title: 0h_0F_rep1

description: 0 hours, 0 mM fructose, Replicate 1

value: 0 hours


title: RNAseq_Red_d6_S1

status: Public on Dec 08 2020

type: SRA

city: Ithaca

first: Karin

middle: Revka Loek

last: van der Burg

state: NY

address: 215 Tower Road, Corson Hall

department: EEB

country: USA

institute: Cornell University

library_source: transcriptomic

data_processing:
Alignment to junonia coenia genome using tophat.
Read counts overlapping genes were calculated with bedtools
Differential expression analysis was performed using DESeq2
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: normalized bigwig files were produced using ucsc script

molecule: total RNA

organism: Junonia coenia

source_name: whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C

extract_protocol:
RNA was isolated from whole wing tissue and poly-A selected using NEB poly-A selection beads
Libraries were prepared using the NEB RNA library prep kit

tag: developmental stage

value: 6 days after pupation

tag: tissue

value: hindwing


title: RRBS_C5

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

library_source: genomic

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
Adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in coverage and ≥10% methylation differences between control groups and arsenite groups using the logistic regression method. DMRs were detected for regions containing ≥3 CpG sites and at least one DMC and with ≥10% absolute mean CpG methylation difference by using an eDMR package on R
DMRs were annotated by using HOMER(http://homer.ucsd.edu/homer/, v4.10).
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Sperm

extract_protocol:
Sperm was lysed in lysis buffer (7.3 mM Tris-HCl (pH 7.5), 7.3 mM NaCl, 18.2 mM EDTA, 1.8% SDS, 1.8% 2-ME, 1.4 mg/ml proteinase K) and DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in 10 mM Tris (pH7.4).
RRBS libraries were prepared as previously described (Matsushita et al.,BMC cancer 18: 317, 2018; Okamura et al. Cancer Sci 110:2629, 2019) with some modifications. Briefly, 100 ng of genomic DNA was sonicated for one second by a Focused-ultrasonicator (Covaris) before restriction enzyme reaction.

tag: strain

value: sperm

tag: dam treatment group

value: control


title: 384h_10F_rep1

type: RNA

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

description: 384 hours, 10 mM fructose, Replicate 1

hyb_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

scan_protocol: Beadchips were scanned using Illumina BeadScan image data acquisition software

data_processing: The scanned data was acquired in R using the package illiminaio. The non-normalized summarized bead-level data was then annotated with R package  illuminaHumanv4.db.

label: biotin

organism: Homo sapiens

source_name: SGBS preadipocyte cells

growth_protocol: SGBS preadipocytes were plated at 2x105 cells in 100 mm dishes, supplemented with 10 ml growth medium, grown to confluence and initiated to differentiate as per. All media used for the growth, differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr).

extract_protocol: For RNA isolation, media was completely aspirated from cells and a total of 700 ul of QIAzol lysis reagent was added to the cells, and the lysed cells were scraped, collected in an Eppendorf vial, sheer disrupted by passing through a tuberculin syringe about 6 time, and the lysates flash frozen.

treatment_protocol: Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose or 5mM of glucose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation. differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr). Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation.

tag: cell line

value: SGBS

tag: time

value: 384 hours

tag: treatment

value: 10 mM  fructose


title: 192h_0F_rep2

description: 192 hours, 0 mM fructose, Replicate 2

label_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

value: 192 hours

value: 0 mM  fructose


title: Individual #12, EtOH, rep2

city: Olsztyn

first: Carsten

last: Carlberg

address: ul. Trylińskiego 18

department: Food Research

country: Poland

institute: Polish Academy of Sciences

data_processing:
Quality control using "afterQC"
Read alignment using "kallisto"
Differential gene expression using "EdgeR"
Genome_build: hg38
Supplementary_files_format_and_content: relative abundance in Excel table

source_name: PBMCs

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

tag: cell type

value: peripheral blood mononuclear cells

tag: agent

value: 0.1percent ethanol

tag: time point


title: Individual #12, EtOH, rep3


title: RRBS_C4


title: ATACseq_Red_5th_S2

data_processing:
Alignment to Junonia coenia genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
Peak calls were performed with F-seq
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: RPM normalized files were produced using deeptools

