quality bases and adapters,
Reads were aligned to the human genome (hg38), together with ERCC RNA spike-in control (Thermo Fisher Scientific) using HISAT2 (version 2.1.0) with ‘--rna-strandness RF -k 5’ parameters.
Assembly: hg38
Supplementary files format and content: text files include read counts for each Sample

extract_protocol:
Generally, to isolate total RNA from cells, the media was aspirated, and the cells were washed once with a proper volume of ice-cold DPBS buffer for each plate. Then total RNA was isolated from cells with TRIzol reagent (Invitrogen) and then extracted following the manufacturer’s protocol through isopropanol precipitation. GlycoBlue Coprecipitant (15 mg ml-1, Thermo Fisher Scientific) was added to the solution during precipitation if needed. Sample collection: five 10-cm plates of HepG2 cells were transfected with IGF2BP1-3 siRNA or METTL1 siRNA or control siRNA at 30% confluency. After 6 h, each 10-cm plate was re-seeded into three 6-cm plates, and each plate was controlled to afford the close numbers of cells. After 48 h, actinomycin D was added to 5 μg ml–1 at 6 h, 3 h, and 0 h before collection. The total RNA was purified with TRIzol (Invitrogen) described before. ERCC RNA spike-in control (Ambion) was added to each sample (0.02 µl per 1 µg total RNA). The total RNA with spike-in controls were then purified to acquire mRNA.
Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
All libraries were sequenced on Illumina Nova Seq with single-end 100 bp read length.

treatment_protocol: AllStars negative control siRNA from Qiagen (1027281) was used as control siRNA in knockdown experiments. IGF2BP1-3 siRNAs were ordered from Dharmacon as pre-desgined. Transfection was achieved by using Lipofectamine RNAiMAX (Invitrogen) for siRNA following the manufacturer’s protocols.

value: IGF2BP3 knockdown

value: actinomycin D treatment

tag: time point

value: 6 hour


title: Primary myotubes, EDA-A2, 24hrs, rep1

city: Sarıyer

first: Samet

last: Agca

state: İstanbul

address: Rumelifeneri Yolu

department: Graduate School of Sciences and Engineering

country: Turkey

institute: Koc University

data_processing:
The quality check of the raw and trimmed data was performed with FastQC (v.0.11.9) and MultiQC (v1.12).
Adaptor sequences and poor-quality sequences were removed with trimGalore (v0.6.5).
Mouse genome index (GRCm39) was created with STAR (v2.7.3a) using genomeGenerate run mode.
Trimmed sequences were mapped onto this index using STAR alignReads run mode. Quality check of alignments was performed with qualimap (v.2.2.1).
Alignments were quantified using HTSeq-count (v0.11.1) Python package.
Assembly: GRCm39
Supplementary files format and content: Contains count values for each sample in txt format

source_name: primary myotubes

growth_protocol: Mouse primary myoblasts were isolated from limb muscles of pups (2-3 days old) and cultured in Ham’s F-10 nutrient mixture (Invitrogen) with 20% FBS (Invitrogen) supplemented with 2.5 ng/ml basic fibroblast growth factor (bFGF) (Sigma) and penicillin/streptomycin (Invitrogen). Myoblasts were then transferred to DMEM (Sigma 5796) supplemented with 5% horse serum and penicillin/streptomycin (Invitrogen) for differentiation.

extract_protocol:
Cells were harvested 72hrs after differentiation. Total RNA was isolated and DNase-treated using Qiazol reagent (Qiagen) and Direct-zol RNA MiniPrep kit (Zymo Research).
Samples were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Differentiated mouse primary myotubes were treated with EDA-A2 for 24 hr (250 ng/ml each)

value: primary myotubes

value: WT

tag: treatment


title: muscle_exercised_saline-treated_rep7

description: Biological replicate 7 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months

value: gastrocnemius muscle


title: Primary myotubes, Control, 24hrs, rep2

value: Control


title: muscle_sedentary_NNMTi-treated_rep7

description: Biological replicate 7 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: HepG2 siIGF2BP3 6h rep1

