title: Pg-Fe rep1

first: Tianyuan

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
llumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,then mapped to mm8 whole genome
Reads Per Kilobase of exon per Megabase of library size(RPKM)were calculated using a protocol from Chepelevet alNucleic Acids Research,2009.
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

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.

value: lung

value: wild type

value: Pg-Fe-hMSC treated


title: Pg-Fe rep2

status: Public on Aug 09 2023

type: SRA

city: Hangzhou

last: Zhang

state: Zhejiang

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: U251DARS-AS1SI1_S4

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

country: USA

institute: UT MD Anderson Cancer Center

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l lncRNA_CRISPRi_sgRNA_library --control-sgrna lncRNA_CRISPRi_sgRNA_CTRL --norm-method control -n sgrna.count --sample-label D0,D21 --fastq files.fq”. MAGeCK test module was then applied with parameters “mageck test -k sgrna.count -c D0 -t D21 --norm-method control --keep-tmp -n D21_D0 --control-sgrna lncRNA_CRISPRi_sgRNA_CTRL”, to identify the lncRNAs that showed a  significant differential selection (|log2(fold-change)| ≥ 1 and p < 0.05) between the D0 and D21 groups. Based on a custom second-best script, the gene-level results were summarized for the lncRNAs accroding to the library map.
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V25 transcriptome with tophat (v2.1.1). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2 (1.22.2).
For the eCLIP data: YeoLab's eCLIP (v0.7.1) was used to call the significant peaks (p < 0.05 & FC > 1.2)

organism: Homo sapiens

growth_protocol: The U87 and U251 cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM, Hyclone #SH30022.01) supplemented with 10% Fetal Bovine Serum (FBS, Gibco#10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI).

extract_protocol:
The genome DNA was extracted by using QIAamp DNA Mini Kit (QIAGEN) for each replicate. Total RNA was isolated from U251 cells using RNeasy Mini Kit (QIAGEN #74104) and was treated with DNase I (QIAGEN #79254).
Two rounds of PCR were employed to prepare the next-generation-sequencing (NGS)-ready sgRNA libraries with the KAPA HiFi HotStart ReadyMix (Roche # KK2602). The RNA-seq library were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594).The eCLIP libraries were generated from U251 cells in biological duplicates with the kit (Eclipse Bioinnovations Inc, #ECEK-0001) according to the standard single-end eCLIP protocol.

treatment_protocol: For eCLIP-seq experiments, U251 cells stably expressing FLAG-tagged YBX1 were crosslinked by 254-nm UV light (400 mJ/cm2) .

tag: cell line

tag: cell type

value: glioblastoma

value: tumor


title: Pg-Fe rep3


title: U251YBX1NC1_S1


title: 3D co-cultured control ATII + MRC5, rep3

city: Southampton

first: Yihua

last: Wang

address: University Road

country: United Kingdom

institute: University of Southampton

data_processing:
Quality control of RNA-seq raw paired data was performed using FastQC  and MultiQC.
Trim Galore was used to trim adapters, reads with low quality (<30) and short length (<50 bp).
RNA-seq reads were mapped to Homo_sapiens.GRCh38.100 using Hisat2 with default codes.
Sam files were transformed into bam files using samtools.
The read counts of each genes were summarized using featureCounts.
Assembly: Homo_sapiens.GRCh38.100
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

source_name: ATII + MRC5

growth_protocol: ATII cells (kindly provided by Prof Julian Downward) were cultured in DCCM-1 (Biological Industries Ltd.) supplemented with 10% NBCS (Life Technologies), 1% penicillin, 1% streptomycin and 1% L-glutamine (from Sigma Aldrich). MRC5 cells were obtained from the European Collection of Authenticated Cell Cultures (ECACC) and were cultured in DMEM (Thermo Fisher Scientific). Both cell culture media were supplemented with 10% FBS (Thermo Fisher Scientific), 1% penicillin/streptomycin and glutamine (Thermo Fisher Scientific). All cells were kept at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop Spectophotometer 2000c (Thermo Fisher Scientific). A total amount of 3 μg RNA per sample was used as input material for library construction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction. Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols (Novogene, UK).

treatment_protocol: Aggregation of 3D cultures was achieved using Nanoshuttle-PL (Greiner Bio-One). Briefly, MRC5 fibroblasts at 80% confluence were treated with Nanoshuttle-PL for 24 h, before trypsinisation as normal. Cells are then pipetted onto cell repellant 96-well plates sat on a magnetic drive and left to incubate at 37 °C and 5% CO2 for a minimum of 3 h on the magnetic drive to enable the spheroid to form. The process was then repeated for control or LKB1-depleted ATII cells so they could then grow around the existing fibroblast spheroid. LKB1-depleted ATII cells were generated by transfection with LKB1 (STK11) siRNA oligos at a final concentration of 35 nM using DharmaFECT 2 reagent (Dharmacon).

value: ATII + MRC5

value: alveolar epithelial type II (ATII) cells + human lung fibroblast

value: WT

value: Control ATII cells co-cultured with MRC5 in 3D for 5 days


title: 3D co-cultured control ATII + MRC5, rep2


title: Fe rep3

value: Fe-hMSC treated


title: U251DARS-AS1NC3_S3


title: U251DARS-AS1NC2_S2


title: Fe rep2


title: Fe rep1


title: Hi-C.alpha4

city: Cleveland

first: Shanshan

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

library_source: genomic

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. For every loop anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range and then map the contact fragments to ~5kb anchor resolution. We used HiCorr to correct bias in raw contacts between every two anchors, and apply DeepLoop on the bias-corrected contact ratio from HiCorr. The file column names are "anchor_loc1", "anchor_loc2", "raw_reads","HiCorr_bias_corrected.ratio","DeepLoop_enhanced"
Genome_build: hg19
Supplementary_files_format_and_content: The file column names are "anchor_loc1", "anchor_loc2", "raw_reads","HiCorr_bias_corrected.ratio","DeepLoop_enhanced"

molecule: genomic DNA

source_name: human islet sorted alpha cells

extract_protocol:
Human islets were purchased from Prodo Labs (Cat# HIR-001). After receiving, the islets were well dispersed and washed with complete PIM(S) media (Prodo Labs, Cat# PIM-S001GMP) by centrifuging at 180g for 2 minutes.  The supernatant was removed with about 2-3ml of media left. The islet pellets were then gently resuspended in complete PIM(S) media, and transferred to a 6-well non-tissue culture treated plate. After recovering in a cell incubator for overnight, the islets were digested to single cells. Briefly, the islets were pelleted and washed with HBSS without Ca++/Mg++ (Sigma, Cat# H6648-1L), and then digested with Accutase (Life Technologies, Cat# A1110501) in a 6-well non-treated plate at 37ºC for about 5 minutes. The digested cells were filtered through a 40?m cell strainer to obtain single cells, and the cell number and viability were observed after washing twice with HBSS. To prepare for low input Hi-C, the single cells were firstly fixed with BD cytofix/ cytoperm buffer (BD, Cat# 51-2090KZ) for 20 minutes and washed with BD perm/ Wash buffer before stained with desired antibodies for alpha cells (BD Biosciences, BV421 mouse anti-glucagon, Cat# 565891) and beta cells (BD Biosciences, Alexa Flour 647 Mouse Anti-Insulin, Cat# 565689). The cells were sorted out using BD FACS ARIA II.
We followed our previous easy Hi-C protocol to generate the eHi-C libraries. In order to make it compatible to low input sorted cells, we made a few changes. Briefly, about 20-30k sorted alpha or beta cells were applied for each library. Nuclei were extracted and digested with HindIII before proximity ligation. The chromatin ligates were then digested DpnII before constructing self-circles. The circuited DNAs were then linearized with a second digestion of HindIII. All the recovered DNAs were used to generate libraries. We followed the standard protocol to generate the libraries with modified Truseq adapters containing a regular sample index (i7) and a random fragment index (i5: NNNNNN).

tag: tag

value: no treat

value: Hi-C


title: 3D co-cultured control ATII + MRC5, rep1


title: Hi-C.alpha5


title: U251DARS-AS1NC1_S1


title: Hi-C.alpha3


title: U87D21R3


title: PF rep3

value: untreated


title: Hi-C.alpha1


title: U87D21R2


title: PF rep2


title: U87D0R1


title: U87D0R2


title: U87D21R1


title: B16F10_H3K27ac_chipseq_aMSH+IFNg_chip_rep2

city: Beijing

first: Yazhong

last: Cui

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National institute of biological sciences, Beijing

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.2.3. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to counts per million, cpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.2.7.1 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools (3.4.3). Score represents the normalized coverage of DNA fragments at a given genomic coordinate. broadPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak (except for Input sample)

growth_protocol: B16F10 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was digested with Micrococcal nuclease and were sonicated for 10 cycles (high energy, 30s on, 30s off) by diagenode instrument.
The chip libraries were constructed and sequenced by Beijing Glbizzia Biotechnology Co., Ltd.

value: mouse melanoma

tag: chip antibody


title: U87D0R3


title: B16F10_H3K27ac_chipseq_aMSH+IFNg_chip_rep1


title: U251D21R3


title: B16F10_H3K27ac_chipseq_IFNg_chip_rep2


title: B16F10_H3K27ac_chipseq_IFNg_chip_rep1


title: Hi-C.alpha2


title: B16F10_H3K27ac_chipseq_aMSH+IFNg_input_rep2


title: U251D21R2


title: B16F10_H3K27ac_chipseq_aMSH+IFNg_input_rep1


title: U251D21R1


title: U251D0R3


title: U251D0R2


title: B16F10_H3K27ac_chipseq_IFNg_input_rep2


title: PF rep1


title: B16F10_ATACseq_aMSH+IFNg_rep2


title: B16F10_H3K27ac_chipseq_IFNg_input_rep1


title: Muscle_Post_Training_Acute_rep23

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from muscle biopsy trained after exercise derived from subject 74