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol
Libraries were prepared as described in the ATAC-seq protocol

value: 5th instar


title: Individual #12, EtOH, rep1


title: RNAseq_Red_72h_S3

value: 72 hours after pupation


title: RNAseq_Red_72h_S2


title: Individual #12, 125D, rep3


title: RRBS_C2


title: RNAseq_Red_72h_S1


title: Individual #12, 125D, rep2


title: Individual #12, 125D, rep1


title: RRBS_C1


title: RNAseq_Red_pp_S3

value: pre pupa


title: RNAseq_Red_pp_S2


title: Individual #9, EtOH, rep3


title: YTHDC1_KO_YTHDC1_ChIP

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

country: China

institute: Fudan university

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

source_name: Embryonic stem cells

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2. For EB differentiation, embryoid bodies (EBs) were allowed to form in the absence of LIF by hanging drops containing ~1,000 mES cells/drop on petri dish lids for 2days, and then collected and transferred to standard mES culture (without LIF and MEK and GSK3β inhibitor) in non-coated petri dishes 5days.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: mESCs were treated with 500μM IAA for 48 hours at 37ºC.

value: Embryonic stem cells

tag: genotype

value: YTHDC1 KO + AID-YTHDC1

value: IAA

tag: antibody


title: Individual #9, EtOH, rep2


title: RRBS_C3


title: RNAseq_Red_5th_S3


title: RNAseq_Red_pp_S1


title: Individual #9, EtOH, rep1


title: IAPEz_ChIRP_Input

data_processing:
Library strategy: ChIRP-Seq
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

extract_protocol:
E14 ES cells were crosslinked with 3% formaldehyde for 30 min at room temperature. Crosslinking was then quenched with 0.125 M glycine for 5 min. Chromatin was then solubilized by sonicating in lysis buffer (50 mM Tris 7.0, 10 mM EDTA, 1% SDS, 0.5 mM DTT, and RNase Inhibitors). Chromatin is diluted in two times volume of hybridization buffer (750mM NaCl, 1% SDS, 50 mM Tris 7.0, 1 mM EDTA, 15% Formamide, 0.5 mM DTT, and RNase Inhibitors). 10 pmol probes were added to 3 ml of diluted chromatin, which was mixed by end-to-end rotation at 37 °C for 6 hr. Streptavidin beads were washed three times in nuclear lysis buffer and added into the reaction, which was mixed for another 45 min at 37 °C. Beads were captured by magnets (Invitrogen) and washed five times with wash buffer (2x SSC, 0.5% SDS, add DTT and PMSF fresh). chromatin was reverse crosslinked at 65 °C overnight. After 1 hour of RNase A (1unit/μl) at 37 °C and Proteinase K (1unit/μl) digestion at 55 °C, DNA samples were then purified using PCR extraction kit (QIAGEN #28006). The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: parental

tag: probe


title: Individual #9, 125D, rep3


title: 0h_0F_rep2

description: 0 hours, 0 mM fructose, Replicate 2

value: 0 hours


title: 192h_8d_10F_rep1

description: 192 hours, 10 mM fructose, Replicate 1


title: YTHDC1_W428A_YTHDC1_ChIP

value: YTHDC1 W428A + AID-YTHDC1


title: 24h _0F_rep3

description: 24 hours, 0 mM fructose, Replicate 3

value: 24 hours


title: 96h_4d_0F_rep1

description: 96 hours, 0 mM fructose, Replicate 1

value: SGBS

value: 96 hours


title: 192h_2.5F_rep3

description: 192 hours, 2.5 mM fructose, Replicate 3

value: 2.5 mM  fructose


title: Arabidopsis pistil_fresh_stage12_rep 1

first: Shi-Xia

last: Yu

address: Dongchuan Road, Shanghai Minhang District No. 800

institute: Shanghai Jiaotong University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Agilent Arabidopsis (V4) Gene Expression Microarray (4*44K, Design ID:021169) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis pistils,removed stigma, stage 12,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown in a 10:10:1 mix of peat substrate: vermiculite: perlite under a 16-h-light/8-h-dark photoperiod at 22 ± 2 °C. For growth on plates, surface-sterilized Arabidopsis seeds were placed on half-strength Murashige and Skoog (MS) basal medium. Plates were kept at 4 °C for 3 days, then transferred to a growth chamber (Percival, Boone, IA, USA) with a 16-h-light/8-h-dark photoperiod at 22 °C.

