title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep2

status: Public on Aug 04 2023

type: SRA

city: Basel

first: Regula

last: Furrer

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Run mode: RAPIDHIGHOUTPUT

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 21.0.5 (Quiagen)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using CLC Genomics Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: mm10
Supplementary files format and content: Excel file (.xlsx) with TPM values for each sample, calculated Log2 fold change and FDR
Supplementary files format and content: GEO-processed-data_Furrer-Handschin_Exercise_RNAseq.xlsx

molecule: polyA RNA

organism: Mus musculus

source_name: Skeletal muscle

extract_protocol:
RNA was isolated with TRIzol reagent (Sigma-Aldrich) and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

tag: strain

tag: tissue

value: Skeletal muscle

tag: genotype

value: wildtype

tag: treatment

value: untrained, acute exercise


title: WT2 iPSC-CMs day 60 AAV-SFRP5 sample 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Demultiplexing of the intensity files using bcl2fastq version 2.17.1.14. Quality check was done via fastqc (v. 0.11.5, Babraham Bioinformatics)
Read alignment was performed using STAR aligner (v2.5.2a)
Read counting was performed using featureCounts
Assembly: hg38 version 89
Supplementary files format and content: RPKM_analysis.xls

molecule: total RNA

organism: Homo sapiens

source_name: UMGi005-A clone 1

extract_protocol: Non stranded mRNA-Seq

tag: cell line

value: UMGi005-A clone 1

tag: cell type

value: iPSC-derived cardiomyocytes

value: WT


title: WT2 iPSC-CMs day 60 AAV-SFRP5 sample 2


title: WT2 iPSC-CMs day 60 AAV-SFRP5 sample 4


title: TE5_WGBS

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

country: China

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

library_source: genomic

data_processing:
Raw reads were mapped to the human genome (GRCh38) by Biscuit align command (version 0.1.4, https://www.githubcom/zwdzwd/biscuit) with default settings. Mapped reads were sorted by genome position, and duplicates were marked using Picard MarkDuplicates tool (version 1.136, http://broadinstitute.github.io/picard/). Biscuit pileup and vcf2bed command were then used to extract DNA methylation information.
All CpG sites with a coverage >= 5 informative reads and outside of the ENCODE blacklist regions were retained for downstream analyses.
Assembly: hg38
Supplementary files format and content: bed include chromosome, start, end, beta value, total coverage (methylated and unmethylated Cytosines), methylated sequence

molecule: genomic DNA

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Following DNA extraction and quality control (QC), 3 ug of DNA which was spiked with 26 ng lambda DNA were fragmented by sonication.
Cytosine-methylated molecular barcodes were ligated to the fragmented DNA. Bisulfite conversion was performed using EZ DNA Methylation-GoldTM Kit (Zymo Research) according to the manufacturer’s instructions. DNA fragments were then PCR amplified by HiFi HotStart Uracil and ReadyMix (Kapa Biosystems). The clustering of the index-coded DNA samples was performed by Illumina cBot Cluster Generation System, followed by sequencing using Illumina Hiseq platform.

value: Esophageal squamous cell carcinoma


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, sedentary


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: ESO26_WGBS

value: Esophageal adenocarcinoma


title: WT2 iPSC-CMs day 60 AAV-GFP sample 4

value: AAV-GFP


title: WT2 iPSC-CMs day 60 AAV-SFRP5 sample 5


title: WT2 iPSC-CMs day 60 AAV-GFP sample 1


title: WT1 iPSC-CMs day 60 AAV-SFRP5 sample 5

source_name: UMGi001-A clone 1

value: UMGi001-A clone 1


title: WT1 iPSC-CMs day 60 AAV-SFRP5 sample 4


title: RNAseq, quadriceps, steady-state, WT-trained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: trained


title: Sensory Neurons SARS_1

city: Cambridge

first: Anthony

last: Flamier

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

data_processing:
Sequence quality was controlled by FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore
Trimmed sequence reads were mapped to hg38 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: iPSC 7095

growth_protocol: iPSC-sensory neurons were maintained in BrainPhys media supplemented with N2/B27 supplements, NT-3, GDNF, and BDNF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPAHypermRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were infected with WA1/2020 SARS-CoV-2 at a MOI of 1 for 48 hours.

value: iPSC 7095

value: iPSC-sensory neurons

value: WA1/2020 SARS-CoV-2 infected

tag: time

value: 48 hrs


title: WT2 iPSC-CMs day 60 AAV-GFP sample 5


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: WT2 iPSC-CMs day 60 AAV-SFRP5 sample 1


title: WT1 iPSC-CMs day 60 AAV-SFRP5 sample 3


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, WT-trained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: WT1 iPSC-CMs day 60 AAV-SFRP5 sample 2


title: RNAseq, quadriceps, steady-state, WT-untrained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: WT2 iPSC-CMs day 60 AAV-GFP sample 3


title: WT1 iPSC-CMs day 60 AAV-GFP sample 5


title: WT1 iPSC-CMs day 60 AAV-GFP sample 4


title: RNAseq, quadriceps, steady-state, WT-trained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, WT-untrained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: WT1 iPSC-CMs day 60 AAV-SFRP5 sample 1


title: WT1 iPSC-CMs day 60 AAV-GFP sample 3


title: RNAseq, quadriceps, steady-state, WT-untrained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, WT-untrained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: WT1 iPSC-CMs day 60 AAV-GFP sample 2


title: RNAseq, quadriceps, steady-state, WT-untrained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: WT2 iPSC-CMs day 60 AAV-GFP sample 2


title: RNAseq, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RNAseq, quadriceps, steady-state, WT-trained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: tridimensional culture 3

city: Chihuahua

first: Mercedes

last: Bermúdez

state: Chihuahua

address: Chihuahua

department: Dentistry

country: Mexico

institute: Universidad autónoma de Chihuahua

library_source: other

data_processing:
The sequencing was performed with a total of 125 M reads for each sample. rRNAs were removed. Reads with Phred Quality Score values greater than 30 across all sequencing cycles were conserved. The filtered reads had a distribution of 6 to 36 bp in length, with a mean of 22 bp, which corresponds to the common size of miRNAs. Reads were aligned to the reference genome (GRCh38), miRBase v22.1, and non-coding RNA database (RNAcentral release 14.0) to classify the different types of small RNAs present in the samples. For the quantification of the miRNAs in the samples, a Bowtie alignment mapping was performed in miRBase v21 and the counting of mature miRNAs was performed with the miRDeep2 Quantifier.
To find the differentially expressed miRNAs (DE-microRNAs) between the experimental groups (3D vs 2D), miRNAs were normalized using TMM (Trimmed mean of M-values), and Principal Component Analysis (PCA) was performed to assess the homogeneity of the experimental replicates. The detection of the DE-miRNAs was performed using Fold Change, and exactTest using edgeR per comparison pair. From the general list, miRNAs with Fold-Change (FC) greater than 2 or less than -2 were filtered with significances values of p < 0.01.

molecule: other

growth_protocol: The human cell line SKBR3 (SK-BR-3, HTB-30. ATCC, USA) derived from a patient with breast carcinoma Her2+ was grown in Dulbecco's modification of Eagle's minimal medium (DMEM/F-12) supplemented with 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin (Invitrogen, USA) at 37 °C, in a 5 % CO2 atmosphere

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's instructions. The quantity and quality of total RNA were evaluated using Nanodrop (ThermoFisher Scientific, USA) and RNA integrity was assessed using agarose gel electrophoresis at 60 V, stained with GelRed 0.5 X, and visualized on a UV transilluminator
MicroRNA expression analysis of SKBR3 cells cultured in 2D and 3D culture was performed by whole Small RNAseq. The TruSeq Small RNA Library Prep kit (Illumina, USA) was used for the preparation of the library.

treatment_protocol: To obtain SKBR3 organoids, a standard On-Top protocol was used [3, 19], briefly, 24-well flat-bottom plates were coated with 150 μL of LDEV-free growth factor-reduced Geltrex (Gibco, USA) and incubated at 37 °C for 30 minutes to promote its gelation. Then, 4.2x104 cells were seeded and DMEM/F-12 supplemented medium was added to incubate for up to 5 days. The only modification was that the medium had no additional 5 % Geltrex as reported. Wells without Geltrex were used as a control (2D), maintaining the rest of the conditions. Similarly, a standard In-Gel protocol was used, briefly, the same number of cells were mixed with Geltrex pregel and then placed in 24-well flat-bottom plates before gelation.[27] Additionally, single cells were diluted to a density of 5x103 cells and placed into ultra-low attachment (ULA) 24-well plates and incubated under the same conditions to let the formation of cell spheroids. Cells were monitored at 72, 96, and 120 h to measure the number and size of spheres using ImageJ software in which regions of interest were surrounded manually around the entire organoid from a bright-field microscopy image, and then in the imageJ module ("Area Measurements of a Complex Object"), the surface area is calculated[28].