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

label: biotin

source_name: Muscle biopsy trained after exercise derived from subject 74

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: no

extract_protocol: RNA extraction was performed using the miRneasy kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, healthy, sedentary (<120 min of physical activity per week) individuals at high risk for T2D with at least one of the following risk factors (BMI>27 kg/m2, family history (first degree) of T2D, former gestational diabetes) were recruited. Criteria for recruitment and design of the exercise intervention were identical in both studies. 44 individuals (19 of study 1 and 25 of study 2) were included for data analysis. One subject participated in both studies and only data obtained in study 2 were used for further analyses. Severe diseases were excluded by anamnesis including medication, monitoring routine laboratory parameters, electrocardiogram, and physical examination.   The participants performed an 8-week supervised aerobic endurance exercise intervention program as described below. Individual training intensity was set at 80% of VO2peak determined before the intervention and kept constant throughout the training program. Insulin sensitivity was assessed after an overnight-fast by 75g-OGTT pre-intervention and 5 days after the last exercise bout; blood samples for clinical routine parameters were obtained before the glucose load. Vastus lateralis muscle biopsies were taken one hour after the 30 min training.

value: muscle


title: Muscle_Post_Training_Acute_rep22

description: Gene expression data from muscle biopsy trained after exercise derived from subject 73

source_name: Muscle biopsy trained after exercise derived from subject 73


title: Muscle_Post_Training_Acute_rep21

description: Gene expression data from muscle biopsy trained after exercise derived from subject 72

source_name: Muscle biopsy trained after exercise derived from subject 72


title: B16F10_ATACseq_aMSH+IFNg_rep1


title: Muscle_Post_Training_Acute_rep20

description: Gene expression data from muscle biopsy trained after exercise derived from subject 71

source_name: Muscle biopsy trained after exercise derived from subject 71


title: Muscle_Post_Training_Acute_rep16

description: Gene expression data from muscle biopsy trained after exercise derived from subject 66

source_name: Muscle biopsy trained after exercise derived from subject 66


title: U251D0R1


title: Muscle_Post_Training_Acute_rep17

description: Gene expression data from muscle biopsy trained after exercise derived from subject 68

source_name: Muscle biopsy trained after exercise derived from subject 68


title: Muscle_Post_Training_Acute_rep19

description: Gene expression data from muscle biopsy trained after exercise derived from subject 70

source_name: Muscle biopsy trained after exercise derived from subject 70


title: Muscle_Post_Training_Acute_rep15

description: Gene expression data from muscle biopsy trained after exercise derived from subject 65

source_name: Muscle biopsy trained after exercise derived from subject 65


title: hiPSC, NKX6.1-GFP/NEUROG3-HA-mCherry, rep1, scRNAseq

city: Illkirch

first: Sara

last: Jiménez

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: SortSeq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made by scDiscoveries
Assembly: Human GRCh38
Supplementary files format and content: UMI counts were adjusted using Poisson counting statistics

source_name: Pancreas

growth_protocol: Cells were seeded at 5.5x10e5 cells/cm2 on Growth Factor Reduced Matrigel (Corning)-coated 24wells in mTESR1 + 5µM Y27632 (Stem Cell Technologies). Differentiation was initiated 24 hours after and performed following the protocol described in Schreiber et al (2021) Molecular Metabolism 53:101313, until the end of Stage 5 (day 13).

extract_protocol:
At day 13 of differentiation, cells were harvested with TrypLE Select (Life Technologies), diluted with 3 volumes of MCDB131-3 medium (Schreiber et al (2021) Molecular Metabolism 53:101313)  containing 5 mM Y27632, centrifuged 4 min at 200g, resuspended at 5.10e6/ml in MCDB131-3 medium containing 5 mM Y27632 and sorted using a FACS Fusion/Aria directly into two 384-well plates provided by Single Cell Discoveries (Utrecht, Netherlands), containing barcoded primers and other reagents. Cells were spun-down and plates stored at -80°C.
Library preparation and single-cell RNA sequencing was performed by Single Cell Discoveries (Utrecht, Netherlands) using their custom SORT-seq protocol adapted from Muraro et al (2016) 3(4):385-394. cDNA libraries were sequenced at 150 k reads/cell on the Illumina NextSeq 500 platform. Number of cells sequenced: 376
SortSeq scRNA-seq

value: Pancreas

value: NKX6.1-GFP/NEUROG3-HA-mCherry hiPSC line, clone 10

value: hiPSC derived pancreatic endocrine progenitors, end of stage 5 (day 13)


title: hiPSC, NKX6.1-GFP/NEUROG3-HA-mCherry, rep2, scRNAseq

description: SortSeq


title: Muscle_Post_Training_Acute_rep18

description: Gene expression data from muscle biopsy trained after exercise derived from subject 69

source_name: Muscle biopsy trained after exercise derived from subject 69


title: Muscle_Post_Training_Acute_rep14

description: Gene expression data from muscle biopsy trained after exercise derived from subject 64

source_name: Muscle biopsy trained after exercise derived from subject 64


title: B16F10_ATACseq_IFNg_rep2


title: B16F10_ATACseq_aMSH_rep2


title: B16F10_ATACseq_IFNg_rep1


title: B16F10_ATACseq_aMSH_rep1


title: Muscle_Post_Training_Acute_rep11

description: Gene expression data from muscle biopsy trained after exercise derived from subject 60

source_name: Muscle biopsy trained after exercise derived from subject 60


title: B16F10_ATACseq_untreat_rep2


title: Muscle_Post_Training_Acute_rep12

description: Gene expression data from muscle biopsy trained after exercise derived from subject 62

source_name: Muscle biopsy trained after exercise derived from subject 62


title: B16F10_ATACseq_untreat_rep1


title: Muscle_Post_Training_Acute_rep13

description: Gene expression data from muscle biopsy trained after exercise derived from subject 63

source_name: Muscle biopsy trained after exercise derived from subject 63


title: AVD-1-833-6029B

city: Baltimore

first: Yuba

middle: R

last: Bhandari

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkins University School of Medicine

hyb_protocol: Biotin-labeled target samples were hybridized to the Affymetrix HT HG-U133+ PM Array

scan_protocol: Target hybridization was processed on the GeneTitan® Instrument according to manufacturer’s instructions provided for Expression Array Plates (P/N 702,933). Images were analyzed using the GeneChip® Command Console Software (GCC) (ThermoFisher)

data_processing: Data was processed using affy_v1.74.0 package with Robust Multichip Average (RMA) normalization in R

source_name: FFPE sample

label_protocol: not provided

extract_protocol:
RNA was extracted from 1 slice (10 µm) from the FFPE samples (Qiagen RNEasy FFPE kit). Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent
Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902,790).

tag: Sex

value: female

tag: age

tag: localization

value: Left

value: colon polyp


title: Muscle_Post_Training_Acute_rep10

description: Gene expression data from muscle biopsy trained after exercise derived from subject 59

source_name: Muscle biopsy trained after exercise derived from subject 59


title: Muscle_Post_Training_Acute_rep9

description: Gene expression data from muscle biopsy trained after exercise derived from subject 58

source_name: Muscle biopsy trained after exercise derived from subject 58


title: Muscle_Post_Training_Acute_rep8

description: Gene expression data from muscle biopsy trained after exercise derived from subject 57

source_name: Muscle biopsy trained after exercise derived from subject 57


title: Zeb1_WT_3

first: Carl

last: Gay

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to mm10 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

growth_protocol: 393P GFP_Vector, 393P Zeb1_deficient, 393P Zeb1 mimetic, and 393P Zeb1 WT cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina. Barcoded libraries were pooled and paired end sequenced on the Illumina HiSeq using the High output V2.5 kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epithelial non-metastatic cell line

tag: replicate

value: Biol rep 3


title: Zeb1_mimetic_3


title: Zeb1_WT_1

value: Biol rep 1


title: AVD-31-3-7961A

value: male


title: Zeb1_WT_2

value: Biol rep 2


title: AVD-31-3-6082A


title: AVD-1-44-7-14441A


title: Zeb1_mimetic_2


title: Zeb1_mimetic_1


title: Zeb1_deficient_3


title: Muscle_Post_Training_Acute_rep4

description: Gene expression data from muscle biopsy trained after exercise derived from subject 53

source_name: Muscle biopsy trained after exercise derived from subject 53


title: Muscle_Post_Training_Acute_rep7

description: Gene expression data from muscle biopsy trained after exercise derived from subject 56

source_name: Muscle biopsy trained after exercise derived from subject 56


title: AVD-31-3-9538C


title: AVD-31-2-7816B

value: Right


title: AVD-1-44-2-2176A


title: Zeb1_deficient_1


title: AVD-1-44-4-9144A


title: GFP_Vector_3


title: GFP_Vector_2


title: Muscle_Post_Training_Acute_rep5

description: Gene expression data from muscle biopsy trained after exercise derived from subject 54

source_name: Muscle biopsy trained after exercise derived from subject 54


title: AVD-1-44-2-5016A


title: Muscle_Post_Training_Acute_rep1

description: Gene expression data from muscle biopsy trained after exercise derived from subject 50

source_name: Muscle biopsy trained after exercise derived from subject 50


title: Muscle_Post_Training_Acute_rep6

description: Gene expression data from muscle biopsy trained after exercise derived from subject 55

source_name: Muscle biopsy trained after exercise derived from subject 55


title: Muscle_Post_Training_Acute_rep2

description: Gene expression data from muscle biopsy trained after exercise derived from subject 51

source_name: Muscle biopsy trained after exercise derived from subject 51


title: Muscle_Baseline_Acute_rep25

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 74

source_name: Muscle biopsy untrained after exercise derived from subject 74


title: Muscle_Post_Training_Acute_rep3

description: Gene expression data from muscle biopsy trained after exercise derived from subject 52