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

value: Liver

value: epithelial-like


title: R820W_M_b

value: HaCaT

value: keratinocyte

value: Mepazine


title: R820W_NT_b

value: Vehicle (DMSO)


title: muscle_exercised_NNMTi-treated_rep7

description: Biological replicate 7 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)

source_name: exercised, NNMTi-treated mouse muscle (methylated)

source_name: exercised, NNMTi-treated mouse muscle (unmethylated)


title: Primary myotubes, Control, 24hrs, rep1


title: HepG2 siIGF2BP3 3h rep2

value: 3 hour


title: muscle_sedentary_saline-treated_rep6

description: Biological replicate 6 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: Primary myotubes, EDA-A2, 24hrs, rep2


title: HepG2 siIGF2BP3 3h rep1


title: HepG2 siIGF2BP3 0h rep2

value: 0 hour


title: WT_NT_b

value: CARD14 WT/WT


title: muscle_exercised_saline-treated_rep8

description: Biological replicate 8 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)


title: KO_NT_a

value: CARD14 KO


title: muscle_exercised_saline-treated_rep6

description: Biological replicate 6 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)


title: NAC+DETD-35_4_technical repeat 2

city: Taipei

first: Lie-Fen

last: Shyur

address: No. 128, Sec. 2, Academia Road

country: Taiwan

institute: Academia Sinica

hyb_protocol: Enriched labeled miRNA targets were hybridized to the Human miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 h of hybridization, non-speciﬁc binding targets were washed away using wash buffer (2× saline sodium citrate solution).

scan_protocol: The arrays were scanned using a DNA Microarray Scanner (Model 4000B, Molecular Devices, Sunnyvale, CA, USA). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing:
GPR files were loaded into R version 2.12.1 to process data analysis. Probes that all replicates within with flags equal to “-50” of all chips were filtered out. Intensity values from repeated probes within one chip are combined by median. CVs (coefficient of variance) of miRNA from repeated probes within one chip are calculated and the intensity values are calculated by median. Intensities were normalized with invariant set normalization method (Cheng Li et al., Genome Biology 2001), then took average of repeated data from the same sample. Selection criteria to identify differentially expressed genes were established at log 2 |Fold change| ≥ 0.8 and P < 0.05.
Average ratios and significant values for each miRNA were calculated based on the normalized intensities by pairwise comparison.

label_protocol: Fluorescent targets were prepared from 2 μg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands). Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA).

extract_protocol: Total RNA was extracted from 1 million of treated MDA-MB-231 cells in each experimental group using the TRIzol® Reagent (Invitrogen,Carlsbad, CA)  according to the manufacturer’s instructions. RNA quantity and purity was assessed using NanoDrop ND-1000 while RNA integrity number (RIN) was assessed using Agilent RNA 6000 Nano assay. A260/A280 ≥ 1.6 and A260/A230 ≥ 1 indicate acceptable RNA purity, while RIN value ≥ 5 indicates acceptable RNA integrity. All the samples meet the above criteria with A260/A280 ranging from 1.78-1.83, A260/A230 ranging from 1.21-1.53, and RIN ranging from 9.7-10.0.

value: triple-negative breast cancer cell line

tag: treatments

value: 1 h NAC treatment (5 mM) followed by 1 h DETD-35 (4 µM) treatment

tag: molecule subtype

value: small RNA


title: R820W_M_a


title: R820W_NT_a


title: NAC+DETD-35_4_technical repeat 1


title: DETD-35_4_technical repeat 2

value: 1 h DETD-35 (4µM) treatment


title: WT_M_a


title: HepG2 siIGF2BP2 6h rep2

city: Shanghai

value: IGF2BP2 knockdown

value: actinomycin D treatment

value: 6 hour


title: muscle_exercised_NNMTi-treated_rep6

description: Biological replicate 6 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)

value: female

value: ~24.5 months

value: gastrocnemius muscle


title: HepG2 siIGF2BP2 3h rep2

value: Liver

value: epithelial-like


title: muscle_sedentary_NNMTi-treated_rep6

description: Biological replicate 6 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: DETD-35_4_technical repeat 1