value: 3D culture


title: Rbf_Mutant_Yki_Overexpression

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Single cell RNA-seq was performed using 10X Genomics Chromium Single Cell 3' v3.1

library_source: transcriptomic single cell

data_processing:
Fastq files generated by NovaSeq were processed using the "count" function in 10X Genomics Cellranger version 6.0.0 with default parameters.
10x Genomics reads were aligned against genome version BDGP6 (From Ensembl) and corresponding gene models were extracted from Ensembl version 90.
Assembly: BDGP6
Supplementary files format and content: Features, barcodes, and matrices from CellRanger 6.0.0 were processed into Seurat objects using the Read10X() and CreateSeuratObject() functions.

organism: Drosophila melanogaster

source_name: RbfYki

growth_protocol: Animals were maintained at 25C in standard cornmeal agar medium vials.

extract_protocol:
Third instar larvae were harvested upon wandering and eye imaginal discs were dissected in cold 1X PBS. Eye discs were then dissected from adjacent tissue at the optic stalk and eye-antennal-border using a microblade. Discs were then deposited in ice-cold 1X Rinaldini solution. Collagenase (Sigma #C9891) was added to a achieve a final concentration of 2.5 mg/mL and Trypsin (Sigma #59418C) to 1X dilution. Tubes were then attached horizontally to a shaker and agitated at 225 rpm for 10 minutes at 37C. Samples were then subjected to approximately 30 pulses of gentle mechanical digestion using a P200 pipette. Cells were then washed twice in 0.04% BSA-PBS and resuspended in 30 uL of 0.04% BSA-PBS. The concentration of cells and their viability was assessed using a hemocytometer and Trypan blue staining.
10x Genomics Chromium Controller on the single cell suspension
10x Genomics: Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: Third instar larval eye disc

tag: description

value: Rbf[120a] mutant eye discs expressing yki[S111A,S168A,S250A] in the posterior compartment using the GMR-GAL4 driver

tag: Sex

value: Male


title: bidimensional culture 2

value: 2D culture


title: Rbf_Mutant_Rep2

source_name: Rbf

value: Rbf[120a] hypomorphic mutant


title: Hth_Yki_Overexpression

source_name: HthYki

value: Eye discs expressing Homothorax and yki[S111A,S168A,S250A] in the posterior compartment using the GMR-GAL4 driver

value: Male and female


title: tridimensional culture 4


title: Yki_Overexpression

source_name: Yki

value: Eye discs expressing yki[S111A,S168A,S250A] in the posterior compartment using the GMR-GAL4 driver


title: bidimensional culture 1


title: RNAseq, quadriceps, steady-state, WT-trained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle

value: wildtype


title: Rbf_Mutant_Rep1


title: Wts_Mutant

source_name: Wts

value: ey-Flp induced homozygous wts[x1] loss-of-function mutant clones

value: ey-Flp/+ or Y; +; 82B wts[x1]/82B GFP


title: Wildtype_Rep2

source_name: WT

value: Wildtype w[1118]


title: Wildtype_Rep1


title: subject 4, 72 hours post-infection

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p14 using kallisto software version 0.45.0
Assembly: GRCh38.p14
Supplementary files format and content: Tab-separated text file containing length, estimated counts, and transcripts per million (TPM) for each gene isoform

source_name: lung

extract_protocol:
RNA was extracted using SV 96 Total RNA Isolation System catalog #Z3500
mRNA libraries were prepared using Illumina TruSeq stranded mRNA sample preparation kit (Illumina #RS-122-2101).

treatment_protocol: Healthy human airway epithelial cell cultures were exposed basolaterally with measles virus expressing GFP at MOI=1 for 4 hrs.

tag: individual

value: subject 4

value: lung

tag: exposure

value: 72 hours post-infection


title: Rbf_Wts_DoubleMutant

source_name: RbfWts

value: Rbf[120a] hypomorphic mutant with ey-Flp induced homozygous wts[x1] loss-of-function mutant clones

value: Rbf[120a], ey-Flp/Y; +; 82B wts[x1]/82B GFP


title: subject 4, 12 hours post-infection

value: 12 hours post-infection


title: subject 4, uninfected

value: no virus


title: subject 4, 24 hours post-infection

value: 24 hours post-infection


title: subject 4, 120 hours post-infection

value: 120 hours post-infection


title: Sakai_Fur_KO_Fe_2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

description: Sakai

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto each reference genome using bowtie with the maximum insert size of 2000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for DESeq(https://bioconductor.org/packages/release/bioc/html/DESeq.html)
Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: The reference genomes used in this study are shown as below,  MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2
Supplementary_files_format_and_content: tab-delimited text files containing TPM values for each sample

organism: Escherichia coli

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli and S. Typhimurium LT2 strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For iron-replete condition, M9 minimal media was supplemented with 0.1 mM FeCl2 ; for iron-depleted condition, M9 minimal media was supplemented with 0.2 mM 2,2’-dipyridyl at early-log phase and continue to culture at 37 oC for additional 2h with vigorous agitation; for regulatory condition, M9 minimal media was supplemented with 1 mL trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2.

value: Sakai

tag: medium

value: glucose M9 minimal

tag: phase

value: mid-log phase

value: Fur deletion


title: subject 3, 48 hours post-infection

value: subject 3

value: 48 hours post-infection


title: Sakai_WT_Fe_2

description: Sakai

value: wild type


title: subject 3, 72 hours post-infection


title: subject 3, 12 hours post-infection


title: subject 4, 48 hours post-infection


title: WT1 iPSC-CMs day 60 AAV-GFP sample 1

value: UMGi001-A clone 1

value: iPSC-derived cardiomyocytes

value: WT

value: AAV-GFP


title: Sakai_Fur_KO_Fe_1

description: Sakai


title: Sakai_WT_Fe_1

description: Sakai


title: subject 3, 120 hours post-infection

value: lung


title: Crooks_WT_Fe_2

description: Crooks

value: Crooks


title: Crooks_Fur_KO_Fe_1

description: Crooks


title: Crooks_Fur_KO_Fe_2

description: Crooks


title: subject 3, uninfected


title: subject 2, 72 hours post-infection

value: subject 2

value: 72 hours post-infection


title: Crooks_WT_Fe_1

description: Crooks


title: subject 2, 48 hours post-infection


title: BL21_Fur_KO_Fe_2


title: BL21_Fur_KO_Fe_1


title: subject 2, 12 hours post-infection

value: 12 hours post-infection


title: subject 2, 24 hours post-infection

value: 24 hours post-infection


title: subject 2, 120 hours post-infection

value: 120 hours post-infection


title: BL21_WT_Fe_2

value: glucose M9 minimal


title: subject 2, uninfected

value: no virus


title: BL21_WT_Fe_1

value: mid-log phase


title: Strain042_Fur_KO_Fe_1

value: Fur deletion


title: subject 1, 48 hours post-infection

value: subject 1

value: 48 hours post-infection


title: Strain042_Fur_KO_Fe_2


title: subject 1, 72 hours post-infection


title: Strain042_WT_Fe_1

value: wild type


title: subject 1, 12 hours post-infection


title: subject 1, 24 hours post-infection


title: Strain042_WT_Fe_2


title: KO11FL_Fur_KO_Fe_2


title: subject 1, 120 hours post-infection


title: subject 1, uninfected


title: KO11FL_Fur_KO_Fe_1


title: shCCR7_2_2

city: Shanghai

first: Zhixin

last: Qiu

address: Dongan Road

institute: Fudan University

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport function to obtain gene expression matrix.
Assembly: hg38
Supplementary files format and content: RNA abundance (Transcripts Per Million, TPM) matrix at the gene level.

source_name: patient-derived cells

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA MiniPrep Kit (catalog R2052) and TRI reagent (catalog R2050) according to the manufacturer’s instructions.
Total RNA was used for library construction using Illumina TruSeq Total RNA Library Prep Kit. The library was sequenced as paired-end 150bp read.

value: patient-derived cells

value: glioblastoma stem cells


title: KO11FL_WT_Fe_1


title: shCCR7_1_2


title: shCCR7_1_1


title: CFT073_Fur_DPD_2

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: Each genome ( MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

tag: myc-tagging

value: Fur myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: shCCR7_2_1


title: CFT073_Fur_Fe_2


title: CFT073_Fur_DPD_1


title: shCONT-1

value: shCONT


title: Navarixin_3

value: Navarixin


title: CFT073_Fur_Fe_1


title: shCONT-2


title: Navarixin_2


title: Navarixin_1


title: Crooks_Fur_DPD_1

value: Crooks


title: Cmp2105_3


title: KO11FL_WT_Fe_2


title: Cmp2105_2


title: BL21_Fur_DPD_1


title: BL21_Fur_Fe_2


title: Cmp2105_1


title: BL21_Fur_DPD_2


title: DMSO_2

value: DMSO


title: BL21_Fur_Fe_1


title: 042_Fur_DPD_2


title: DMSO_1


title: 042_Fur_DPD_1


title: LEC cell 24

data_processing:
Raw FASTQ reads were mapped using STAR and transcript expression levels were qunatified using featureCount.
Assembly: hg38
Supplementary files format and content: RNA count matrix at the gene level.

source_name: lymphatic endothelial cell line

extract_protocol:
The cells were sorted and the SMART-seq protocol were applied according to the  user manul (Takara).
The library was construction using Illumina Nextera XT DNA Library Prep Kit.