source_name: Muscle biopsy trained after exercise derived from subject 52


title: Muscle_Baseline_Acute_rep24

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 73

source_name: Muscle biopsy untrained after exercise derived from subject 73


title: AVD-1-44-4-3163B


title: AVD-31-4-8148A


title: AVD-1-44-2-4422B


title: AVD-1-44-3-6340A


title: Muscle_Baseline_Acute_rep22

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 71

source_name: Muscle biopsy untrained after exercise derived from subject 71


title: Muscle_Baseline_Acute_rep23

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 72

source_name: Muscle biopsy untrained after exercise derived from subject 72


title: Zeb1_deficient_2


title: Muscle_Baseline_Acute_rep21

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 70

source_name: Muscle biopsy untrained after exercise derived from subject 70


title: AVD-1-835-1951A


title: AVD-1-44-4-4765A


title: GFP_Vector_1


title: Muscle_Baseline_Acute_rep20

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 69

source_name: Muscle biopsy untrained after exercise derived from subject 69


title: KI 4

city: Jinan

first: Moke

last: Liu

address: Jingsi road No.544

institute: Shandong Provincial Hospital

data_processing:
Clustering and sequencing. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Quality control. The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base 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.
Reads mapping to the reference genome. 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.
Quantification of gene expression level.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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for  samples

source_name: liver

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-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, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. 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 (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: liver

tag: development stage


title: KI 3


title: KI 2


title: KI 1


title: Muscle_Baseline_Acute_rep19

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 68

source_name: Muscle biopsy untrained after exercise derived from subject 68


title: Muscle_Baseline_Acute_rep18

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 67

source_name: Muscle biopsy untrained after exercise derived from subject 67


title: Control 2


title: AVD-1-24-5-1731A

source_name: FFPE sample


title: Control 1


title: AVD-1-44-5-10888A


title: Muscle_Baseline_Acute_rep15

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 64

source_name: Muscle biopsy untrained after exercise derived from subject 64


title: D2 primary oviductal muscle cell IgG-1

city: Bethesda

first: qiliang

last: Xin

address: 50 South Dr

department: NIDDK

institute: NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with Bowtie2 against Mus musculus genome sequence
filter for uniquely mapped and non-duplicated reads
call peaks with macs2
Assembly: GRCm38.p5
Supplementary files format and content: peaks called in excel files
Library strategy: CHIC-seq

source_name: primary oviductal muscle cell

growth_protocol: The mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Oviduct isolated from 8-12 weeks aged control and knockout mice.

extract_protocol:
Oviduct were isolated and cut into small pieces (1-2 mm) and incubated (30-45 min) in rotation at 37 ℃ in pre-warmed DMEM/F12 (1:1) (Gibco), 12 mM HEPES (Gibco), 1% penicillin/streptomycin (Gibco), 2 mg/ml trypsin (Sigma), 400 U/ml collagenase type I (Invitrogen), and 5 U/ml dispase (Invitrogen). The digested cells were passed through a 70-mm filter to obtain a homogenous population of smooth muscle cells. Cells were plated in 100 mm dishes, containing DMEM and Ham F-12 media (1:1) (Gibco) with 12% charcoal-stripped fetal bovine serum (FBS) and antibiotics (penicillin-streptomycin, Thermo Fisher, 100 µg/mL). After 4 h, the medium was replaced with DMEM/F-12 (1:1) containing 10% FBS. 2 h later, the cells were gently washed twice with PBS and samples were prepared for CHIC-seq.  50-100K cell was isolated for CHIC-Seq.
Small cell number ChIC-seq assays were performed as previous reported. ChIC-seq libraries were constructed using 50,000 mouse primary oviduct muscle cells. Cells were fixed with 1% formaldehyde solution at RT for 5 minutes. Reaction was terminated by adding 1:10 volume of 1.25 M glycine. The fixed cells were kept in -80 ℃ after three washes with ice cold PBS. For ChIC reaction and library preparation, cells were incubated and rinsed with 500 ml antibody binding buffer (1xTE pH 7.5+150 mM NaCl+0.1% Trition X100) twice and re-suspended in 100 ml antibody binding buffer. To prepare ProteinA-MNase and antibody complex, Pbrm1 (Abcam,  ab196022), Brg1 (Abcam, ab110641), H3K27ac (Abcam, ab4729), H3K4me1 (Abcam, ab176877)) bounded PA-MNase (Ab+PA-MNase) and were incubated at a molecular ratio of 1:2 on ice for 30 min in 50 ml antibody binding buffer. This complex mixed with 50 ml resuspended cells and incubated for 1.5 h on ice. Cells were washed three times with 1 ml wash buffer (1xTE pH 7.5+400 mM NaCl+1% Triton X-100) and rinsed with 400 ml rinsing buffer (10 mM Tris pH 7.5+10 mM NaCl+0.1% Triton X-100). The MNase digestion was initiated by re-suspending rinsed cells in 40 ml reaction buffer (20 mM Tris, pH 7.4, 10 mM NaCl, 2 mM CaCl2, 0.1% Tx100) and incubated at 37 ℃ for 3 min. The reaction was stopped by adding 80 ml stop buffer (20 mM Tris, pH 8.0, 10 mM EGTA, 20 mM NaCl, 0.2% SDS) and 1 ml proteinase K, then incubated at 65 ℃ for overnight. DNAs were purified by phenol-chloroform extraction. The purified DNA was used for library preparation. For all ChIC-seq libraries, PCR was performed for 13-15 cycles and DNA fragments from 200 bp to 500 bp were isolated and sequenced on NovaSeq 6000 (Illumina).

treatment_protocol: Mate with stud male for pregrancy.

value: primary oviductal muscle cell

value: WT

value: Day 2 of pregrancy

tag: time

value: Day 2

tag: antibody

value: anti-IgG


title: D2 primary oviductal muscle cell IgG-3


title: Muscle_Baseline_Acute_rep16

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 65

source_name: Muscle biopsy untrained after exercise derived from subject 65

value: muscle


title: Muscle_Baseline_Acute_rep13

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 62

source_name: Muscle biopsy untrained after exercise derived from subject 62


title: Control 3


title: Muscle_Baseline_Acute_rep12

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 61

source_name: Muscle biopsy untrained after exercise derived from subject 61


title: AVD-1-44-3-6578B


title: AVD-1-834-10279A


title: Muscle_Baseline_Acute_rep17

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 66

source_name: Muscle biopsy untrained after exercise derived from subject 66


title: AVD-1-842-5650A


title: AVD-1-842-1920A


title: AVD-1-45-2-1523B


title: AVD-1-834-10715B


title: AVD-31-3-9289A


title: Muscle_Baseline_Acute_rep11

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 60

source_name: Muscle biopsy untrained after exercise derived from subject 60


title: Muscle_Baseline_Acute_rep9

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 58

source_name: Muscle biopsy untrained after exercise derived from subject 58


title: D2 primary oviductal muscle cell IgG-2


title: Muscle_Baseline_Acute_rep14

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 63

source_name: Muscle biopsy untrained after exercise derived from subject 63


title: Muscle_Baseline_Acute_rep10

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 59

source_name: Muscle biopsy untrained after exercise derived from subject 59


title: AVD-1-835-3340B


title: Muscle_Baseline_Acute_rep8

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 57

source_name: Muscle biopsy untrained after exercise derived from subject 57


title: AVD-1-44-5-11713B


title: D2 primary oviductal muscle cell Brg1-WT1


title: AVD-1-44-2-3298B


title: D2 primary oviductal muscle cell Brg1-WT3


title: D2 primary oviductal muscle cell Baf180-WT3


title: Muscle_Baseline_Acute_rep7

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 56

source_name: Muscle biopsy untrained after exercise derived from subject 56


title: D2 primary oviductal muscle cell Baf180-WT2


title: human astrocyte cultured with NCI-H69 #3

city: Stanford

first: Fangfei

last: Qu

state: CA California

address: SIM1 G2065, 265 Campus Drive

institute: Stanford University

data_processing:
RNA quantification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.28.1
Genome_build: GRCh38
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

source_name: human astrocytes co-cultured with NCI-H69

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

value: astrocyte

tag: coculture

value: with NCI-H69


title: AVD-31-3-7032A

value: female

value: unknown


title: D2 primary oviductal muscle cell Baf180-WT1


title: D2 primary oviductal muscle cell Brg1-WT2


title: Muscle_Baseline_Acute_rep6

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 55

source_name: Muscle biopsy untrained after exercise derived from subject 55


title: AVD-1-833-6862A

value: Left

value: colon polyp


title: D2 primary oviductal muscle cell    IgG-3


title: human astrocyte cultured with NCI-H69 #1


title: human astrocyte cultured with NCI-H69 #2


title: Muscle_Baseline_Acute_rep4

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 53

source_name: Muscle biopsy untrained after exercise derived from subject 53


title: D2 primary oviductal muscle cell    IgG-2


title: human astrocyte cultured with NCI-H82 #3

source_name: human astrocytes co-cultured with NCI-H82

value: with NCI-H82


title: D2 primary oviductal muscle cell    IgG-1


title: D2 primary oviductal muscle cell H3K4Me1-WT3


title: human astrocyte cultured with NCI-H82 #2


title: Muscle_Baseline_Acute_rep5

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 54

source_name: Muscle biopsy untrained after exercise derived from subject 54


title: human astrocyte cultured with NCI-H82 #1


title: Muscle_Baseline_Acute_rep3

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 52

source_name: Muscle biopsy untrained after exercise derived from subject 52


title: D2 primary oviductal muscle cell H3K4Me1-WT2

source_name: primary oviductal muscle cell


title: human astrocyte cultured alone #3

source_name: human astrocytes cultured alone

value: no


title: D2 primary oviductal muscle cell H3K4Me1-WT1


title: human astrocyte cultured alone #2


title: Muscle_Baseline_Acute_rep2

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 51

source_name: Muscle biopsy untrained after exercise derived from subject 51


title: human astrocyte cultured alone #1


title: Muscle_Baseline_Acute_rep1

description: Gene expression data from muscle biopsy untrained after exercise derived from subject 50

source_name: Muscle biopsy untrained after exercise derived from subject 50


title: AVD-31-4-5590B

source_name: FFPE sample


title: AVD-1-64-6-78A

value: male


title: AVD-31-4-3389A


title: AVD-1-44-6-7560A


title: AVD-1-63-6-2157A


title: Muscle_Post_Training_rep23

description: Gene expression data from muscle biopsy post training derived from subject 73

source_name: Muscle biopsy post training derived from subject 73

treatment_protocol: As described in the paper. Briefly, healthy, sedentary (<120 min of physical activity per week) individuals at high risk for T2D with at least one of the following risk factors (BMI>27 kg/m2, family history (first degree) of T2D, former gestational diabetes) were recruited. Criteria for recruitment and design of the exercise intervention were identical in both studies. 44 individuals (19 of study 1 and 25 of study 2) were included for data analysis. One subject participated in both studies and only data obtained in study 2 were used for further analyses. Severe diseases were excluded by anamnesis including medication, monitoring routine laboratory parameters, electrocardiogram, and physical examination.   The participants performed an 8-week supervised aerobic endurance exercise intervention program as described below. Individual training intensity was set at 80% of VO2peak determined before the intervention and kept constant throughout the training program. Insulin sensitivity was assessed after an overnight-fast by 75g-OGTT pre-intervention and 5 days after the last exercise bout; blood samples for clinical routine parameters were obtained before the glucose load. Vastus lateralis muscle biopsies were taken after end of the OGTT before and five days after the 8-week intervention.