title: muscle_sedentary_NNMTi-treated_rep5

description: Biological replicate 5 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: HepG2 siIGF2BP2 6h rep1


title: muscle_sedentary_saline-treated_rep5

description: Biological replicate 5 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: muscle_exercised_saline-treated_rep5

description: Biological replicate 5 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)


title: NAC+DET_4_technical repeat 1

value: 1 h NAC treatment (5 mM) followed by 1 h DET (4 µM) treatment


title: NAC+DET_4_technical repeat 2


title: HepG2 siIGF2BP3 0h rep1

value: IGF2BP3 knockdown


title: HepG2 siIGF2BP2 3h rep1

value: 3 hour


title: WT_M_b

value: HaCaT

value: keratinocyte

value: CARD14 WT/WT

value: Mepazine


title: DET_4_technical repeat 2

value: triple-negative breast cancer cell line

value: 1 h DET (4µM) treatment

value: small RNA


title: Adrenal Medulla P15 stem cells

city: London

first: Cynthia

middle: Lillian

last: Andoniadou

state: -- Select State/Province --

address: Dept of Craniofacial Development, Guy's Hospital, Tower Wing, Floor 27

country: United Kingdom

institute: King's College London

description: Sox2 enriched

data_processing:
barcode processing
gene counting and aggregation
cell ranger-4.0.0
Assembly: mm10
Supplementary files format and content: tab separated values and matrix files

source_name: Adrenal Medulla

extract_protocol:
Mouse adrenals were dissected on ice, surrounding fat and excess adrenal cortex were removed manually. Medullae were placed in an enzymatic digestion mix containing 50μg/ml DNAse I (Sigma, D5025), 10mg/ml Collagenase II (Worthington, LS004177), 2.5μg/ml Fungizone (Gibco, 15290026), 0.1X Trypsin-EDTA (Sigma, 59418C) in 1X Hank’s Balanced Salt Solution (HBSS) (Gibco, 14025050) and incubated at 37°C for 15 minutes. Enzymes were inactivated by addition of 10 times volume of serum-containing Base Media: DMEM/F-12 (Gibco, 31330-038) + 5% FBS (Merk, F0804) + 50U/ml Penicillin-Streptomycin (Gibco, 15070063). The cell suspension was centrifuged at 281g for 5 minutes at room temperature, washed twice in PBS and pellets were resuspended in a solution of HBSS 2.5% FBS. An aliquot of 10,000 viable cells were used for the experiment. For Sox2 enriched dataset, cells were sorted for GFP expression.
Following manifacturer's indications for 10X Genomics Single Cell RNAseq 3' v3.1

value: Adrenal Medulla

value: stem cells


title: HepG2 siIGF2BP2 0h rep2

value: IGF2BP2 knockdown

value: actinomycin D treatment

value: 0 hour


title: muscle_sedentary_saline-treated_rep4

description: Biological replicate 4 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months

value: gastrocnemius muscle


title: serum_sedentary_NNMTi-treated_rep6

description: Biological replicate 6 of 7. Serum from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)