value: lymphatic endothelial cell line


title: 042_Fur_Fe_2


title: LEC cell 23


title: LEC cell 21


title: LEC cell 22


title: 042_Fur_Fe_1


title: Crooks_Fur_DPD_2


title: LEC cell 20


title: Crooks_Fur_Fe_2


title: LEC cell 19


title: KO11FL_Fur_Fe_2


title: KO11FL_Fur_DPD_1


title: Crooks_Fur_Fe_1


title: W_Fur_DPD_2

value: W


title: KO11FL_Fur_Fe_1


title: LEC cell 17


title: LEC cell 18


title: DMSO_3


title: W_Fur_DPD_1


title: W_Fur_Fe_2


title: LEC cell 13


title: muscle, 24 months old, PGC-1α transgenic, rep_6

first: Laura

middle: Maria

last: de Smalen

state: Basel-Stadt

data_processing:
Reads were subjected to 3’ adapter and poly(A)/poly(T) trimming using Cutadapt v1.16. Reads shorter than 10 nucleotides were discarded.
Reads were mapped to the mouse genome assembly GRCm38 (release 100) with the annotation from Ensembl database using salmon v1.1.0.
Differential expression analysis was performed with EdgeR for genes that had at least 1 count per million in all of the 5-6 biological replicates.
Assembly: GRCm38 (release 100)
Supplementary files format and content: Tab-separated values file containing count matrix comprised of TPM values for all samples.

source_name: gastrocnemius muscle

extract_protocol:
M. gastrocnemius muscles were crushed and tissue was further homogenized using Lysing matrix D tubes (MP Biomedicals) in TRI Reagent (Sigma). RNA was purified using chloroform phase separation and ethanol cleanup.
Libraries were prepared from total RNA using an Illumina TruSeq RNA Library Prep Kit (version 2).

value: gastrocnemius muscle

value: bulk tissue

value: PGC-1{alpha} transgenic

tag: age

value: 24 months old

value: male


title: muscle, 24 months old, PGC-1α transgenic, rep_5


title: KO11FL_Fur_DPD_2


title: muscle, 24 months old, PGC-1α transgenic, rep_3


title: LEC cell 11


title: LEC cell 10


title: LEC cell 12


title: muscle, 24 months old, PGC-1α transgenic, rep_4


title: LEC cell 9


title: muscle, 24 months old, PGC-1α knockout, rep_6

value: PGC-1{alpha} knockout


title: LEC cell 7


title: LEC cell 8


title: LEC cell 6


title: muscle, 24 months old, PGC-1α knockout, rep_5


title: LEC cell 16


title: muscle, 24 months old, PGC-1α knockout, rep_4


title: LEC cell 5


title: LEC cell 15


title: LEC cell 14


title: LEC cell 2


title: W_Fur_Fe_1


title: LEC cell 4


title: muscle, 24 months old, wildtype, rep_6

value: WT


title: muscle, 24 months old, PGC-1α knockout, rep_1


title: LEC cell 1


title: muscle, 24 months old, wildtype, rep_3


title: muscle, 24 months old, wildtype, rep_2


title: muscle, 24 months old, wildtype, rep_4


title: muscle, 24 months old, PGC-1α transgenic, rep_2


title: ESO26, H3K36me2

data_processing:
Raw reads were mapped to GRCh38 (ENSEMBL release 84) using BWA mem program (version 0.7.15) with the default options. Then the mapped reads were sorted using SAMtools program (version 1.3.1), followed by removing PCR duplicates and blacklist regions by Picard MarkDuplicates tool and bedtools (version 2.27.1).
MACS2 (Model-Based Analysis of ChIP-Seq, version 2.1.2) were applied to call peaks with ''--broad -p 0.01 --extsize=146 --nomodel'' for H3K36me2.
Bigwig files were generated by deepTools bamCompare function (version 3.1.3) with “--operation subtract --normalizeUsing CPM --extendReads 146 --binSize 20".
The input files of EAC (ESO26) and ESCC cell lines (KYSE70 and TE5) were obtained from our previous datasets GSE132680 and GSE106563, respectively.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: RPMI-1640 medium (Gibco, USA), supplemented with 10% FBS (Omega Scientific, USA) and 1% penicillin-streptomycin (Thermo Scientific, USA). Cells were cultured at 37C at 5% CO2.

extract_protocol:
Ten million esophageal cancer cells were harvested and transferred into 15 ml tubes, followed by fixing with 4 ml of 1% paraformaldehyde for 10 min under room temperature. After quenching and cell lysis, chromatin was sonicated using a Covaris sonicator.
Debris was removed by centrifuge and supernatants were diluted five times with the buffer containing 0.01% SDS, 1% Triton X-100, 1.2 mM EDTA pH 8.0, 150 nM NaCl. 1 ug of the H3K36me2 antibody (Cell Signaling Technology, USA, Cat# 2901S) was added and incubated by rotation at 4℃ overnight. Protein G Dynabeads (Life Technologies, USA) were added the next morning and incubated by rotation for an additional 4 hours. Dynabeads were next washed with 1X wash buffer followed by cold TE buffer. DNAs were reverse crosslinked, purified, followed by library preparation and deep sequencing using the Illumina HiSeq platform.

value: Esophageal adenocarcinoma

tag: chip antibody

value: H3K36me2 (Cell Signaling Technology, USA, Cat# 2901S)


title: GSC20_IgGisotype_Control_3

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport function to obtain gene expression matrix.
Genome_build: hg38
Supplementary_files_format_and_content: RNA count and abundance (Transcripts Per Million, TPM) matrix at the gene level.

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA MiniPrep Kit (catalog R2052) and TRI reagent (catalog R2050) according to the manufacturer’s instructions
Total RNA was used for library construction using Illumina TruSeq Stranded Total RNA Library Prep Kit. The library was sequenced as paired-end 150bp read.

value: IgGisotype

value: glioblastoma stem cells


title: muscle, 24 months old, PGC-1α transgenic, rep_1


title: KYSE70, H3K36me2

value: Esophageal squamous cell carcinoma


title: TE5, H3K36me2


title: muscle, 24 months old, wildtype, rep_1


title: muscle, 3 months old, PGC-1α transgenic, rep_6

value: 3 months old


title: muscle, 24 months old, wildtype, rep_5


title: muscle, 24 months old, PGC-1α knockout, rep_3


title: GSC20_IgGisotype_Control_1


title: muscle, 24 months old, PGC-1α knockout, rep_2


title: GSC20_CCL21_3


title: LEC cell 3


title: muscle, 3 months old, PGC-1α transgenic, rep_4


title: GSC20_CCL21_2


title: muscle, 3 months old, PGC-1α transgenic, rep_5


title: muscle, 3 months old, PGC-1α transgenic, rep_3


title: muscle, 3 months old, PGC-1α transgenic, rep_2


title: GSC20_CCL21_1


title: muscle, 3 months old, PGC-1α transgenic, rep_1


title: muscle, 3 months old, PGC-1α knockout, rep_5


title: 36A3h-R2

city: Hangzhou

first: Zhu

last: Yibing

state: Zhe Jiang

address: Xihu

department: Life Of Science

institute: Zhejiang University

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1).
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website UCSC. Then Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: sacCer3
Supplementary_files_format_and_content: all.fpkm_anno.txt (Matrix table with raw gene counts and FPKMs for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: cell

growth_protocol: Yeast cells grown to log phase in YPL medium from 0.1 OD.

extract_protocol:
RNA was harvested using Lucigen MasterPure Yeast RNA Purification Kit
1 μg total RNA was used for following library preparation. Next generation sequencing library preparations were constructed according to the Illumina protocol

treatment_protocol: Cells were washed with SL medium once and then transferred to SL medium for culturing.

tag: strain

value: switch to minimal medium for 3h


title: S23h-R2


title: 36A3h-R1


title: muscle, 3 months old, PGC-1α knockout, rep_4

tag: tissue


title: S23h-R1

tag: genotype


title: R13h-R2

tag: treatment


title: GSC20_IgGisotype_Control_2


title: WT3h-R2


title: muscle, 3 months old, PGC-1α knockout, rep_2


title: muscle, 3 months old, PGC-1α knockout, rep_1


title: WT3h-R1


title: muscle, 3 months old, wildtype, rep_5


title: 36A1h-R2

value: switch to minimal medium for 1h


title: ILCs_CCRL2_KO

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

description: BD Single-Cell Kit_mm

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SevenBridges platform with the pipeline BD WTA Multiplex Rhapsody Analysis Pipeline Version 1.9.1 (https://www.sevenbridges.com/)ata processing step
Supplementary files format and content: mm10
Supplementary files format and content: Comma-separated values files

extract_protocol:
Mice were sacrificed and lungs and tumors harvested. The innate lymphoid cell populations (NK, ILC1 and ILC2) were sorted from lung tumors by using a Becton Dickinson FACS Aria Fusion (BD Biosciences) and Single cell sequencing libraries were generated using BD Rhapsody™ Single-Cell Analysis system (BD) according to the manufacture’s protocol. Both cell viability and counts were then evaluated by the BD Rhapsody scanner, and only samples with high viability (> 85 %) were used for sequencing. Each genotype was loaded in a dedicated BD Rhapsody cartridge.
RNA was extracted according to the manufacter’s instructions (BD Rhapsody™ Single-Cell Analysis System ).
Library was performed according to the manufacter’s instructions (BD Rhapsody™ Single-Cell Analysis System ).