title: Muscle_Post_Training_rep24

description: Gene expression data from muscle biopsy post training derived from subject 74

source_name: Muscle biopsy post training derived from subject 74


title: SUBr1 cell line

source_name: primary cancer cells isolated from SCLC patient brain metastasis

value: SCLC cell line NCI-H82


title: NCI-H82 co-cultured with human astrocytes #3

value: with human astrocytes


title: AVD-1-834-2705A


title: AVD-31-3-10195A

value: Right


title: Muscle_Post_Training_rep22

description: Gene expression data from muscle biopsy post training derived from subject 72

source_name: Muscle biopsy post training derived from subject 72


title: D2 primary oviductal muscle cell H3K27ac-WT3

value: primary oviductal muscle cell

value: WT


title: Muscle_Post_Training_rep20

description: Gene expression data from muscle biopsy post training derived from subject 70

source_name: Muscle biopsy post training derived from subject 70


title: Muscle_Post_Training_rep21

description: Gene expression data from muscle biopsy post training derived from subject 71

source_name: Muscle biopsy post training derived from subject 71


title: AVD-31-2-2950A

value: transverse colon


title: AVD-1-24-4-3593B


title: Muscle_Post_Training_rep19

description: Gene expression data from muscle biopsy post training derived from subject 69

source_name: Muscle biopsy post training derived from subject 69


title: NCI-H82 co-cultured with human astrocytes #2


title: AVD-1-44-4-8020A


title: AVD-1-44-5-8125A


title: D2 primary oviductal muscle cell H3K27ac-WT2

value: Day 2 of pregrancy

value: Day 2


title: D2 primary oviductal muscle cell Pbrm1 KO2

data_processing:
quality trim sequences and removing adapter sequences with cutadapt
aligning the reads with Bowtie2 against Mus musculus genome sequence
filter for uniquely mapped and non-duplicated reads
call peaks with macs2
IDR filter for conservertive peaks
Assembly: GRCm38.p5
Supplementary files format and content: conservertive reproduciable peaks in BED format

extract_protocol:
Oviduct were isolated and cut into small pieces (1-2 mm) and incubated (30-45 min) in rotation at 37 ℃ in pre-warmed DMEM/F12 (1:1) (Gibco), 12 mM HEPES (Gibco), 1% penicillin/streptomycin (Gibco), 2 mg/ml trypsin (Sigma), 400 U/ml collagenase type I (Invitrogen), and 5 U/ml dispase (Invitrogen). The digested cells were passed through a 70-mm filter to obtain a homogenous population of smooth muscle cells. Cells were plated in 100 mm dishes, containing DMEM and Ham F-12 media (1:1) (Gibco) with 12% charcoal-stripped fetal bovine serum (FBS) and antibiotics (penicillin-streptomycin, Thermo Fisher, 100 µg/mL). After 4 h, the medium was replaced with DMEM/F-12 (1:1) containing 10% FBS. 2 h later, the cells were gently washed twice with PBS and samples were prepared for ATAC-seq.  50-100K cell was isolated for ATAC-Seq.
ATAC-seq libraries were constructed (Buenrostro et al., 2013) using 50,000 mouse primary oviduct muscle cells. Cells were centrifuged (500 x g, 5 min, 4 °C), washed with 500 ml PBS and re-suspended in 50 ml of cold lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.1% digitonin), incubated on ice for 3 min, and diluted with 1 ml wash buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). After centrifugation (500 x g, 10 min, 4 °C), pelleted nuclei were re-suspended in 50 µl of transposition reaction consisting of 2x tagmentation buffer (25 µl), water (5 µl), PBS (16.5 µl), 10% Tween-20 (0.5 µl), 1% digitonin (0.5 µl) and 2.5 ml Tn5 Transposase enzyme (Illumina). After incubation (45 min, 37 °C) with gentle mixing, DNA was purified using a phenol/chloroform extraction kit protocol (Sigma-Aldrich) and eluted with 10 ml of elution buffer. Transposed DNA was amplified using barcoded PCR primers and cycling conditions of 72 °C for 5 min and 98 °C for 30 s followed by 12 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min. DNA fragments of nucleosome free regions (between primer-dimers and mono-nucleosome bands) corresponding to sequence insert <100 bp or >1000 bp were removed by double-sided beads purification. Libraries were eluted with 15 ml elution buffer for analysis of size distribution and 50 bp paired-end sequencing was provided by the NIDDK Genomic Core Facility.

value: Pbrm1 cKO


title: NCI-H82 co-cultured with human astrocytes #1


title: AVD-1-62-2-2403A


title: D2 primary oviductal muscle cell Pbrm1 KO1


title: AVD-31-3-2015A


title: D2 primary oviductal muscle cell H3K27ac-WT1


title: NCI-H82 cultured alone #2

source_name: NCI-H82 cultured alone


title: Muscle_Post_Training_rep18

description: Gene expression data from muscle biopsy post training derived from subject 68

source_name: Muscle biopsy post training derived from subject 68

value: muscle


title: Muscle_Post_Training_rep17

description: Gene expression data from muscle biopsy post training derived from subject 67

source_name: Muscle biopsy post training derived from subject 67


title: D2 primary oviductal muscle cell Pbrm1 KO3


title: NCI-H82 cultured alone #1


title: Muscle_Post_Training_rep16

description: Gene expression data from muscle biopsy post training derived from subject 65

source_name: Muscle biopsy post training derived from subject 65


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 20C replicate 3

city: Abu Dhabi

first: Daniel

middle: Michael

last: Ripley

address: NYUAD

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Reads filtered using sortmeRNA and DeconSeq , and reads with low quality scores removed using Trimmomatic
Transcripts assembled in Trinity 2.8.4; (Transcripts generated from all 6 samples in Trinity in fasta format)
abundance estimates generated using Kallisto
Supplementary_files_format_and_content: Abundance estimates for each individual, in .tsv format

organism: Scyliorhinus canicula

extract_protocol:
total RNA of the tissue was extracted using the Qiagen kit with homogenisation
TruSeq® Stranded mRNA assay (Illumina, Inc.)

tag: embryonic temperature

value: ventricle


title: AVD-1-842-2602A

value: female


title: D2 primary oviductal muscle cell WT2


title: AVD-1-46-3-4830B

value: Left


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 15C replicate 3


title: Muscle_Post_Training_rep15

description: Gene expression data from muscle biopsy post training derived from subject 64

source_name: Muscle biopsy post training derived from subject 64


title: D2 primary oviductal muscle cell WT1

source_name: primary oviductal muscle cell


title: AVD-1-63-6-325A

value: colon polyp


title: BMDM, KO, M2, rep3

city: Shanghai

first: Yuanwen

address: No.221 Yan’an West Road

department: Department of Gastroenterology

institute: Huadong Hospital Affiliated to Fudan University

data_processing:
Raw reads in fastq format of RNA-seq were firstly processed using Trimmomatic (v0.36) and the low-quality reads were removed to obtain the clean reads for subsequent analyses.
Clean reads were aligned to the mouse genome (GRCm39) using hisat2 (v2.2.1.0) with the default parameter settings.
The aligned reads were assembled into transcripts using stringtie2 (v1.3.3b).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes counts for each Sample

source_name: Primary bone marrow-derived macrophages (BMDM)

extract_protocol:
Total RNA was isolated via TRIzol reagent. A total amount of 500 ng RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were subsequently constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Prep-/-

value: IL4 (20 ng/ml) and IL13 (20ng/ml) for 24hrs


title: D2 primary oviductal muscle cell WT3


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 15C replicate 2


title: Muscle_Post_Training_rep14

description: Gene expression data from muscle biopsy post training derived from subject 63

source_name: Muscle biopsy post training derived from subject 63


title: BMDM, KO, M2, rep2

value: Primary bone marrow-derived macrophages (BMDM)


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 20C replicate 2


title: BMDM, KO, M2, rep1


title: Muscle_Post_Training_rep13

description: Gene expression data from muscle biopsy post training derived from subject 62

source_name: Muscle biopsy post training derived from subject 62


title: AVD-1-44-6-2365A

source_name: FFPE sample

value: male


title: BMDM, KO, M1, rep3

value: LPS (50ng/ml) for 24hrs


title: Muscle_Post_Training_rep12

description: Gene expression data from muscle biopsy post training derived from subject 61

source_name: Muscle biopsy post training derived from subject 61


title: AVD-1-72-4-4475A


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 15C replicate 1


title: AVD-1-19-5-7276A


title: 200720130106_R08C01

type: genomic

description:
LESION: adenoma at baseline
AGE: age (years)
IS_FEMALE: 1=F, 0=M
ADEN_GRADE: grading score adenoma
ADEN_SIZE: size (mm)
ADEN_LEFT: adenoma located at left colon
ADEN_3PLUS: 3 or more adenomas in patient
ADEN_LT_1CM: adenoma larger than 1 cm
ADEN_HAS_HGD: adenoma has high grade dysplasia