value: serum


title: HepG2 siIGF2BP2 0h rep1

value: Liver

value: epithelial-like


title: DET_4_technical repeat 1


title: Infected mice, day 2, rep4

city: Helsinki

first: Tomas

last: Strandin

address: Haartmaninkatu 3

department: Virology

country: Finland

institute: University of Helsinki

data_processing:
Illumina Bcl2fastq2 Conversion Software (version v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.   Sample specific read files were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v.0.39). Trimmed reads were aligned to mouse genome using STAR aligner (v.2.7.6a) in two-pass mode. Reference genome and gene annotations were based on GENCODE release v44 (GRCh38.p14). Counts per gene were then collected using featureCounts from Subread package (v2.0.1).   ------------------------------------------------ References: Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905. Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.   In addition we used FastQC (version 0.11.9) and MultiQC (v1.9) to check the quality of the data
Conversion and Demultiplexing: Illumina Bcl2fastq2 Conversion Software (version v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.
Quality Control and Trimming: Sample-specific read files were trimmed for adaptor sequences and masked for low-complexity or low-quality sequences using Trimmomatic (v0.39) .
Quality Assessment: FastQC (version 0.11.9) and MultiQC (v1.9) were used to check the quality of the data.
Read Alignment: Trimmed reads were aligned to the mouse genome using STAR aligner (v2.7.6a) in two-pass mode .
Quantification: Counts per gene were collected using featureCounts from the Subread package (v2.0.1) .
Assembly: The reference genome and gene annotations were based on GENCODE release v44 (GRCh38.p14).
Supplementary files format and content: Gene expression table (.txt): A table with gene expression levels for each sample. The table includes gene identifiers and normalized read counts for each gene across all samples.
Supplementary files format and content: MultiQC Report (html): A comprehensive report generated by MultiQC that summarizes the quality control metrics for both raw and aligned sequence data. This includes per-base sequence quality, GC content, sequence duplication levels, overrepresented sequences, and alignment statistics.
Supplementary files format and content: FeatureCounts: generated by the featurecounts tool.Text files (format). Contains raw read counts for each gene in each sample, summary of read assignment results including counts of successfully assigned reads and unassigned reads, and log file with details of the featureCounts run, parameters used, and summary of the process.

source_name: Mice lung neutrophils

extract_protocol:
RNA was extracted from the samples using the Trizol method followed by RNA isolation using the RNeasy micro kit.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (# E7760) combined with NEBNext Poly(A) mRNA Isolation Module (NEB #E7490)
Library preps were started with 25 ng input and 14x cycles were used in the indexing PCR. Library pool was sequenced as 1.3 pM with 1% PhiX in NextSeq 500 high output 1x75bp flowcell.

value: Mice lung neutrophils

value: Neutrophils

value: SARS-Cov-2 infected


title: HepG2 siIGF2BP1 6h rep2

value: IGF2BP1 knockdown

value: 6 hour


title: WT_NT_a

value: HaCaT

value: keratinocyte

value: CARD14 WT/WT

value: Vehicle (DMSO)


title: HepG2 siIGF2BP1 6h rep1

value: actinomycin D treatment


title: Infected mice, day 2, rep3


title: muscle_exercised_NNMTi-treated_rep5

description: Biological replicate 5 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)


title: muscle_sedentary_NNMTi-treated_rep4

description: Biological replicate 4 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: vehicle_technical repeat 2

value: triple-negative breast cancer cell line

value: 1 h vehicle (0.5% DMSO) treatment

value: small RNA


title: NAC+vehicle_technical repeat 1

value: 1 h NAC treatment (5 mM) followed by 1 h vehicle (0.5% DMSO) treatment


title: NAC+vehicle_technical repeat 2


title: muscle_exercised_saline-treated_rep4

description: Biological replicate 4 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months

value: gastrocnemius muscle


title: mouse lung, Kras_prtn3, replicate2

city: zhengzhou

first: renle

last: du

address: 94 Weijin Road

institute: Nankai University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file for each sample

source_name: lung

extract_protocol:
Total RNA was extracted using Trizol
RNA transcriptome profiles were generated by the Beijing Genomics Institute (BGI) using the DNA Nanoball sequence (DNBSEQ) platform.

value: lung


title: mouse lung, Kras_prtn3, replicate1


title: Adrenal Medulla P15

description: Medulla

value: Adrenal Medulla

value: multiple

value: wild type


title: muscle_exercised_NNMTi-treated_rep4

description: Biological replicate 4 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)


title: Infected mice, day 2, rep2

value: Mice lung neutrophils

value: Neutrophils

value: SARS-Cov-2 infected


title: Infected mice, day 4, rep4


title: Infected mice, day 2, rep1


title: HepG2 siIGF2BP1 3h rep1

value: Liver

value: epithelial-like

value: IGF2BP1 knockdown

value: 3 hour


title: HepG2 siIGF2BP1 3h rep2

value: actinomycin D treatment


title: mouse lung, Kras, replicate2


title: muscle_sedentary_NNMTi-treated_rep3

description: Biological replicate 3 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: Infected mice, day 4, rep3