treatment_protocol: TK-Ccrl2 WT and TK-Ccrl2 KO, at 8 weeks of age, were intranasally inoculated with 2.5 × 10^7 infectious particles of replication-deficient adenoviral vector (in 50 μL DMEM with 10 mmol/L CaCl2) with cytomegalovirus promoter driving the expression of the Cre recombinase protein (Ad5CMVCre) to induce sporadic mutations and lung tumor development. Mice were sacrificed 10 weeks after the adenovirus inoculation

value: Lung_Kras G12D/+ /p53 LoxP_TK_Ccrl2_wt

value: Innate Lymphoid Cells


title: ILCs_CCRL2_WT

description: BD Single-Cell Kit_mm

value: Lung_Kras G12D/+ /p53 LoxP_TK_Ccrl2_ko


title: S21h-R2


title: muscle, 3 months old, wildtype, rep_4

value: gastrocnemius muscle

value: bulk tissue


title: 36A1h-R1


title: Metrnf/f LysM (cKO), rep2

city: hangzhou

first: Xin-Jiang

last: Lu

address: Zijingang Campus, Zhejiang University, No.866, Yuhang Tang Road

department: Department of Physiology, and Department of Hepatobiliary and Pancreatic Surgery of The First Affiliated Hospital,

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

extract_protocol:
We sorted LSK cells (Lin-Sca-1+c-Kit+) from two Metrnf/f and two Metrnf/f, LysM mice by FACS. After sorting, total RNA was extracted from the tissue using TRIZOL Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and quantified using a Nanodrop ND-2000 spectrophotometer (Thermo Scientific, Waltham, MN, USA). Highquality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) is used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: 12 weeks

value: Metrn-cKO

value: LSK cells


title: Metrnf/f (WT), rep2

value: wild type


title: S21h-R1


title: Metrnf/f LysM (cKO), rep1


title: muscle, 3 months old, wildtype, rep_2

value: WT

value: male


title: muscle, 3 months old, wildtype, rep_3


title: G112_ClQ 30µM_24 hrs_rep2

type: RNA

city: Mainz

first: Ella

middle: L

last: Kim

state: Select an option…

address: Langenbeckstraße 1

department: Neurosurgery

institute: University Medical Center Mainz

hyb_protocol: Following fragmentation, 0.3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data analysis consisted of between-array normalization, probe summary, global clustering and PCA-analysis, fitting the data to a linear model and detection of differential gene expression. To ensure that the intensities had similar distributions across arrays, quantile-normalization was applied to the log2-transformed intensity values as a method for between-array normalization. As for the summary of probes a median polish procedure was chosen. Significant changes in the expression of genes between the groups was analyzed by Empirical Bayes statistics by moderating the standard errors of the estimated values. P-values obtained from the moderated t-statistic were corrected for multiple testing with the Benjamini–Hochberg method. P-value adjustments guarantee a smaller number of false positive findings by controlling the false discovery rate (fdr). For each gene, the null hypothesis suggesting there is no differential expression between degradation levels was rejected when its fdr was lower than 0.05. Samples were assessed in a blinded manner.

label: biotin

source_name: human glioblastoma stem cells, 24 hrs, 30 µM chloroquine

label_protocol: cDNA was synthesized using 5 μg of total RNA. The synthesis of the double-stranded cDNA was performed using the WT Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA, USA) and the cleanup was done using the GeneChip® Sample Cleanup module (Affymetrix). In vitro transcription was conducted using the WT Target Labeling Kit (Affymetrix). The total amount of the reaction product was purified using the GeneChip® cRNA Sample Cleanup Module (Affymetrix) and quantified with the NanoDrop ND-1000 (Nanodrop (Thermo), Wilmington, DE USA). cDNA synthesis (ss) was done with the WT Target Labeling Kit (Affymetrix) and the total ssDNA (5.5 μg) was cleaved 35–200 bp fragments enzymatically. The degree of fragmentation and the length distribution of the ssDNA were analyzed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent Technologies). Following fragmentation, a terminal labeling reaction (Biotin) was conducted using the WT Labeling Kit (Affymetrix).

growth_protocol: Glioblastoma stem cell lines were maintained in serum-free NeuroBasal Complete medium supplemented with B27 component and growth factors bFGF and EGF (10 and 20 ng/mL, respectively).

extract_protocol: RNA isolation was performed using the Trizol (Invitrogen) method according to the manufacturer’s instructions. The samples were treated with DNAse I (Sigma-Aldrich, St. Louis, MO USA). RNA quality was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) microfluidic electrophoresis and only samples with comparable RNA integrity numbers were processed for microarray analysis.

treatment_protocol: Single cell suspensions were prepared by trituration one day before treatment 30 µM ClQ solved in PBS or radiation with 2Gy of IR. Control samples were processed in parallel using the same procedure except the treatment. 24 hrs after the treatment ClQ-treated, IR-treated or untreated control cells were collected by centrifugation, washed twice with PBS, pelleted and snap-frozen in liquid nitrogen. Frozen cell pellets were kept at -80°C until RNA extraction and hybridization on Affymetrix microarrays.

value: cell line established from glioblastoma WHO grade IV

value: mutated TP53 (hotspot mutation R273H)

value: human glioblastoma stem cells

value: 30 uM chloroquine


title: Metrn f/f (WT), rep1


title: G112_ClQ 30µM_24 hrs_rep3


title: R13h-R1

value: switch to minimal medium for 3h


title: muscle, 3 months old, PGC-1α knockout, rep_3

value: PGC-1{alpha} knockout

value: 3 months old


title: R11h-R2

value: switch to minimal medium for 1h


title: G112_untreated 24 hrs_rep3

source_name: human glioblastoma stem cells, untreated

value: untreated


title: muscle, 3 months old, wildtype, rep_6

value: gastrocnemius muscle

value: bulk tissue


title: R11h-R1


title: CFT073_Fur_KO_Fe_2

organism: Escherichia coli O157:H7

value: glucose M9 minimal

value: mid-log phase

value: Fur deletion


title: Control mouse endothelial cells rep 2

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

data_processing:
vast-tools version v2.3.0 compare, which maps to the mm9 genome of mouse, and maps the reads to the mouse genome, providing counts of junction mapped reads.
Assembly: mm9
Supplementary files format and content: Tab separated text file with splicing junction counts

source_name: endothelial cells

extract_protocol:
MoEC overexpressing or knockdown for NOVA2 were cultured in DMEM-high glucose with 1mM sodium pyruvate (Euroclone Cat# ECB7501L) supplemented with 10% FBS (Euroclone Cat# ECS500L), 2 mM L-glutamine (Euroclone, Cat# ECB3000D), 100 U/L penicillin/streptomycin (Euroclone Cat# #ECB3001D), 25 mM HEPES (Euroclone, Cat# #ECM0180), 100 g/mL heparin (from porcine intestinal mucosa, Merck Millipore Cat# H3149), 5 μg/mL EC growth supplement (ECGS from bovine pituitary gland, Merck Millipore Cat# E2759) under puromycin selection (3 μg/ml, InvivoGen Cat# ant-pr-1). Since NOVA2 expression is regulated by EC density, for the splicing analysis of NOVA2 targets moEC overexpressing HA-tagged NOVA2 were grown as sparse (500.000 cells in 100 mm Petri dishes), while NOVA2-knockdown moEC were seeded as confluent monolayers (500.000 cells in 35 mm Petri dishes).
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. After treatment with DNase (Ambion), 2–3 μg of RNA was retro-transcribed with mix of d(T)18 oligos and random hexamers or gene-specific primers (Supplementary Table 10) and Superscript III RT (Invitrogen)

treatment_protocol: Mouse endothelial cells (moEC) stably overexpressing or knockdown for NOVA2, as well as their relative controls (named HA and shRNA:Ctr, respectively) were generated by lentiviral transduction of HA-NOVA2 and control HA (pLenti-GIII-CMV human NOVA2-HA, THP Medical Products) or shRNA vectors for NOVA2 and control shRNA (GIPZ shRNAs from Open Biosystems) as described in Nat. Commun. 2015, 6, 8479, doi:10.1038/ncomms9479

value: endothelial cells

value: lentiviral transduction of control HA


title: Control mouse endothelial cells rep 1


title: G112_untreated 24 hrs_rep2


title: WT1h-R2

value: WT


title: CFT073_Fur_KO_Fe_1


title: G112_untreated 24 hrs_rep1

value: cell line established from glioblastoma WHO grade IV


title: Nova2 over expression mouse endothelial cells rep 2

value: lentiviral transduction of HA-NOVA2


title: #1095_ClQ 30µM_24 hrs_rep3

value: mutated TP53 (phenotype p53 null)

value: human glioblastoma stem cells


title: Nova2 over expression mouse endothelial cells rep 1


title: 36A0h-R2


title: CFT073_WT_Fe_1

value: wild type


title: CFT073_WT_Fe_2


title: #1095_ClQ 30µM_24 hrs_rep2

value: 30 uM chloroquine


title: RRBS, quadriceps, sedentary-2, mTG-sed, biol rep4

description: Run mode: RAPIDHIGHOUTPUT

data_processing:
The reads were quality- and adapter-trimmed with the Trim Galore! wrapper of cutadapt and controlled with FastQC.
Conversion rates were calculated with custom scripts, counting the amount of G's and C's in non-GC context resulting in values above 99% for all libraries.
The reads were mapped to the mm10 version of the mouse genome with BWA and methylCtools.
The reads were locally realigned and the quality values were recalibrated before calling the methylation levels using the mm10 SNPs and InDels from dbSNP v138.
Differential loci was detected with MethylKit testing in 500 bp sliding windows with at least 3 CpGs, only including those with a coverage of at least 10x. Differentially methylated regions (DMRs) were defined as ±10% with a q-value < 0.01.
Assembly: mm10
Supplementary files format and content: processed data file contains the differntially methylated regions (defines as ±10% with a q-value < 0.01) that are assigned to the closest gene of each experimental condition compared to the relative control.