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Data belonging to both 450K and EPIC platform was normalized using "preprocessFunnorm" subroutine from "Minfi" package version 1.42.0.
850k_matrix.txt: methylation β-values (ratio of the methylated probe intensity and the overall intensity)

label: Cy3, Cy5

extract_protocol: DNA was extracted from 2-3 slices (10 µm) from the FFPE samples (Qiagen), quantified using PicoGreen and checked for quality using the Illumina FFPE QC Kit. The DNA was then subjected to bisulfite conversion (EZ DNA methylation kit, Zymo Research) and controlled by two in-house qPCRs. Next, 250 ng DNA was subjected to Illumina’s FFPE restoration protocol. Data were processed in two batches: the first batch was profiled on Illumina Infinium 450K beadchips, the second batch was run on Infinium EPIC (850K) beadchips.

tag: patientid

tag: lesion

tag: bmi


title: BMDM, KO, M1, rep1

tag: genotype

tag: treatment


title: 200720130106_R07C01


title: Muscle_Post_Training_rep10

description: Gene expression data from muscle biopsy post training derived from subject 59

source_name: Muscle biopsy post training derived from subject 59

tag: tissue


title: Muscle_Post_Training_rep11

description: Gene expression data from muscle biopsy post training derived from subject 60

source_name: Muscle biopsy post training derived from subject 60


title: Muscle_Post_Training_rep9

description: Gene expression data from muscle biopsy post training derived from subject 58

source_name: Muscle biopsy post training derived from subject 58


title: AVD-1-44-4-7307B


title: AVD-1-44-5-8225A

value: Right


title: 200720130106_R06C01


title: BMDM, KO, M0, rep3

tag: cell type

value: No treatment


title: Ventricle tissue from a juvenile Scyliorhinus canicula incubated at 20C replicate 1


title: AVD-1-833-6148A


title: BMDM, KO, M0, rep2


title: Muscle_Post_Training_rep7

description: Gene expression data from muscle biopsy post training derived from subject 56

source_name: Muscle biopsy post training derived from subject 56


title: AVD-1-834-10319A


title: 200720130106_R04C01


title: BMDM, KO, M0, rep1


title: Muscle_Post_Training_rep5

description: Gene expression data from muscle biopsy post training derived from subject 54

source_name: Muscle biopsy post training derived from subject 54


title: BMDM, KO, M1, rep2


title: AVD-1-44-3-6472B


title: 200720130106_R03C01


title: BMDM, Hete, M2, rep3

value: Prep+/-


title: AVD-1-20-6-4831B


title: 200720130106_R02C01


title: Muscle_Post_Training_rep6

description: Gene expression data from muscle biopsy post training derived from subject 55

source_name: Muscle biopsy post training derived from subject 55


title: BMDM, Hete, M2, rep2


title: 200720130106_R01C01


title: Muscle_Post_Training_rep8

description: Gene expression data from muscle biopsy post training derived from subject 57

source_name: Muscle biopsy post training derived from subject 57


title: AVD-1-835-2920A


title: Muscle_Post_Training_rep4

description: Gene expression data from muscle biopsy post training derived from subject 53

source_name: Muscle biopsy post training derived from subject 53


title: Muscle_Post_Training_rep3

description: Gene expression data from muscle biopsy post training derived from subject 52

source_name: Muscle biopsy post training derived from subject 52


title: BMDM, Hete, M1, rep3


title: AVD-31-2-5501A


title: AVD-1-44-1-4073B


title: BMDM, Hete, M2, rep1


title: 200720130067_R07C01


title: 200720130067_R05C01


title: AVD-1-44-2-9868B


title: 200720130067_R04C01


title: Huh7-HBx cells with Doxycycline treatment, m6A enriched

city: Suzhou

first: Enakshi

last: Sivasudhan

address: 111, Ren'ai Road, Suzhou Industrial Park

institute: Xi'an Jiaotong Liverpool University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore v.2.9 (parameter --stringency 3)
Trimmed data were analyzed quality control using fastqc.
Tremmed sequence reads were mapped to GRCh38/hg38 using hisat2 v.2.1.0 (parameter -p 20)
Sam files were convert to Bam files using samtools v.1.7.
Bam files were used to call peaks and call differential anaylsis by using exomePeak2.
Assembly: hg38
Supplementary files format and content: A txt file include peaks calling results using exomePeak2.
Library strategy: MeRIP-Seq

molecule: polyA RNA

growth_protocol: Huh7 cells were grown in DMEM media containing 10% FBS and maintained in 5% CO2 at 37 C.

extract_protocol:
MeRIP sample preparations were carried out as described in riboMeRIPTM m6A Transcriptome Profilling Kit (C1105 1-1) and RNA was harvested using the Trizol method following manufacturer's instructions.
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB)

treatment_protocol: Huh7 cells were stably transfected with HBx using lentiviral based inducible system.

tag: cell line

value: Liver cancer cells

value: IP

value: With HBx


title: Huh7-HBx cells with Doxycycline treatment, Input control

value: Input


title: 200720130067_R03C01


title: BMDM, Hete, M1, rep1


title: Muscle_Post_Training_rep1

description: Gene expression data from muscle biopsy post training derived from subject 50

source_name: Muscle biopsy post training derived from subject 50

value: muscle


title: BMDM, Hete, M0, rep3


title: 200720130067_R01C01


title: Huh7-HBx cells without Doxycycline treatment, m6A enriched

value: Without HBx


title: BMDM, Hete, M0, rep2


title: Muscle_Baseline_rep24

description: Gene expression data from muscle biopsy before training derived from subject 73

source_name: Muscle biopsy before training derived from subject 73


title: Muscle_Baseline_rep23

description: Gene expression data from muscle biopsy before training derived from subject 72

source_name: Muscle biopsy before training derived from subject 72


title: Muscle_Baseline_rep25

description: Gene expression data from muscle biopsy before training derived from subject 74

source_name: Muscle biopsy before training derived from subject 74


title: Huh7-HBx cells without Doxycycline treatment, Input control


title: 200722330054_R08C01


title: 200722330054_R06C01


title: BMDM, Hete, M0, rep1

source_name: Primary bone marrow-derived macrophages (BMDM)


title: BMDM, Hete, M1, rep2


title: BMDM, PREP, binding, M2

data_processing:
Paired-end reads of CUT&Tag-seq were aligned to mm10 genome using Bowtie2 (v2.3.4.3) with options: --end-to-end --sensitive. Deeptools (3.3.2) was used to generate the read coverage track (command bamCoverage with normalization by RPKM), and calculate scores per genome regions (command computeMatrix) .
For peak calling of CUT&Tag-seq, bigwig files containing RPKM-normalized CUT&Tag signal produced by bamCoverage were firstly converted to bedGraph files by bigWigToBedGraph in UCSC Toolkit. Peak calling was then performed using command bdgpeakcall in macs2 (v2.1.4) with cutoff options (-c 160 -l 320 -g 20). Peak annotations and metagene profiles were performed with R package ChIPseeker (v1.30.3)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (NovoProtein, Cat. #N259) was used for CUT&Tag library preparation according to the manufacturer’s recommendations. Briefly, 1 × 105 cells were bound to Concanavalin A (ConA)–coated magnetic beads and were incubated with a primary rabbit anti-prolyl endopeptidase (1:100, Abcam, CAT. #ab58988) for 2 h at room temperature (RT). Then cells were shifted to incubation with ChiTag Goat anit-Rabbit IgG antibody (1:200) antibody for 1 h at RT.
After washing by Wash buffer, cells were incubated with NovoNGS® ChiTag™ pAG-Tn5 for 1 h at RT. After washing by ChiTag Buffer, cells were resuspended in 50 μl of Tagmentation Buffer and incubated for 1 h at 37°C, followed by heat inactivation at 55°C for 10 min to stop the reaction. DNA fragments were extracted by Tagment DNA Extract Beads and amplified by using N5&N7 primers and 5×AmpliMix. After DNA purification by NovoNGS® DNA Clean Beads, libraries were sequenced on Illumina NovaSeq 6000 for generation of 150-bp paired-end reads.


title: AVD-1-44-3-9228A

tag: Sex

value: female


title: BMDM, PREP, binding, M1


title: HepG2-HBx cells with Doxycycline treatment, bio rep 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter - paired)
Tremmed sequence reads were mapped to GRCh38/hg38 using hisat2 v.2.1.0 (parameter --rna-strandness FR -p 20)
Sam files after mapped to the genome were convert to Bam files using samtools v.1.7.
Generate read counts by using featureCount v.1.6.2
Reads counts were used for differential anaylsis using DESeq2 v.1.26.0.
Assembly: hg38
Supplementary files format and content: A txt file include raw counts for each sample.

growth_protocol: Huh7 and HepG2 cells were grown in DMEM media containing 10% FBS and maintained in 5% CO2 at 37 C.

extract_protocol: RNA was harvested using the Trizol method following manufacturer's instructions.

treatment_protocol: Huh7 and HepG2 cells were stably transfected with HBx using lentiviral based inducible system.