title: mouse lung, Kras, replicate1


title: HepG2 siIGF2BP1 0h rep1

value: 0 hour


title: HepG2 siControl 6h rep2

value: control knockdown

value: 6 hour


title: vehicle_technical repeat 1

value: triple-negative breast cancer cell line

value: 1 h vehicle (0.5% DMSO) treatment

value: small RNA


title: muscle_exercised_saline-treated_rep3

description: Biological replicate 3 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months

value: gastrocnemius muscle


title: Infected mice, day 4, rep2

value: Mice lung neutrophils


title: muscle_exercised_NNMTi-treated_rep3

description: Biological replicate 3 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)


title: RNA-seq analysis of PEF-piPSCs-2

city: Yangling

first: Shuai

last: YU

address: No.22 Xinong Road,

institute: Northwest A&F University

data_processing:
Clean reads were aligned to pig genome Ssc11.1, and the expression level was normalized as RPKM with gene annotation file.
Differential expression genes and functional enrichment for Gene Ontology (GO) and KEGG were plotted by http://www.bioinformatics.com.cn, an online platform for data analysis and visualization
Genome_build: pig genome Ssc11.1 (NCBI)
Supplementary_files_format_and_content: Results_RNA-seq of SCs-piPSCs and SCs.txt (RPKMs)

organism: Sus scrofa

extract_protocol:
Total RNA of the RNA samples was isolated from cell pellets by Trizol reagent (TaKaRa) and RNA-seq library was generated according to the manufacturer’s recommendations.
Paired-end 150 bp sequencing was performed on DNBSEQ (Illumina) at BGI Technology Corporation (China).

value: PEF-piPSCs


title: Infected mice, day 4, rep1

value: Neutrophils

value: SARS-Cov-2 infected


title: muscle_sedentary_saline-treated_rep3

description: Biological replicate 3 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: HepG2 siControl 6h rep1

value: Liver

value: epithelial-like


title: HepG2 siIGF2BP1 0h rep2

value: IGF2BP1 knockdown


title: RNA-seq analysis of PEF-piPSCs-1


title: RNA-seq analysis of SCs-2

value: testis

value: Sertoli cells (SCs)


title: muscle_sedentary_NNMTi-treated_rep2

description: Biological replicate 2 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: HepG2 siControl 3h rep2

value: control knockdown

value: actinomycin D treatment

value: 3 hour


title: Control mice, rep 4

value: Non infected


title: HepG2 siControl 3h rep1


title: Control mice, rep 3


title: RNA-seq analysis of SCs-1


title: muscle_exercised_NNMTi-treated_rep2

description: Biological replicate 2 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)


title: muscle_exercised_saline-treated_rep2

description: Biological replicate 2 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)


title: muscle_sedentary_saline-treated_rep2

description: Biological replicate 2 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)


title: HepG2 siControl 0h rep2

value: 0 hour


title: Control mice, rep 2


title: RNA-seq analysis of SCs-piPSCs-2

value: SCs-piPSCs


title: Control mice, rep 1


title: HepG2 siControl 0h rep1


title: muscle_sedentary_saline-treated_rep1

description: Biological replicate 1 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous saline treatment (5 milliliters per kg body weight)

value: female

value: ~24.5 months


title: RNA-seq analysis of SCs-piPSCs-1


title: RNA MOLM-13 CTRL shRNA rep2

status: Public on Jul 12 2024

first: Srikanth

last: Kodali

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: MOLM-13 counts.xlsx

data_processing:
FASTQ files were aligned to the reference genome using STAR with default settings
Duplicates were removed using samtools 1.12
Differential expression analysis was performed using R package DESeq2
Assembly: GRCh38
Supplementary files format and content: .xlsx files include read counts for each sample.

source_name: Blood

growth_protocol: Cells were cultured in RPMI 1640 supplemented with fetal bovine serum (FBS), L-glutamine, beta-mercaptoethanol, and antibiotics.