source_name: Skeletal muscle

extract_protocol:
The isolated genomic DNA (gDNA) was purified according to the manufacturer’s instructions using the DNeasy Blood & Tissue Kit (Qiagen).
RRBS (Reduced Representation Bisulfite Sequencing) library was prepared with the Premium RRBS Kit (Diagenode) according to the manufacturer’s instructions with 100 ng of gDNA as starting material.

value: Skeletal muscle

value: PGC-1alpha muscle-specific transgenic

value: untrained, sedentary


title: #1095_ClQ 30µM_24 hrs_rep1


title: #1095_untreated 24 hrs_rep3

value: untreated


title: RRBS, quadriceps, sedentary-2, mTG-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: S20h-R1


title: WT1h-R1

value: switch to minimal medium for 1h


title: RRBS, quadriceps, sedentary-2, mTG-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, sedentary-2, mTG-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: 36A0h-R1


title: G112_ClQ 30µM_24 hrs_rep1

value: mutated TP53 (hotspot mutation R273H)


title: muscle, 3 months old, wildtype, rep_1

value: gastrocnemius muscle

value: bulk tissue

value: 3 months old

value: male


title: Sakai_Fur_DPD_2

value: Sakai

value: Fur myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: S20h-R2


title: #1095_untreated 24 hrs_rep1

value: cell line established from glioblastoma WHO grade IV

value: mutated TP53 (phenotype p53 null)


title: Sakai_Fur_DPD_1


title: Sakai_Fur_Fe_1


title: #993_IR 2Gy_24 hrs_rep3

source_name: human glioblastoma stem cells, 24 hrs after 2Gy radiation

value: wild type TP53

value: human glioblastoma stem cells

value: 24 hrs after 2Gy radiation


title: RRBS, quadriceps, sedentary-2, WT-sed, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle

value: wildtype


title: #1095_untreated 24 hrs_rep2

value: untreated


title: Sakai_Fur_Fe_2


title: R10h-R2


title: MG1655_fe_dpd_2

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Assembly: Reference genomes (E.coli EDL933 =  AE005174.2 / Klebsiella pneumoniae MGH78578 = CP000647.1 / Salmonella enterica Typhimurium LT2 = NC_003197.2 / E.coli SMS-3-5 = NC_010498.1 / Shigella flexneri 2a. 2457T = AE014073.1 / E.coli  UMN026 = CU928163.2 / Yersina pseudotuberculos IP32953 = NZ_CP009712.1 )
Supplementary files format and content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

source_name: bacterial cells

growth_protocol: glycerol stocks of bacterial myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked bacterial cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.


title: RRBS, quadriceps, sedentary-2, mTG-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT

value: PGC-1alpha muscle-specific transgenic

value: untrained, sedentary


title: #993_IR 2Gy_24 hrs_rep1


title: RRBS, quadriceps, sedentary-2, WT-sed, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: #993_ClQ 30µM_24 hrs_rep3

value: 30 uM chloroquine


title: R10h-R1


title: MG1655_fe_1


title: MG1655_fe_2


title: #993_ClQ 30µM_24 hrs_rep1


title: RRBS, quadriceps, sedentary-2, WT-sed, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: #993_ClQ 30µM_24 hrs_rep2


title: StrainW_Fur_KO_Fe_2

description: StrainW

organism: Escherichia coli K-12

value: W

value: glucose M9 minimal

value: mid-log phase

value: Fur deletion


title: yWZ703_yeast_chr04_9_07

city: New York

first: Weimin

last: Zhang

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description: synIV final strain

data_processing:
Sequencing reads were trimmed using trimmomatic/0.38.
Trimmed reads were aligned to references using bowtie2/2.2.9.
Bam files were generated using samtools/1.9
The resulting alignments were used to identify single nucleotide variants (SNVs) and short indels using a new freebayes protocol, whereas structural variants and copy number changes were identified by combining GRIDSS with a new copy number calling algorithm specifically designed to work on haploid strains. Finally, mutational and coverage data were organized into VCF and bigWig files for downstream analysis and easy visualization.
Assembly: BY4741, or synIV design reference
Supplementary files format and content: csv files for single nucleotide variation and structural variation
Library strategy: WGS

growth_protocol: Yeast cells were grown in YPD medium. Overnight cultured yeast cells were harvested by centrifugation at 3000xg for 2 min at room temperature.

extract_protocol:
Yeast genomic DNA was extracted by using Fungi/Yeast Genomic DNA Isolation Kit (Norgen, 27300). The concentration of the genomic DNA was determined by using aQubit dsDNA Assay Kit.
Whole genome sequencing libraries were prepared using the NEBNext Ultra II FS DNA library prep kit (NEB, E7805).

value: his3{delta}1 leu2{delta}0 ura3{delta}0

tag: mating type

value: a


title: WT0h-R2

value: WT


title: yWZ608_rightside-out_linear

description: Linear synIV with CEN4 in its native location


title: StrainW_WT_Fe_2

description: StrainW

value: wild type


title: StrainW_WT_Fe_1

description: StrainW


title: MG1655_fe_dpd_1

value: Fur myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: #993_IR 2Gy_24 hrs_rep2

value: cell line established from glioblastoma WHO grade IV

value: wild type TP53

tag: cell type

value: human glioblastoma stem cells

value: 24 hrs after 2Gy radiation


title: StrainW_Fur_KO_Fe_1

description: StrainW


title: RRBS, quadriceps, sedentary-2, WT-sed, biol rep2

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle

value: wildtype


title: WT0h-R1

value: untreated


title: RRBS, quadriceps, sedentary-2, WT-sed, biol rep1

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, sedentary


title: yWZ645_CEN4relocation_linear

description: Linear synIV with CEN4 relocated to telomere joint point


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: PGC-1alpha muscle-specific knockout

value: untrained, acute exercise


title: yWZ687_yeast_chr04_9_06

description: synIV draft strain


title: #993_untreated 24 hrs_rep2


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: #993_untreated 24 hrs_rep1


title: yWZ638_rightside-out_circle

description: Circular synIV with CEN4 in its native location

value: his3{delta}1 leu2{delta}0 ura3{delta}0 LEU2


title: #993_untreated 24 hrs_rep3


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: N2-iRGC, week 4, rep 2

city: Taipei

first: Yu-Hui

last: Wong

state: Taiwan

address: (NYCU) No. 155, Sec. 2, Linong St., Beitou Dist.

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The fastq format reads underwent quality filter (score >= Q15, qualified percentage > 60%) and adapter trimming using fastp (0.20.1).
The remain reads were mapped to Human Genome Reference GRCh38 using STAR (2.7.5a) to generate output in the BAM file format.
Expected counts were then estimated using RSEM (1.3.1).
Downstream analysis of the expected counts was performed in R Statistical Software (v4.2.1; R Core Team 2022) using DESeq2 (1.36.0).
Assembly: Human Genome Reference GRCh38
Supplementary files format and content: tab-delimited text file includes expected counts for each samples

growth_protocol: Human iPSCs are maintained in Essential 8™ mediumor StemFlex™ medium (Gibco).