value: With Doxycycline


title: HepG2-HBx cells with Doxycycline treatment, bio rep 1


title: 200722330054_R04C01

tag: age


title: Muscle_Baseline_rep22

description: Gene expression data from muscle biopsy before training derived from subject 71

source_name: Muscle biopsy before training derived from subject 71


title: HepG2-HBx cells without Doxycycline treatment, bio rep 2

value: Without Doxycycline


title: Muscle_Post_Training_rep2

description: Gene expression data from muscle biopsy post training derived from subject 51

source_name: Muscle biopsy post training derived from subject 51


title: Muscle_Baseline_rep21

description: Gene expression data from muscle biopsy before training derived from subject 70

source_name: Muscle biopsy before training derived from subject 70


title: Muscle_Baseline_rep19

description: Gene expression data from muscle biopsy before training derived from subject 68

source_name: Muscle biopsy before training derived from subject 68


title: AVD-31-4-4138A

source_name: FFPE sample

tag: localization

value: Left

value: colon polyp


title: Muscle_Baseline_rep20

description: Gene expression data from muscle biopsy before training derived from subject 69

source_name: Muscle biopsy before training derived from subject 69


title: HepG2-HBx cells without Doxycycline treatment, bio rep 1


title: 200722330054_R03C01

description:
LESION: adenoma at baseline
AGE: age (years)
IS_FEMALE: 1=F, 0=M
ADEN_GRADE: grading score adenoma
ADEN_SIZE: size (mm)
ADEN_LEFT: adenoma located at left colon
ADEN_3PLUS: 3 or more adenomas in patient
ADEN_LT_1CM: adenoma larger than 1 cm
ADEN_HAS_HGD: adenoma has high grade dysplasia


title: BMDM, PREP, binding, M0

value: Primary bone marrow-derived macrophages (BMDM)


title: Muscle_Baseline_rep18

description: Gene expression data from muscle biopsy before training derived from subject 67

source_name: Muscle biopsy before training derived from subject 67


title: Huh7-HBx cells with Doxycycline treatment, bio rep 2


title: Control-2

description: brain cells isolated from sham brain injection control

data_processing:
Sequenced reads were demultiplxed and aligned to the mm10 genome using CellRanger 6.0 software
The cell count matrix was generated using CellRanger count function.
The output matrices of replicates corrsponding to the same treatment were aggregated using the Cellranger aggr function with default parameters
Assembly: mm10
Supplementary files format and content: The processed files are folders containing the following three files:aggregated_treatment_barcodes.tsv.gz, aggregated_treatment_features.tsv.gz and aggregated_treatment_matrix.mtx.gz

source_name: brain cell

growth_protocol: SCLC mouse brain allograft

extract_protocol:
FACS sort for GFP- DAPI- cells
3'V3.1 Dual index kit for 10X scRNA seq

value: brain cell

tag: brain region

value: sham injection


title: 200722330054_R02C01


title: Muscle_Baseline_rep17

description: Gene expression data from muscle biopsy before training derived from subject 66

source_name: Muscle biopsy before training derived from subject 66


title: 200722330054_R05C01


title: Huh7-HBx cells with Doxycycline treatment, bio rep 1


title: 200722330054_R01C01


title: Muscle_Baseline_rep16

description: Gene expression data from muscle biopsy before training derived from subject 65

source_name: Muscle biopsy before training derived from subject 65


title: Control-1


title: Huh7-HBx cells without Doxycycline treatment, bio rep 2


title: 200722330053_R07C01


title: Tumor edge-1

description: brain cells isolated from SCLC brain allograft tumor edge

value: SCLC brain allograft tumor edge


title: Huh7-HBx cells without Doxycycline treatment, bio rep 1


title: 200722330053_R08C01


title: Tumor edge-2


title: Tumor core-2

description: brain cells isolated from SCLC brain allograft tumor core

value: SCLC brain allograft tumor core


title: 200722330053_R06C01


title: 200722330053_R05C01


title: Muscle_Baseline_rep14

description: Gene expression data from muscle biopsy before training derived from subject 63

source_name: Muscle biopsy before training derived from subject 63


title: T24 cells, siRNA2 bio rep 2

city: Guangzhou

first: Ning

last: Jiang

state: Guangdong

address: Industrial middle 253, Haizhu district

institute: Southern Medical University

data_processing:
FastQC software for quanlity control
Adaptor sequence was trimmed using cutadapt software from sequenced reads which were masked for low-complexity or low-quality sequence
Trimmed sequences were mapped to hg38 whole genome unsing STAR software
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted using RNAiso Plus (Takara), using Oligo dT beads to enrich mRNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder cancer cells


title: T24 cells, siRNA2 bio rep 1


title: T24 cells, siRNA1 bio rep 2


title: Muscle_Baseline_rep13

description: Gene expression data from muscle biopsy before training derived from subject 62

source_name: Muscle biopsy before training derived from subject 62


title: 200722330053_R04C01


title: Muscle_Baseline_rep15

description: Gene expression data from muscle biopsy before training derived from subject 64

source_name: Muscle biopsy before training derived from subject 64


title: Muscle_Baseline_rep12

description: Gene expression data from muscle biopsy before training derived from subject 61

source_name: Muscle biopsy before training derived from subject 61


title: 200722330053_R03C01


title: Tumor core-1


title: T24 cells, siRNA1 bio rep 1


title: Muscle_Baseline_rep10

description: Gene expression data from muscle biopsy before training derived from subject 59

source_name: Muscle biopsy before training derived from subject 59


title: T24 cells, siControl bio rep 2


title: 200722330053_R02C01


title: 200722330053_R01C01


title: T24 cells, siControl bio rep 1


title: Muscle_Baseline_rep11

description: Gene expression data from muscle biopsy before training derived from subject 60

source_name: Muscle biopsy before training derived from subject 60


title: 200722330034_R07C01


title: 200722330034_R06C01


title: Extracellular vesicles pool 2

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

data_processing:
Data was processed in R computing environment (version 4.1.3).
Quality of sequencing was assessed by FastQC. Raw data was processed to eliminate adapters and to clean lecture sequences based on their size using bbduk package.
miRNAs were aligned using subread software and annotated with miRbase using human genome reference HG38.
Normalization of number of lectures per sample was performed calculating Trimmed mean M-values in edgeR, obtaining Counts Per Million (CPM).
Assembly: HG38
Supplementary files format and content: Column-delimited excel file include CPM values for each sample

source_name: Extracellular vesicles secreted by cultured cells

extract_protocol:
Total RNA from extracellular vesicles was extracted with miRNeasy Mini Kit (Qiagen).
Libraries of miRNAs were prepared using NEXTFLEX® Small RNA-Seq v3 for Illumina Platforms (Bioo Scientific®) following manufacturer's protocols.

value: primary human endometrial epithelial cells

value: 10−8 M β-estradiol and 10−7 M progesterone hormonal treatment


title: Extracellular vesicles pool 3


title: Muscle_Baseline_rep8

description: Gene expression data from muscle biopsy before training derived from subject 57

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

source_name: Muscle biopsy before training derived from subject 57

extract_protocol: RNA extraction was performed using the miRneasy kit (Qiagen)


title: 200722330034_R05C01


title: Extracellular vesicles pool 1


title: Muscle_Baseline_rep9

description: Gene expression data from muscle biopsy before training derived from subject 58

source_name: Muscle biopsy before training derived from subject 58


title: Muscle_Baseline_rep7

description: Gene expression data from muscle biopsy before training derived from subject 56

source_name: Muscle biopsy before training derived from subject 56


title: 200722330034_R04C01


title: 200722330034_R03C01


title: 200722330034_R02C01


title: NPM1C-KI-LK-ATAC-seq_2

first: Huacheng

last: Luo

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq and HiC-seq reads  were aligned to the hg19 or mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Assembly: mm9, hg19
Supplementary files format and content: tab-delimited text files include count values for RNA-seq, and peaks for ATAC-seq, and interaction contact file for HIC-seq samples.

organism: Mus

source_name: Bone marrow Lin-  Kit+ cells

growth_protocol: Total bone marrow LK cells were isolate from WT and NPM1C+ KI mice, and were sorted with Lin- and Kit+ markers.  Human OCI-AML3 leukemia cells were culture with alpha-MEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.  HiC-seq libraries were prepared according to KAPA HyperPrep Kits (KK8500).

treatment_protocol: Immediately extract total RNA from OCI-AML3 AML cells with and without Selinexor (KPT-330, XPO1 inhibitor) treatment.

tag: cell types

value: Mouse-derived Bone marrow cells

value: Bone marrow

tag: cell subtype

value: Lin-  Kit+ cells


title: 200722330034_R01C01

source_name: FFPE sample


title: WT_6_04

city: Birmingham

first: Hayden

last: Pacl

state: AL

address: 845 19th St S, BBRB 308

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Illumina BCL image files were converted to FASTQ files using Illumina's bcl2fastq version 2.18.12 software
STAR (version 2.7.5b) was used to align the raw FASTQ files to the mouse genome using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment (BAM) files using HTSeq-count (version 0.11.3) using parameters -r pos -t exon -i gene_id -a 10 -s no - f bam
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: Excel file (tab-delimited) containing Ensembl ID#s and raw transcript abundances associated with each ID# and sample

source_name: Whole lung

extract_protocol:
RNA was isolated from the lungs of Mtb-infected mice stored in RNAlater (Thermo Fisher Scientific, AM7024) at -80 °C using the RNeasy plus Mini Kit (Qiagen, 74134) according to the manufacturers protocol.
RNA passing quality control was converted to a sequencing ready library using the NEBNext Ultra II Directional RNA library kit with polyA selection as per the manufacturer’s instructions (New England Biolabs).
The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems) prior to cluster generation.

value: Whole lung

value: LDHAfl/fl:LysM-/- (WT)

value: Infection with Mtb

tag: time point

value: 4 weeks


title: PA14 delta-amrZ delta-ptsP cells, biol rep 1

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

data_processing:
Sequence reads were processed and trimmed using FastQC and Cutadapt
Sequence reads were aligned to genome using Bowtie 2.
Differential gene expression analysis was processed using EdgeR.
All software was set using default parameters.
Assembly: NC_008463
Supplementary files format and content: Excel file includes gene list with max group means, log2 and raw fold changes, P values and false discovery rate (FDR) P-values

organism: Pseudomonas aeruginosa

source_name: whole cells

growth_protocol: P. aeruginosa strains as noted were grown for 3 d on M6301-1% agar at 25C in a standard microbiological incubator

extract_protocol:
Total RNA was extracted using the NEB Monarch total RNA extraction kit according to the manufacturer's protocol for gram-negative bacteria. Ribosomal RNA was removed using the Ribo-Zero kit.
Libraries were constructed using the NEB directional kit according to the manufacturer's protocol.