extract_protocol:
RNAs were extracted using the miRNeasy Micro Kit (QIAGEN).
RNA libraries were constructed according to NEBNext® Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cells were transduced with control or DDX6 shRNA-expressing lentiviruses and selected with puromycin

value: Blood

value: AML

value: WT

value: shRNA


title: RNA MOLM-13 DDX6 shRNA rep1

description: MOLM-13 counts.xlsx

value: DDX6 knockdown


title: RNA MOLM-13 CTRL shRNA rep1

description: MOLM-13 counts.xlsx


title: RNA HEL CTRL shRNA rep2

description: HEL counts.xlsx

value: HEL


title: RNA HEL DDX6 shRNA rep1

description: HEL counts.xlsx


title: RNA HEL CTRL shRNA rep1

description: HEL counts.xlsx


title: muscle_exercised_saline-treated_rep1

description: Biological replicate 1 of 10. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous saline treatment (5 milliliters per kg body weight)

value: gastrocnemius muscle


title: muscle_sedentary_NNMTi-treated_rep1

description: Biological replicate 1 of 9. Gastrocnemius muscle from a female mouse after being sedentary for 8 weeks and given subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] adminsitered at 10 milligrams per kilogram body weight)


title: G58R OMA1+/- liver, treated with control ASO, biological rep1

description: RNA expression from mouse liver

value: adult

value: liver

value: control ASO


title: MOLM-13 DDX6 shRNA rep2

data_processing:
Raw sequencing reads were mapped to the human reference genome (GRCh38) using Bowtie2 version 2.2.6, followed by peak calling with software MACS2 version 2.1.0
Quality control (QC) metrics were collected to determine library complexity, signal to noise ratios, and reproducibility according to the current ENCODE QC standards.
Sample-based peaks were then combined using the Irreproducibility Discovery Rate (IDR) framework to generate the final optimal IDR peak set, and fed into R package DESeq2 to generate a normalized reads count matrix while adjusting for effective library sizes.
Log-transformed read counts were used for downstream differential peak analysis.
Assembly: GRCh38
Supplementary files format and content: .csv files including log-transformed differential accessiblity fold changes.

extract_protocol:
Cells were lysed (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.2 % IGEPAL CA-630) and nuclei were extracted.
Transposition was performed, DNA was isolated, PCR-amplified, and size-selected.


title: MOLM-13 CTRL shRNA rep1


title: MOLM-13 CTRL shRNA rep2


title: HEL DDX6 shRNA rep2


title: MOLM-13 DDX6 shRNA rep1


title: HEL CTRL shRNA rep2


title: HEL CTRL shRNA rep1


title: RNA MOLM-13 DDX6 shRNA rep2

description: MOLM-13 counts.xlsx


title: GP muscle from KIC mouse 1 uninjected

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
FastQC tool (version 0.11.8) was used for quality control of RNA-seq raw fastq data to evaluate low quality or adaptor portion of the reads for trimming. Read were trimmed with Trimmomatic (Version 0.39) and aligned to mm10 reference genome using HiSAT2 (Version 2.1.0) with default settings. The raw count matrix was generated using featureCounts (Version 1.6.2) with bam files as input.
Assembly: mm10
Supplementary files format and content: .txt RawCount

source_name: GP

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring only high quality RNA is used (RIN Score 8 or higher).  The Qubit fluorimeter is used to determine the concentration prior to staring library prep. One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.

value: GP

value: KIC, mixed background (C57BL/6 with FVB)

value: 66 days

value: no treatment


title: GP muscle from KIC mouse 1 shMyog

value: AAV9-shMyog intramuscular injection


title: GP muscle from KIC mouse 2 shMyog


title: GP muscle from control mouse 3 shMyog

value: control, mixed background (C57BL/6 with FVB)

value: Ink4afl/fl (Control)