extract_protocol:
Total RNA of iRGCs from days 7, 14 and 28 were extracted using RNA Mini Kit (Geneaid).
1 μg of total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol:
Human iPSCs for RGC differentiation are infected with lentiviruses encoding ubiquitously driven reverse tetracycline transactivator (rtTA) and Tet-On promoter driven ATOH7, BRN3B and SOX4 sequentially.
The differentiation process was started by addition of 2 μg/mL doxycycline, defined as day 0. Cells were then cultured in Medium-1: DMEM/F12 (Gibco) supplemented with N-2 (Gibco), 0.1 mM NEAA and 200 ng/mL mouse laminin (Gibco) with various other supplementary substances, namely brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), and forskolin (10 μM, Sigma-Aldrich). On day 1, Medium-1 was refreshed and 1 μg/mL puromycin and 2 μg/mL zeocin were added to allow selection of successfully induced cells.
On day 2, the cells were then dissociated using 0.5 mM EDTA in DPBS and replated onto poly-L-lysine- and laminin-coated culture plates for culture in Medium-2: DMEM/F12 + Neurobasal (1:1) supplemented with N-2, B-27, GlutaMAX (Gibco) and 200 ng/mL mouse laminin (Gibco) with supplementary substances. Zeocin selection was continued until day 6. On day 4 after doxycycline induction, Medium-2 was refreshed with 25 μM AraC to inhibit proliferation of undifferentiated cells.
On day 6, after 48 hrs of AraC treatment, Medium-2 was replaced by Medium-3: Neurobasal supplemented with N-2, B27 and GlutaMAX with supplementary substances. Hereafter, the cells were cultured in Medium-3 and medium was half refreshed every 3-4 days until day 15 or day 20, when the cells were used for downstream applications.The supplementary substances included doxycycline (2 μg/mL), brain-derived neurotrophic factor (BDNF, 10 μg/mL, PeproTech), ciliary neurotrophic factor (CNTF, 10 μg/mL, PeproTech), neurotrophin-3 (NT-3, 10 μg/mL, PeproTech), basic fibroblast growth factor (bFGF, 5 μg/mL, PeproTech), insulin (5 μg/mL, PeproTech) and forskolin (10 μM, Sigma-Aldrich)

tag: cell line

value: hiPSC-derived retinal ganglion cells


title: W3110_Fur_KO_Fe_2

value: glucose M9 minimal

value: mid-log phase

value: Fur deletion


title: yWZ635_CEN4relocation_circle

description: Circular synIV with CEN4 relocated to telomere joint point

value: his3{delta}1 leu2{delta}0 ura3{delta}0 URA3

value: a


title: W3110_WT_Fe_1

value: wild type


title: W3110_WT_Fe_2


title: N2-iRGC, week 2, rep 2


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep1

first: Regula

last: Furrer

description: Run mode: RAPIDHIGHOUTPUT


title: yWZ647_3_BS08000A

data_processing:
Samples were first processed by removing the Illumina barcodes and adaptor sequences using Trimmomatic v0.33.
Processed reads were then aligned to the S288C transcriptome reference and a custom synIV transcriptome reference (in which chromosome IV transcripts had been replaced with their synthetic versions) using the program Kallisto v0.43.0.
All data analyses were carried out in Rstudio v1.1.456.
Assembly: S288C
Supplementary files format and content: normalized_counts.txt

growth_protocol: Yeast cells were grown in approporate medium overnight. The next day overnight yeast culture was diluted to A600=0.1 into 5 mL of fresh liquid medium. Yeast cells were immediately harvested when A600 reached to 0.8-1.0.

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (QIAGEN, 74106).
1 mg of total RNA was used as input for RNA library preparation following vendor's instructions (NEB E7770, E7490).

treatment_protocol: For the chromosome tethering assay, 10 nM estradiol was supplemented after diluting the yeast cells to A600=0.1, and grow for 5-6 h until the wild-type strains reached to A600=1

value: is3{delta}1 leu2{delta}0 ura3{delta}0


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: W3110_Fur_DPD_2

value: Fur myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: N2-iRGC, week 1


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: W3110_Fur_DPD_1


title: W3110_Fur_KO_Fe_1

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto each reference genome using bowtie with the maximum insert size of 2000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for DESeq(https://bioconductor.org/packages/release/bioc/html/DESeq.html)
Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: The reference genomes used in this study are shown as below,  MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2
Supplementary_files_format_and_content: tab-delimited text files containing TPM values for each sample

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: W3110_Fur_Fe_2


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: N2-iRGC, week 4, rep 1


title: yWZ646_3_BS07997A

value: his3{delta}1 leu2{delta}0 ura3{delta}0


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: N1-iRGC, week 4, rep 2


title: W3110_Fur_Fe_1


title: N2-iRGC, week 2, rep 1


title: N1-iRGC, week 2, rep 2


title: yWZ647_2_BS07999A


title: yWZ646_1_BS07995A


title: yWZ646_2_BS07996A


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: N1-iRGC, week 4, rep 1


title: N1-iRGC, week 2, rep 1


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: Allele-iPSC, rep 2

source_name: Allele

value: Allele

value: hiPSC


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: PGC-1alpha muscle-specific knockout

value: untrained, sedentary


title: RRBS, quadriceps, steady-state, mKO-trained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: trained


title: yWZ647_1_BS07998A


title: yWZ636_2_BS07990A


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, mKO-untrained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: yWZ638_1_BS07992A

value: his3{delta}1 leu2{delta}0 ura3{delta}0 LEU2


title: yWZ638_3_BS07994A


title: yWZ638_2_BS07993A


title: Allele-iPSC, rep 1

description: AlliPSSF


title: yWZ636_1_BS07989A


title: RRBS, quadriceps, steady-state, mKO-trained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: yWZ636_3_BS07991A


title: N1-iRGC, week 1

value: hiPSC-derived retinal ganglion cells


title: Allele-iRGC, week 1


title: RRBS, quadriceps, steady-state, mKO-trained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: Allele-iRGC, week 4, rep 2


title: Allele-iRGC, week 2, rep 2


title: yWZ608_3_BS07988A


title: Allele-iRGC, week 4, rep 1


title: RRBS, quadriceps, steady-state, mKO-untrained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: BY4741_2_BS07984A

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Allele-iRGC, week 2, rep 1


title: RRBS, quadriceps, steady-state, mKO-trained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: yWZ608_1_BS07986A


title: RRBS, quadriceps, steady-state, mKO-trained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: L1/L2 split-seq

description: split-seq

data_processing:
Libraries were combined using Parse Biosciences pipeline
The demultiplexing, barcoded processing, gene counting and aggregation were made using the pipeline provided by Parse Biosciences
Assembly: hg38
Supplementary files format and content: Tab-separated matrix file and cell metadata with gene list

source_name: iPSC-sensory neurons and HEK293T cells

extract_protocol:
Extraction was done according to manufacturer's instructions (Kit WT-mini from Parse Biosciences)
Library construction was done according to manufacturer's instructions (Kit WT-mini from Parse Biosciences)
A total of 2 sublibraries were sequenced for scRNA-seq by split-seq

value: iPSC-sensory neurons and HEK293T cells

value: multiplexed (none; mock; heat-inactivated SARS-CoV-2; Infection with WA1/2020 SARS-CoV-2; Infection with delta variant SARS-CoV-2; Infection with omicron variant SARS-CoV-2)


title: BY4741_3_BS07985A

value: a


title: RRBS, quadriceps, steady-state, mKO-untrained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: wildtype

value: untrained, acute exercise


title: BY4741_1_BS07983A


title: int1-rep3

first: James

middle: J

last: Bieker

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

description:
Int1 sample 3
Table S5
Table S6
Table S7

data_processing:
Statistical analysis and representations were performed in R with package DESeq2.
75 nt single reads, 57-79 million reads per sample
Read mapping and quantification using Salmon
Differential gene expression using DESeq and edgeR
Assembly: hg38
Supplementary files format and content: Table S5, genes down regulated in int1-edited samples compared to scr control, tab-delimited xls file that includes samples 1-3 of scr and int1 (filtered based on padj<0.05 and |log2|>1.0)
Supplementary files format and content: Table S6, genes up regulated in int1-edited samples compared to scr control, tab-delimited xls file that includes samples 1-3 of scr and int1 (filtered based on padj<0.05 and log2>1.0)
Supplementary files format and content: Table S7, genes altered in expression in int1-edited cells compared to control (padj=NA have been removed; otherwise unfiltered)
Supplementary files format and content: salmon files contain quant.sf data

source_name: erythroid

growth_protocol: Human CD34+ cells were purchased from AllCells or obtained from the Yale Cooperative Center of Excellence in Hematology. These were differentiated ex vivo under three-phase protocols. Briefly, CD34+ cells were thawed on day 0 into X-VIVO 15 (Lonza, 04–418Q) supplemented with 100 ng/ml human stem cell factor (SCF), 100 ng/ml human thrombopoietin, and 100 ng/ml recombinant human Flt3-ligand. Transfection was performed before the expansion phase I, and cells were allowed to recover for 24-48 hrs in X-VIVO media prior to switching to phase I. The base erythroid differentiation medium (EDM) consists of IMDM supplemented with 330 μg/ml holo-human transferrin, 10 μg/ml recombinant human insulin, 2 IU/ml heparin, 5% human Octoplas AB plasma (OctaPharma), 3 IU/ml erythropoietin, 1% L-glutamine, and 1% penicillin/streptomycin. During phase I (days 0-7), EDM was further supplemented with 10E–6 M hydrocortisone, 100 ng/ml human SCF, and 5 ng/ml human IL-3. During phase II (days 7–11), EDM was supplemented with 100 ng/ml human SCF alone. During phase III (days 11–18), EDM had no additional supplements. All analyses were performed after harvesting the cells on day 18.

extract_protocol:
Total RNA from all samples was isolated with Triazol.
RNA seq analysis was performed using NEBNext polyA selection (Cat. # E7490S) and RNA Library Prep Kit (Cat. # E7770L).

treatment_protocol: AsCpf1 protein (enhanced) was purchased from IDT. RNP were freshly formed by mixing 105 pmol of Cpf1 protein with 120 pmol of gRNA (IDT) for 15 at room temperature and kept on ice until use. CD34+ cells were transfected with the Amaxa 4D Nucleofector with program EO-100.