value: whole cells

value: delta-amrZ delta-ptsP


title: PA14 delta-amrZ delta-ptsP cells, biol rep 3


title: PA14 delta-amrZ delta-ptsP cells, biol rep 2


title: NPM1C-KI-LK-ATAC-seq_1

city: Hangzhou


title: WT-LK-ATAC-seq_2


title: 200722330031_R07C01


title: WT_5_30

value: 30 weeks


title: Muscle_Baseline_rep6

description: Gene expression data from muscle biopsy before training derived from subject 55

source_name: Muscle biopsy before training derived from subject 55

value: muscle


title: Muscle_Baseline_rep4

description: Gene expression data from muscle biopsy before training derived from subject 53

source_name: Muscle biopsy before training derived from subject 53


title: 200722330031_R08C01

description:
LESION: adenoma at baseline
AGE: age (years)
IS_FEMALE: 1=F, 0=M
ADEN_GRADE: grading score adenoma
ADEN_SIZE: size (mm)
ADEN_LEFT: adenoma located at left colon
ADEN_3PLUS: 3 or more adenomas in patient
ADEN_LT_1CM: adenoma larger than 1 cm
ADEN_HAS_HGD: adenoma has high grade dysplasia


title: 200722330031_R05C01


title: WT_5_04


title: WT-LK-ATAC-seq_1


title: WT_4_04


title: Muscle_Baseline_rep3

description: Gene expression data from muscle biopsy before training derived from subject 52

source_name: Muscle biopsy before training derived from subject 52


title: Muscle_Baseline_rep1

description: Gene expression data from muscle biopsy before training derived from subject 50

source_name: Muscle biopsy before training derived from subject 50


title: WT_3_30


title: 200722330031_R04C01


title: NPM1C-KI-LK-RNA-seq_2


title: NPM1C-KI-LK-RNA-seq_1


title: Muscle_Baseline_rep2

description: Gene expression data from muscle biopsy before training derived from subject 51

source_name: Muscle biopsy before training derived from subject 51


title: 200722330031_R02C01


title: WT-LK-RNA-seq_2


title: KO_6_04

value: LDHAfl/fl:LysM+/- (KO)


title: WT-LK-RNA-seq_1


title: 200722330031_R01C01


title: Prmt5-CKO EAE SP scRNA-seq

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
For single-cell RNA-seq, cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Genome_build: GRCm38
Supplementary_files_format_and_content: For single-cell RNA-seq, MTX file and TSV file contain counts for each barcodes and genes. "matedata.csv" contain contains genotype information for the cells.

source_name: Spleen

extract_protocol:
Single-cell suspensions were harvested from fresh tissues according to standard procedures. For single-cell RNA-seq, single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
For single-cell RNA-seq, RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Prmt5 CKO and control mice (3 mice per group) were induced EAE by MOG35–55/CFA immunization, on the day the score peaked, cells were isolated from spleen.

tag: strain

value: spleen cells

value: CD4-Cre+ PRMT5fl/fl


title: KO_5_30


title: Muscle_Baseline_rep5

description: Gene expression data from muscle biopsy before training derived from subject 54

source_name: Muscle biopsy before training derived from subject 54


title: KO_5_04


title: 200722330026_R08C01


title: WT EAE SP scRNA-Seq

value: wild type


title: Prmt5-CKO EAE SP scATAC-seq

data_processing:
Cell Ranger ATAC version 3.0.2 (10x Genomics) was used to perform demultiplexing and read alignment. scATAC-seq data from two types of mice (Control and Prmt5-CKO) underwent quality control analysis and filtering based on the number of fragments in peaks, the fraction of fragments in peaks, the ratio of fragments in the blacklist, transcriptional start site enrichment score and the nucleosome banding pattern.
Genome_build: GRCm38
Supplementary_files_format_and_content: ATAC-seq fragments captured by the assay, analyzed by Cell ranger

extract_protocol:
Single-cell suspensions were harvested from fresh tissues according to standard procedures.  For single-cell ATAC-seq, nuclei were prepared as outlined in the 10X Genomics Chromium single cell ATAC-seq solution protocol.
For single-cell ATAC-seq, libraries were prepared for sequencing following the 10X Genomics single cell ATAC-seq solution protocol and prepared for sequencing using standard Illumina protocols


title: 200722330026_R05C01


title: 200722330026_R06C01


title: KO_4_04


title: WT EAE SP scATAC-Seq


title: Liver, Control (NASH Diet)_9

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

description: Data can be used by nSolver Software

hyb_protocol: Hyb protocol from NanoString Technologies, Inc.

scan_protocol: Scan protocol from NanoString Technologies, Inc.

data_processing: Gene expression data was normalized and log-transformed prior to differential gene expression analysis and pathway signature score computation using NanoString Technologies’ nSolver 4.0 software (version 4.0.70) and the embedded PLAGE algorithm.

label: Nanostring label

source_name: Liver

label_protocol: Label protocol from NanoString Technologies, Inc.

extract_protocol: Liver tissue (~15 mg) was lysed in 1 mL TRIzol reagent (Invitrogen) using ceramic beads and a Precellys 24 homogenizer (Bertin Technologies). Samples were spun down for 10 mins at 12 000 g at 4 ºC. 200 µL of chloroform was added and shaken vigorously before spinning samples again at same settings. Supernatant was placed in new tubes and an equal amount of 70% ethanol was added then vortexed. Solutions were loaded onto RNeasy columns and manufacturer’s instructions were followed including a DNAse I digestion step (Qiagen).

treatment_protocol: At 8 weeks of age, mice were moved into specific-pathogen free (SPF) microisolators in a room maintained at ~29 ºC and fed a high-fat, high-fructose diet (NASH Diet; ND; 40% fat from mostly palm, 20% fructose, 0.02% cholesterol). Due to fructose being supplemented in the diet, diet was changed every few weeks. 16 weeks later, mice were grouped by matching body weight and adiposity randomly and placed on respective interventional arms. Adiposity was assessed based on time-domain NMR using a Bruker Minispec LF90II. Control mice were continued on diet alone, vehicle-treated mice (Vehicle) were given subcutaneous saline injections every second day 1-2 hrs before the dark cycle, bempedoic acid-treated mice (BemA) had the drug supplemented in the diet at a dose of 10 mg/kg, liraglutide-treated mice (Lira) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle, and combination-treated mice (Lira+BemA) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle with bempedoic acid supplemented in the diet at a dose of 10 mg/kg.

tag: diet

value: NASH diet

value: Saline

value: mouse liver


title: Liver, Control (NASH Diet)_8

description: Data can be used by nSolver Software


title: KO_3_30


title: KO_6_30


title: 200722330026_R04C01

tag: patientid


title: Liver, Control (NASH Diet)_7

description: Data can be used by nSolver Software


title: 200722330026_R03C01

tag: lesion


title: SP CD8 Prmt5-CKO_77

data_processing:
For RNA-Seq, before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to the mouse genome (GRCm38) using Hisat2. HTseq was used to obtain gene counts, and the FPKM method was used to determine gene expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: For RNA-Seq, Matrix table with raw gene counts/fpkm for every gene and every sample.

extract_protocol:
Single-cell suspensions were harvested from fresh tissues according to standard procedures and surface-stained in FACS buffer with monoclonal antibodies. Related T cell subsets from mice spleen or thymus were sorted with FACS Aria II Cell Sorter.  For bulk RNA-seq, total RNA was extracted from tissue by Trizol reagent.
For bulk RNA-seq, complementary DNA (cDNA) libraries were prepared using the NEBNextTM Ultra Directional RNA Library Prep Kit, NEBNext Poly (A) mRNA Magnetic Isolation Module, and NEBNext Multiplex Oligos according to the manufacturer’s instructions. The products were purified and enriched by PCR to create the final cDNA libraries.

value: T cells


title: Liver, Control (NASH Diet)_6

description: Data can be used by nSolver Software


title: SP CD8 WT_80


title: 200722330022_R08C01

tag: bmi


title: Male Bladder tumor pool 5

city: Los Angeles

first: Saravana Kumar

last: Kailasam Mani

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description:
10x Genomics
MB5

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated files containing features
Supplementary files format and content: Tab-separated files containing barcodes
Supplementary files format and content: Matrix files containing expression data

source_name: Bladder

extract_protocol:
Tumors were cut into approximately 0.5-2mm3 samples, transferred to a gentleMACS C-tube (Miltenyi Biotec) containing 2.3 ml of cold DMEM media. Once all the tumors had been processed, 100ul of Enzyme D, 50ul of Enzyme R, and 12.5ul of Enzyme A were added to each gentleMACS C-tube. The C-tubes were attached to the gentleMACS Dissociator with heater and incubated for 30 min at 37°C.  Once the dissociation program completed, the cell suspension was passed through a pre-wetted 40um cell strainer (Falcon), washed with cold PBS and centrifuged for 5 min at 500g at 4°C. Samples were depleted of red blood cells (RBC) using ACK Lysing buffer (Gibco). Cells were centrifuged and resuspend with 5mL FACS buffer. Dead Cell Removal Kit (Miltenyi Biotec) was further used to remove dead cells. We obtained the single-cell suspension and detected live cells using a hemocytometer with trypan blue.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bladder

value: 32-50 weeks old

value: Male

value: BBN


title: 200722330022_R07C01


title: Male Bladder tumor pool 4

description:
10x Genomics
MB4


title: SP CD8 WT_63

tag: genotype


title: SP CD4 Prmt5-CKO_77


title: Liver, Control (NASH Diet)_5

description: Data can be used by nSolver Software

tag: treatment


title: Liver, Control (NASH Diet)_4

description: Data can be used by nSolver Software

tag: tissue


title: Male Bladder tumor pool 2

description:
10x Genomics
MB2


title: 200722330022_R05C01


title: Liver, Control (NASH Diet)_3

description: Data can be used by nSolver Software


title: 200722330022_R03C01


title: 200722330022_R02C01


title: SP CD8 Prmt5-CKO_66

tag: cell type


title: Female Bladder tumor pool 5

description:
10x Genomics
FB5

value: Female


title: Liver, Control (NASH Diet)_2

description: Data can be used by nSolver Software


title: SP CD4 WT_82


title: 200722330021_R08C01


title: SP CD4 WT_63


title: Liver, Lira injections (NASH Diet)_5

description: Data can be used by nSolver Software

value: Liraglutide (70 µg/kg)


title: Liver, Control (NASH Diet)_1

description: Data can be used by nSolver Software


title: DA3/EPOR Escaped rep 3

city: Toronto

first: Sam

last: Benchimol

state: ON

address: 4700 Keele St.