title: GP muscle from control mouse 3 uninjected


title: RNA HEL DDX6 shRNA rep2

description: HEL counts.xlsx

value: Blood


title: GP muscle from control mouse 2 shMyog


title: GP muscle from control mouse 2 uninjected


title: hindlimb muscle from control mouse 3, 8 months

source_name: hindlimb muscles

value: hindlimb muscles

value: 8 months

value: control


title: GP muscle from control mouse 1 shMyog


title: muscle_exercised_NNMTi-treated_rep1

description: Biological replicate 1 of 7. Gastrocnemius muscle from a female mouse after 8 weeks of progressive weighted wheel running and subcutaneous nicotinamide N-methyltransferase inhibitor treatment (5-amino-1-methylquinolinium [also known as RT001, 5A-1MQ] administered at 10 milligrams per kilogram body weight)

value: female

value: ~24.5 months


title: hindlimb muscle from control mouse 1, 8 months


title: hindlimb muscle from control mouse 2, 8 months


title: GP muscle from control mouse 1 uninjected


title: hindlimb muscle from control mouse 3, postnatal day 3


title: hindlimb muscle from control mouse 2, postnatal day 2


title: hindlimb muscle from control mouse 1, postnatal day 1


title: hindlimb muscle from control mouse 3, E17.5 age


title: hindlimb muscle from control mouse 2, E17.5 age


title: HEL DDX6 shRNA rep1

value: HEL

value: AML

value: DDX6 knockdown

value: shRNA


title: hindlimb muscle from control mouse 1, E17.5 age


title: hindlimb muscle from pooled control mice 2, E15.5 age


title: hindlimb muscle from pooled control mice 3, E15.5 age


title: Biliary epithelial cells PC depleted, rep 3

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Base call data generated by Illumina NextSeq 2000
Read quality assessed using FastQC (v.0.11.9) and MultiQC (v.1.3.dev0)
Adapter, poly-G and low-quality base trimming with Cutadapt (v.1.16)
Read alignment with STAR (v.2.7.1a)
Read counting with featureCounts (Rsubread Bioconductor package v.2.0.1)
Differential expression computed using DESeq2 (v.1.34.0)
Assembly: GRCm38.100
Supplementary files format and content: Tab separated matrix table with raw gene counts for all genes and samples

source_name: biliary epithelium

extract_protocol:
Mouse livers were perfused with saline, dissected down to approximately 2-4 mm3 portions and covered with a mix of 0.125 mg/ml Collagenase (Sigma-Aldrich) and Dispase (Life Technologies) in 2% FCS Advanced DMEM/F-12 (Thermo Fisher). This mix was incubated 1 hour at 37ºC and individual bile ducts were manually picked up, cleaned twice with 5%FCS DMEM/F-12 (Thermo Fisher) and transferred to Matrigel (Corning) for subsequent culture. Bile ducts were grown as three-dimensional organoids for 4 to 5 passages and then transferred to a two-dimensional culture in plates covered with 1mg/ml collagen (Sigma).
500ng of each total-RNA sample was used for RNA-seq library preparation, using the NEBNEXT Ultra II Directional RNA Library Prep Kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the manufacturer’s protocol. AMPure XP beads (Beckman Coulter #A63881) were used to purify the cDNA library. Multiple indexing adapters were ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 10 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing. Following amplification, libraries were purified using AMPure XP beads. Completed libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626).

value: biliary epithelium

value: Biliary epithelial cells


title: Biliary epithelial cells PC depleted, rep 2


title: GP muscle from KIC mouse 2 uninjected

value: GP

value: KIC, mixed background (C57BL/6 with FVB)

value: 66 days


title: Biliary epithelial cells PC depleted, rep 1


title: Biliary epithelial cells PC competent, rep 3


title: hindlimb muscle from pooled control mice 1, E15.5 age

value: no treatment


title: Biliary epithelial cells PC competent, rep 2


title: GP muscle from KIC mice [scRNA]