tag: cell harvest

value: differentiation d18

tag: starting cells

value: erythroid

value: int1 indel

value: int1 crispr RNP


title: SynIV_HEH1ZF_HEH2ZF_1_BS18944A

value: his3{delta}1 leu2{delta}0 ura3{delta}0 YKL162C-A::ZEV-NatMX4, pWZ758, pWZ759


title: SynIV_HEH1ZF_HEH2ZF_2_BS18945A


title: SynIV_HEH1ZF_HEH2ZF_3_BS18946A


title: int1-rep1

description:
Int1 sample 1
Table S5
Table S6
Table S7


title: RRBS, quadriceps, steady-state, mKO-untrained, biol rep4

address: Spitalstrasse 41

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle


title: RRBS, quadriceps, steady-state, mKO-untrained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT

value: PGC-1alpha muscle-specific knockout


title: int1-rep2

description:
Int1 sampe 2
Table S5
Table S6
Table S7


title: scr-rep2

description:
Scr sample 2
Table S5
Table S6
Table S7

value: WT

value: scrambled crispr RNP


title: yWZ608_2_BS07987A

value: his3{delta}1 leu2{delta}0 ura3{delta}0


title: SynIV_HEH1_HEH2_3_BS18943A

value: his3{delta}1 leu2{delta}0 ura3{delta}0 YKL162C-A::ZEV-NatMX4, pWZ802, pWZ803


title: scr-rep3

description:
Scr sample 3
Table S5
Table S6
Table S7


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, steady-state, mKO-untrained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, sedentary


title: BY4741_HEH1ZF_HEH2ZF_3_BS18940A

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 YKL162C-A::ZEV-NatMX4, pWZ758, pWZ759


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-4h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: SynIV_HEH1_HEH2_2_BS18942A


title: MDA-MB-231_EtOH_rep3

city: Boulder

first: Jennifer

middle: F

last: Kugel

state: CO

address: 596 UCB

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
Reads were mapped to the human genome (hg38 assembly) using HISAT2 in the L, 0, 0.15 alignment mode plus trimming 61 bps off the 3ʹ end and trimming 10 bps off the 5’ end where read quality decreased.
Tag directories in HOMER were created from the SAM files generated by HISAT2.
bedGraph files were generated using the makeUCSCfile command in HOMER.
Meta-analyses and per-gene quantification of mapped reads were performed using the suites of tools available in HOMER, Bedtools, and Galaxy.
Assembly: hg38
Supplementary files format and content: Processed data files are bedgraph files of each biological replicate and input

extract_protocol:
Total RNA was extracted using TRIzol. 100 μg of total RNA was added to a 250 μL MTS-biotin labeling reaction with 1X Biotinylation buffer (10mM HEPES, pH 7.5, 1 mM EDTA) and 5μg of MTSEA biotin-XX (Biotium) dissolved in 20% DMF. Reactions were nutated at room temperature for 30 min in the dark, then phenol/chloroform extracted, followed by ethanol precipitation. The RNA pellets were dissolved in 50 μL of dH2O and incubated at 65°C for 10 min followed by rapid cooling on ice. Biotinylated 4sU-labeled RNA was separated from unlabeled RNA using the μMacs Streptavidin Kit (Miltenyi). 100 μL of μMacs Streptavidin Microbeads were added to the 50 μL of RNA and nutated at room temperature for 15 min. Meanwhile, μMacs μColumns (Miltenyi) were equilibrated twice with 100uL of Equilibration Buffer for nucleic acid applications (Miltenyi). Samples were applied to the μColumns and flow-throughs were collected. The μColumns were then washed twice with 500 μL of high salt wash buffer (100mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20). 4sU-labeled RNA was eluted from the μColumns with 100 μL of freshly prepared 100 mM DTT. A second elution was performed 5 min later with another 100 μL of 100 mM DTT. The eluates were ethanol precipitated and RNA pellets were resuspended in 20 μL of dH2O.
Sequencing libraries were constructed using the CORALL Total RNA-Seq Library Prep Kit with RiboCop (Lexogen).

treatment_protocol: Cells were treated with 0.3% (60 mM) EtOH or left untreated for 6 h. At 4 h into the incubation, 200 μM 4sU (final concentration) was added to the cells.

value: epithelial triple-negative breast cancer cells

value: 4sU, ethanol


title: SynIV_HEH1_HEH2_1_BS18941A

value: a


title: MDA-MB-231_EtOH_rep2


title: scr-rep1

description:
Scr sample 1
Table S5
Table S6
Table S7


title: MDA-MB-231_notreat_rep3


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep5

city: Basel

institute: University of Basel

description: Run mode: RAPIDHIGHOUTPUT

value: wildtype

value: untrained, acute exercise


title: BY4741_HEH1ZF_HEH2ZF_2_BS18939A


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: MDA-MB-231_notreat_rep2


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: MDA-MB-231_EtOH_rep1


title: BY4741_HEH1_HEH2_2_BS18936A

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 YKL162C-A::ZEV-NatMX4, pWZ802, pWZ803


title: BY4741_HEH1_HEH2_3_BS18937A


title: BY4741_HEH1_HEH2_1_BS18935A


title: MDA-MB-231_notreat_rep1


title: MCF7_EtOH_rep3

value: epithelial breast cancer cells


title: RRBS, quadriceps, acute-exercise, WT-untrained-ex-0h, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: synIV_yWZ645

data_processing:
A multistep, parameter-free approach was use to map the Hi-C read with Bowtie2, as described previously (PMID: 22941365).
Normalized contact maps were 5 kb-binned
Normalized contact maps were plotted using MatLab2018
Assembly: S288C
Supplementary files format and content: bin.txt files

growth_protocol: Yeast cells were inoculated into 10 mL of YPD overnight, and the next day approximately 80-100 OD cells were subcultured into 150 mL YPD for 2.5 hours of growth at 30°C.

extract_protocol:
Crosslinked cells were harvested and suspended in 10 mL spheroplast buffer (1M sorbitol, 5 mM DTT, 250 U zymolyase 100T (US Biological, Z1004)) for 40 min incubation at 30°C. Spheroplasts were washed with 10 mL of 1M sorbitol once and resuspended in 2 mL of 0.5% SDS at 65°C for 20 min. MboI (NEB, R0147) was used for overnight digestion of all the genomic DNA from fixed yeast cells at 37°C. The digestion product was centrifuged at 18000xg for 20 min and the pellet was subsequently suspended in 200 mL cold water. DNA sticky ends were filled with biotin-14-dCTP (Invitrogen, 19518018) by Klenow enzyme (NEB, M0210L) at 37°C for 80 min. Biotinylated DNA was ligated with T4 ligase (Thermo Scientific, EL0014) at room temperature for 2 hours.
Ligation product was reverse cross-linked by 0.5 mg/mL proteinase K (Thermo Scientific, EO0492) in 25 mM EDTA buffer at 65°C for 4 hours. The reverse crosslinked sample was purified using the large fragment DNA recovery kit (Zymo Research, D4046). Purified Hi-C library was used as input material for Illumina sequencing library prep kit (NEB, E7805).

treatment_protocol: Cells were crosslinked by 3% [v/v] formaldehyde for 20 min at room temperature and subsequently quenched with glycine for 15 min at 4°C.


title: RRBS, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep5

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: MCF7_EtOH_rep2


title: synIV_yWZ636

value: his3{delta}1 leu2{delta}0 ura3{delta}0 URA3


title: MCF7_EtOH_rep1


title: RRBS, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: synIV_yWZ635


title: BY4741_HEH1ZF_HEH2ZF_1_BS18938A


title: RRBS, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: synIV_yWZ638

value: his3{delta}1 leu2{delta}0 ura3{delta}0 LEU2


title: synIV_yWZ631


title: RRBS, quadriceps, acute-exercise, WT-untrained-ctrl, biol rep1

description: Run mode: RAPIDHIGHOUTPUT

value: Skeletal muscle


title: MCF7_notreat_rep2


title: MCF7_notreat_rep1


title: MCF10A_EtOH_rep3

value: non-tumorigenic epithelial breast cells


title: RRBS, quadriceps, steady-state, WT-trained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: trained


title: RRBS, quadriceps, steady-state, WT-trained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: synIV_yWZ536


title: synIV_yWZ556


title: MCF10A_EtOH_rep2

value: WT


title: BY4741_WZ

description: Wild-type control

value: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: MCF10A_notreat_rep3


title: RRBS, quadriceps, steady-state, WT-trained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: BY4741_LLS

description: Wild-type control


title: RRBS, quadriceps, steady-state, WT-trained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT


title: MCF7_notreat_rep3


title: MCF10A_notreat_rep2


title: Muscle stem cells, PSB-KD-1, 2

city: Montréal

first: Nicolas

middle: A

last: Dumont

state: QC

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Saint-Justine

data_processing:
GenPipes an open-source Python-based Workflow Management System (WMS)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GenPipes
Trimmed sequence reads were mapped to mm10
Read count extraction and normalization were performed using Genpipes
Assembly: mm10
Supplementary files format and content: csv file with raw values for each Sample

source_name: Muscle

growth_protocol: mdx muscle stem cells were maintained in HAMF-10 supplemented with 20% fetal bovine serum (FBS), FGF2, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Untreated murine muscle stem cells (MuSCs) and PSB-KD107 treated cells were harvested, and total mRNA was extracted using RNeasy Kit (Qiagen, ID:73404) according to the manufacturer’s instructions
the sequencing libraries and Illumina NovaSeq 6000 for 100-bp PE reads sequencing were performed at the genome Quebec platform

treatment_protocol: mdx MuSCs were treated for 2-days with PSB-KD107 (10 μM) or vehicle.