institute: York University

data_processing:
Genome Quebec performed base calling
First 13 bases of sequenced reads trimmed using Trimmomatic due to low-quality sequence, then mapped to grcm38 (mm10) whole genome using HiSAT2  --dta --rna-strandness RF -1.
Reads were counted using HTSEQ
Normalization of counts and differential expression was calculated using EdgeR, as described by Chen et al., (2008).
Genome_build: grcm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for read genes fo each Sample

source_name: DA3/EPOR cells

growth_protocol: DA3/EPOR cells were grown in RPMI 1640 supplemntented with 1U EPO and 10% FBS

extract_protocol:
Total RNA was isolated using Monarch Total RNA Miniprep Kit (New England BioLabs) as described by the manufacturer. A poly-A tail selection was performed by Genome Quebec
RNA libraries were prepared for sequencing by Genome Quebec

treatment_protocol: Senescent and Escaped DA3/EPOR cells were treated with 200ng/ml Doxorubicin for 24 hours and allowed to recover in Doxorubicin free media for 3 and 9 days, respectively.

tag: cell line

value: DA3/EPOR cells

tag: group

value: Escaped

tag: disease

value: Leukemia


title: Female Bladder tumor pool 3

description:
10x Genomics
FB3

tag: age

tag: Sex


title: Female Bladder tumor pool 4

description:
10x Genomics
FB4


title: Male Bladder tumor pool 3

description:
10x Genomics
MB3


title: DA3/EPOR Escaped rep 1


title: Female Bladder tumor pool 1

description:
10x Genomics
FB1


title: Liver, Lira injections (NASH Diet)_4

description: Data can be used by nSolver Software


title: Liver, Lira injections (NASH Diet)_3

description: Data can be used by nSolver Software


title: 200722330021_R05C01

first: Yuba

address: 1650 Orleans Street

institute: The Johns Hopkins University School of Medicine

data_processing:
Data belonging to both 450K and EPIC platform was normalized using "preprocessFunnorm" subroutine from "Minfi" package version 1.42.0.
850k_matrix.txt: methylation β-values (ratio of the methylated probe intensity and the overall intensity)

extract_protocol: DNA was extracted from 2-3 slices (10 µm) from the FFPE samples (Qiagen), quantified using PicoGreen and checked for quality using the Illumina FFPE QC Kit. The DNA was then subjected to bisulfite conversion (EZ DNA methylation kit, Zymo Research) and controlled by two in-house qPCRs. Next, 250 ng DNA was subjected to Illumina’s FFPE restoration protocol. Data were processed in two batches: the first batch was profiled on Illumina Infinium 450K beadchips, the second batch was run on Infinium EPIC (850K) beadchips.


title: Female Bladder tumor pool 2

description:
10x Genomics
FB2


title: Liver, Lira injections (NASH Diet)_2

description: Data can be used by nSolver Software


title: 200722330021_R06C01


title: DA3/EPOR Senescent rep 3

value: Senescent


title: Male Bladder tumor pool 1

description:
10x Genomics
MB1


title: SP CD4 Prmt5-CKO_73


title: MUTSU2_AllGFP-S5

city: Syracuse

first: Samantha

middle: Jane

last: England

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

description: 10x Genomics

data_processing:
We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software (https://www.10xgenomics.com)
We analyzed the data using Partek Flow Genomic Analysis Software (https://www.partek.com/partek-flow/). Multiplets were removed by filtering out cells with >12,000 counts and >2,500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million (CPM) algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis (PCA), graph-based clustering and Uniform Manifold Approximation and Projection (UMAP) plotting, using the NN-Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine-tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single-cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild-type, evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow, we used the statistically robust Hurdle Model two-part model with default parameters.
We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above.
Assembly: Lawson Lab zebrafish transcriptome V4.3.2 (https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/)
Supplementary files format and content: Tab-separated and matrix files.

organism: Danio rerio

source_name: Spinal Cord

growth_protocol: Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tg(evx1:EGFP)SU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf, as confirmed by analysis of morphological criteria, including head-trunk angle, head and eye size.

extract_protocol:
Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP-positive embryos were used for dissections and FACS at 48 hpf.  Embryos were deyolked, dissected and dissociated as described in GSE145916, with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord, and posteriorly, immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System (Worthington Biochemical Corporation, LK003150), trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately after homogenising the digested tissue mixture with a sterile p200 tip, we passed each sample through a 40 µm Flowmi cell strainer (Merck, BAH136800040) into a sterile microcentrifuge tube. After Papain inactivation, samples were resuspended in 1 ml Leibovitz’s L-15 medium (ThermoFisher Scientific, 21083027) + 0.5% FBS and stored on ice. Immediately before FACS, DAPI (Merck, D9542) and Draq5 (BioLegend, 424101) were added at a final concentration of 5 µg/ml and 5 µM respectively.  FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al., (2008) with the following modifications. Ice-cold samples were filtered through 35 µm mesh strainers in to 5 ml round-bottomed polystyrene tubes (Corning Falcon, 352235). All FAC-sorting and collection steps were performed at +4oC, using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates (forward scatter height x forward scatter width, followed by side scatter height x side scatter width) were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI-negative (sick cells are DAPI-permeant and excluded) and Draq-5 positive (only healthy nuclei are Draq-5 permeant) cells.  EGFP-positive cells were sorted and fixed using a methanol fixation protocol modified from the 10x Genomics Sample Preparation Demonstrated Protocol “Methanol Fixation of Cells for Single Cell RNA Sequencing” (https://www.10xgenomics.com). EGFP-positive cells were sorted directly in to 5 ml round-bottomed tubes containing 3.5 mls of freshly made, pre-chilled, 90% methanol (for HPLC, >99%, Merck, 34860)/10% Dulbecco’s Phosphate-Buffered Saline (DPBS, No calcium, No magnesium, Merck, D8537) fixative. A tube of EGFP-negative cells was also collected to assess fixation efficiency. Sorted cells were incubated on ice for 1 hour before assessing fixation efficiency of the EGFP-negative control tube using Trypan Blue (ThermoFisher Scientific, 15250061) and a hemocytometer. Samples with intact, fully fixed cells, containing little or no cell debris were stored at +4oC for up to six days prior to rehydrating and performing single-cell capture with the 10x Genomics Chromium system (please see below).  To rehydrate our fixed EGFP-positive 48 hpf evx1i232;evx2sa140;Tg(evx1:EGFP)SU2 cells, we first centrifuged each sample at 300 rcf for 10 minutes at +4oC using a swing-bucket centrifuge. Next, we carefully removed the majority of the supernatant with a sterile p1000 tip, until approximately 100 µl remained in the tube. Samples were kept on ice at all times. Each cell pellet was then gently resuspended by adding 2 ml of freshly made, pre-chilled Rehydration Buffer (1x Dulbecco’s Phosphate-Buffered Saline, no calcium, no magnesium (Merck, D8537), 1.0% UltraPure BSA (ThermoFisher Scientific, AM2616), 0.5 u/µl Roche Protector RNase Inhibitor (Merck, 3335402001)) and gently pipetting 10 times. It is important to avoid making foam. We repeated the centrifugation and resuspension in Rehydration Buffer steps as previously. After the second Rehydration step, we again centrifuged at 300 rcf for 10 minutes at +4oC before carefully removing all but 30-40 µl of supernatant. Using a sterile p200 tip, we carefully resuspended the cell pellet and immediately measured the cell concentration in triplicate using a Bio-Rad TC20 automated cell counter (Bio-Rad, 1450102). We also checked a small aliquot under a conventional microscope to ensure we had single cell suspensions. As described by 10x Genomics in their Sample Preparation Demonstrated Protocol “Methanol Fixation of Cells for Single Cell RNA Sequencing” (https://www.10xgenomics.com), we too recovered approximately 50% of the sorted cells after rehydration.
We isolated single cells using a 10x Genomics Chromium system, aiming for capture of 10,000 cells per well (Chromium Next GEM Chip G Single Cell Kit, 1000127). We prepared libraries using a 10x Genomics Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit (v3.1, 10x Genomics, 1000128) and sequenced them on an Illumina NextSeq500 to a depth of at least 50,000 reads per cell (Illumina NextSeq 500/500 High Output Kit, v2.5, 150 cycles, 20024907).

value: Spinal Cord

value: V0v spinal interneurons

value: evx1i232/+;evx2sa140/+ incross


title: Liver, Lira injections (NASH Diet)_1

description: Data can be used by nSolver Software

value: NASH diet


title: 200722330021_R03C01

last: Bhandari


title: MUTSU2_OtherGFP-G8

description: 10x Genomics


title: 200722330021_R07C01


title: DA3/EPOR Senescent rep 2


title: AVD-1-842-4378A

data_processing: Data was processed using affy_v1.74.0 package with Robust Multichip Average (RMA) normalization in R

extract_protocol:
RNA was extracted from 1 slice (10 µm) from the FFPE samples (Qiagen RNEasy FFPE kit). Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent
Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902,790).

value: male

tag: localization

value: Right

value: colon polyp


title: Liver, BemA 10mg/kg diet + Lira injections_5

description: Data can be used by nSolver Software

value: Bempedoic acid (10 mg/kg) + Liraglutide (70 µg/kg)

value: mouse liver