description: 10x Genomics

data_processing:
10X Cell Ranger Arc (version 2.0.0) was used to perform sample demultiplexing for both the snRNA-seq and snATAC-seq data. Raw base call files (BCL) from the Nextseq 500 were demultiplexed with the Cell Ranger Arc mkfastq pipeline into FASTQ files. We used this command to demultiplex ATAC and GEX flow cells. FASTQ files were processed further using the Cell Ranger ARC count pipeline to perform alignment, filtering, barcode counting, peak calling and counting of ATAC and GEX molecules with the mouse mm10 (Sequence: GRCm38 Ensembl 93) genome used as the reference and default parameters. Further quality filtering was performed using the Seurat R package (version 4.0.4) and Signac (1.4.0) performed in R version (4.1.0). Any barcodes (nuclei) with between 25,000 and 400 reads from RNA (nCount_RNA) and between 70,000 and 400 reads from snATAC-seq were analyzed. Cells with >20% of the reads coming from mitochondrial genes were also filtered to remove potential dead cells from analysis.  We obtained 4899 nuclei from the cachexic samples and 3293 from the control samples. After performing unsupervised clustering analysis and integrating the snRNA-seq and snATAC-seq datasets and careful inspection with known cell markers, we annotated each cluster and merged clusters that did not show clear distinctions as the same cell type.
Assembly: mm10
Supplementary files format and content: .h5 10X count

extract_protocol:
Skeletal muscles were dissected, snap-frozen, and stored in liquid nitrogen until the single nucleus multi-ome procedure was performed. Three control and three KIC GP muscles were pooled together. Muscles were thawed for 5 min on ice and minced with scissors in 1 mL cold lysis buffer (10 mM Tris- HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NonidetTM P40, 1 mM DTT, 1 U/μl RNase inhibitor in Nuclease-Free Water). Cold lysis buffer was then added, and muscles were lysed for 5 min at 4 °C. Cold wash buffer (PBS, BSA 2%, and 0.2 U/μl RNase inhibitor from Roche) was added, and the lysate was dounced with a loose dounce homogenizer for 20 strokes. The homogenate was then filtered with 70 μm and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 x g at 4 °C. Nuclei were then resuspended in wash buffer and 2 μL of Nuclear Pore Complex antibody (Biolegend, 682203) to stain all nuclei. After 15 min, nuclei were pelleted by centrifugation for 5 min at 500 x g at 4 °C. Nuclei were then resuspended in wash buffer and filtered with 30 μm cell strainers.  Nuclei were FACS sorted to exclude debris with a BD FACSAria III and the BD FACSDIVA and Flowjo v10.8.1 software. Nuclear Pore Complex-positive nuclei were collected for each condition and pelleted by centrifugation for 10 min at 500 x g at 4 °C. Nuclei were then resuspended in ATAC lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% NonidetTM P40, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1U/μl RNase inhibitor in Nuclease- Free Water). After 2 min, ATAC wash buffer (10 mM Tris- HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1 mM DTT, 1% BSA, 1U/μl RNase inhibitor in Nuclease-Free Water) was added. Nuclei were then pelleted by centrifugation for 10 min at 500 x g at 4 °C and resuspended in diluted nuclei buffer from 10x Genomics.  Nuclei concentrations were quantified with an automatic hemocytometer, and were adjusted to 2000 nuclei/μL with wash buffer. We loaded ~ 5000 nuclei per condition into the 10x Chromium Chip. We used the Next GEM single-cell Multiome ATAC+ Gene expression kit according to manufacturer’s protocol.
SnRNA-seq libraries were constructed by performing the following steps: cDNA Amplications, SPRIselect cleanup, Fragmentation, End repair and A tailing, SPRIselect cleanup, and Adaptor ligation, SPRIselect cleanup, Sample index PCR and SPRIselect cleanup size selection. Fragment size estimation was assessed with Agilent TapeStation D1000 (Agilent) and quantified using the QubitTM dsDNA High-Sensitivity HS assay (ThermoFisher Scientific).

value: mixed background (C57BL/6 with FVB)

value: 66 days mouse age


title: Biliary epithelial cells PC competent, rep 1


title: GP muscle from control mice [scRNA]

description: 10x Genomics

value: Ink4afl/fl (Control)


title: GP muscle from 48 hour fasted mouse 2

value: control, mixed background (C57BL/6 with FVB)

value: 48 hours fasting (no food)


title: GP muscle from 48 hour fasted mouse 3


title: GP muscle from KIC mouse 3