value: Muscle

value: mdx cells

value: Satellite cells


title: Muscle stem cells, PSB-KD-1, 3


title: RRBS, quadriceps, steady-state, WT-untrained, biol rep5

description: Run mode: RAPIDHIGHOUTPUT

value: untrained, sedentary


title: RRBS, quadriceps, steady-state, WT-trained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: MCF10A_notreat_rep1


title: MCF10A_EtOH_rep1

value: 4sU, ethanol


title: RRBS, quadriceps, steady-state, WT-untrained, biol rep4

description: Run mode: RAPIDHIGHOUTPUT


title: Muscle stem cells, control 3

value: Control


title: RRBS, quadriceps, steady-state, WT-untrained, biol rep3

description: Run mode: RAPIDHIGHOUTPUT

value: wildtype


title: HepG2_1000cells_2

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

data_processing:
UMI processed using umi-tools version 0.5.4
Unmethylation, methylation, and hydroxymethylation reads were separated and the tags were removed using Cutadapt version 1.5
Reads were aligned to the human genome using bowtie2 version 2.3.4.1
PCR duplicates were removed using umi-tools version 0.5.4
Assembly: hg38
Supplementary files format and content: bed files containing chromosome, start, end, 5C ratio, 5mC ratio, 5hmC ratio and coverage for each CCGG site
Library strategy: LM-PCR WGA

extract_protocol:
For bulk samples, DNA was extracted using Qiagen Dneasy Blood and Tissue kit. Single cells were stained with Calcein-AM dye and isolated into tubes.
Bulk samples undergo DARESOME protocol and single cells undergo scDARESOME. Cells were lysed and protease treated prior to HpaII digestion. Digested unmethylated sites were ligated with unmethylation-tag (U-tag) adapters. Excess adapters were then removed using NEB Thermolabile USER II enzyme. This was followed by the second round of digestion with MspI and NlaIII enzymes. Hydroxymethylation-tag (H-tag) and Nla-tag (N-tag) adapters were ligated with the digested fragments. Excess adapters and oligonucleotides were removed with Thermolabile USER. 5hmC CCGG sites were glucosylated by glusyl transferese. The samples then undergo MspI digestion, methylated CCGG sites are digested and liagated to Methylated-tag (M-tag). The Read1 and Read2 Illumina sequencing adapters were added through PCR. The amplified library was size selected using BluePippin and quantified using Kapa Library Quantification kit.

value: Liver cell line

tag: disease

value: Hepatocellular carcinoma


title: Muscle stem cells, control 2


title: HepG2_1000cells_1


title: Muscle stem cells, PSB-KD-1, 1


title: H1ES_1000cells_2

value: ES Cell line


title: RRBS, quadriceps, steady-state, WT-untrained, biol rep1

description: Run mode: RAPIDHIGHOUTPUT


title: RRBS, quadriceps, steady-state, WT-untrained, biol rep2

description: Run mode: RAPIDHIGHOUTPUT


title: H1ES_1000cells_1


title: Lw_c02, control, scRNAseq

city: Beijing

first: Xiaoxiao

last: Wang

address: No.11 Xizhimen South Street

institute: Peking Univeristy People's Hospital

description:
10x Genomics
Sample 8, bacodes with_8

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version 2.20). Sample demultiplexing, barcode processing and single-cell 3’ gene counting were performed by using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger, version 5.0.1), and scRNA-seq data were aligned to the Ensembl genome GRCh38/GRCm38 reference genome.
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

source_name: liver

extract_protocol:
Liver tissues of mice were obtained from wild-type mice (N=2) and NASH mice with fibrosis (HFD+F+CCl4, N=3; WD+F+CCl4, N=3) and were transferred into a sterile RNase-free tube containing calcium-free and magnesium-free 1x phosphate buffered solution (PBS) on ice. Tissues were transferred into the culture dish and cut it into 0.5 mm 2 pieces,  and washed with 1 × PBS. Liver tissues were dissociated into single cells in dissociation solution 0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I ) in 37 water bath. The overall cell viability was higher than 85%.
Single cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer s instructions of 10X Genomics Chromium Single Cell 3 kit ( V3 ) .The following cDNA amplification and library construction steps were p erformed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired end multiplexing run,150bp) by LC Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: liver

value: hepatocytes, cholangiocytes, hepatic stellate cells (HSCs), endothelial cells, DCs, monocytes, Kupffer cells, T cells, B cells, and granulocytes


title: HepG2_sc_4


title: Lw_h03, NASH model, scRNAseq

description:
10x Genomics
Sample 6, bacodes with_6

value: high-fat diet, fructose solution plus intraperitoneal injection of CCl4


title: HepG2_sc_5


title: HepG2_sc_3


title: NUGQ3

city: Barcelona

first: Malgorzata

middle: Ewa

last: Rogaska

address: C/ del Dr. Aiguader, 88

country: Spain

institute: CRG

data_processing:
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.2.2 , available on github (https://github.com/vastgroup/vast-tools)
Alternative splicing analysis: From the primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed using a 2-tailed unpaired Wilcoxon–Mann–Whitney test. The FDR was estimated using the Benjamini–Hochberg method. A p-value < 0.05 fdr<0.12 and PSI difference >5 was considered significant
Assembly: hg38
Supplementary files format and content: All files are in tab-delimited format. File dPSI.txt contains filtered PSI values and results of differential AS analysis with dPSI per event and associated p-value

growth_protocol: NUGC4 cells were cultured in RPMI medium (GIBCO Cat# 31870-025) and HFE145 cells in DMEM medium (Lonza, Cat#12-733F), supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin, under standard tissue culture conditions (37oC, 5% CO2)

extract_protocol:
Total RNA was extracted with the TRIzol® reagent (Thermo Fisher Scientific, Inc)
lluminaRNA Sample Prep Kit (TruSeq® Stranded mRNA Library Prep, Cat#20020594) was used with 1ug of total RNA for the construction of sequencing libraries RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IQGAP1KO cells for all the above cell lines were generated with the CRISPR/Cas9 approach


title: SMZ1_HiChIP_rep2

city: Salt Lake City

first: Xiaoyang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Assembly: hg19
Supplementary files format and content: mango text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, PETs, the adjusted P-value
Library strategy: HiChIP

extract_protocol:
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)

value: T-cell lymphoma


title: SMZ1_HiChIP_rep1


title: Lw_h02, NASH model, scRNAseq

description:
10x Genomics
Sample 5, bacodes with_5


title: NUGQ2


title: HepG2_sc_2


title: NUGQ1


title: LT2_Fur_KO_Fe_2

first: Ye

last: Gao

address: 9500 Gilman Dr.

organism: Salmonella enterica

source_name: bacteria cells

value: Typhimurium LT2

value: glucose M9 minimal

value: mid-log phase

value: Fur deletion


title: Lw_h01, NASH model, scRNAseq

description:
10x Genomics
Sample 4, bacodes with_4

value: WT


title: HepG2_sc_1


title: NUG3


title: Lw_w03, NASH model, scRNAseq

description:
10x Genomics
Sample 3, bacodes with_3

value: western diet, fructose solution plus intraperitoneal injection of CCl4


title: LT2_Fur_KO_Fe_1


title: Lw_w02, NASH model, scRNAseq

description:
10x Genomics
Sample 2, bacodes with_2


title: H1ES_sc_5


title: NUG2


title: Muscle stem cells, control 1

value: Muscle

value: mdx cells

value: Satellite cells


title: H1ES_sc_4


title: Lw_w01, NASH model, scRNAseq

description:
10x Genomics
Sample 1, bacodes with_1


title: NUG1


title: H1ES_sc_3


title: Lw_c01, control, scRNAseq

description:
10x Genomics
Sample 7, bacodes with_7

value: Control


title: Mouse_P21_3

value: Cerebellum


title: N2-iPSC, rep 2

value: hiPSC


title: H1ES_sc_2

value: ES Cell line


title: N1-iPSC, rep 2


title: Mouse_P21_1


title: H1ES_sc_1


title: LT2_Fur_DPD_2

data_processing:
Library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the each reference genome using bowtie with default options to generate SAM output files
MACE program was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, manual curation was performed based on the signal-to-noise(S/N) ratio value.
The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: Each genome ( MG1655 =  NC_000913.2 / W3110 = NC_007779.1 / W  = NC_017635.1 , NC_017636.1 , NC_017637.1 / KO11FL = NC_017660.1 , NC_017661.1 / 042 = NC_017626.1 , NC_017627.1 / BL21 = NC_012971.2 / Crooks = NC_010468.1  / Sakai  = NC_002695.1 , NC_002127.1 , NC_002128.1  / CFT073 = NC_004431.1 / LT2 = NC_003197.2 , NC_003277.2 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

value: Fur myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: LT2_Fur_DPD_1