extract_protocol: RNA was prepared using the RNasey Mini Kit (Qiagen p/n 74104) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The stigma was removed, and collected under a stereoscope microscope. More than 3 μg pistils was collected at stage 9-10 (S1), stage 11 (S2), and stage 12 (S3) with three biological replicates

value: stage 12

tag: tissuse

value: Pistil removed stigma


title: Arabidopsis pistil_fresh_stage12_rep 3

source_name: Arabidopsis pistils,removed stigma, stage 12,replicate 3


title: Arabidopsis pistil_fresh_stage11_rep 3

source_name: Arabidopsis pistils,removed stigma, stage 11,replicate 3

value: stage 11


title: IAPEz_ChIRP

value: IAPEz-int DNA


title: RNAseq_Red_5th_S1

value: 5th instar

value: hindwing


title: Individual #9, 125D, rep2

value: peripheral blood mononuclear cells


title: YTHDC1_WT_YTHDC1_ChIP

value: Embryonic stem cells

value: YTHDC1 WT + AID-YTHDC1


title: Arabidopsis pistil_fresh_stage11_rep 2

source_name: Arabidopsis pistils,removed stigma, stage 11,replicate 2


title: rescue_Mut_total_RNA_rep2

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5) with parameter “-k 1” to keep only one locus when a read mapped to multiple genomic regions.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).

value: METTL3 KO+Mut METTL3


title: Individual #9, 125D, rep1


title: SL96966

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

data_processing:
Raw fastq data were aligned to mouse transcriptome by kallisto v0.43
Kallisto counts were imported through Tximport to get unnormalized gene expressions
Normalized counts were extracted from DESeq2
Genome_build: Rat ensembl release 90
Supplementary_files_format_and_content: csv file with unnormalized gene counts from Tximport

organism: Rattus norvegicus

source_name: Female Rat age at 16 month, acyclic menopause cycle

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: status

value: Hippocampus

tag: Sex

value: Female


title: Individual #5, EtOH, rep3

value: 0.1percent ethanol


title: rescue_Mut_total_RNA_rep1


title: rescue_WT_total_RNA_rep2

value: METTL3 KO+WT METTL3


title: Arabidopsis pistil_fresh_stage11_rep 1

source_name: Arabidopsis pistils,removed stigma, stage 11,replicate 1


title: SL96965


title: RNAseq_Red_5th_S2


title: Arabidopsis pistil_fresh_stage12_rep 2

source_name: Arabidopsis pistils,removed stigma, stage 12,replicate 2


title: Arabidopsis pistil_fresh_stage 9-10_rep 3

source_name: Arabidopsis pistils,removed stigma, stage 9-10,replicate 3

value: stage 9-10


title: Individual #5, EtOH, rep2


title: rescue_WT_total_RNA_rep1


title: SL96964


title: Individual #5, EtOH, rep1


title: Individual #5, 125D, rep3


title: METTL3_KO_total_RNA_rep2

value: METTL3 KO


title: SL96962


title: Individual #5, 125D, rep2


title: SL96963


title: Arabidopsis pistil_fresh_stage 9-10_rep 1

source_name: Arabidopsis pistils,removed stigma, stage 9-10,replicate 1


title: h12 vs h13

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: deltaNp63 knockdown keratinocyte

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The cells were cultured as a monolayer in keratinocyte-SFM supplemented with 5 ng/ml human recombinant epidermal growth factor 1-53 and 50 μg/ml bovine pituitary extract (Gibco, Carlsbad, CA) at 37ºC in a humidified atmosphere with 5% CO2. NHEKs were maintained for 3 or 4 passages in these conditions.

extract_protocol: Total NHEK RNA was purified using RNeasy Mini Kit and RNase-free DNase (Qiagen, Hilden Germany) according to the manufacturer’s protocol. Extracted total RNA was reverse-transcribed into cDNA using a RevertAid RT kit containing random hexamer primers (Thermo Fisher Scientific, Woburn, MA).

treatment_protocol: Human ΔNp63-specific siRNA was obtained from Invitrogen (Carlsbad, CA; sense: 5′-ACAAUGCCCAGACUCAAUU-3′; antisense: 5′-AAUUGAGUCUGGGCAUUGU-3′). Scrambled sequence siRNA for the negative control was purchased from Invitrogen. Transfections were performed using Lipofectamine RNAiMAX (Invitrogen) in Opti-MEM (GIBCO) at 40 nmol/L according to the manufacturer's instructions. The culture medium was replaced at 6 h after siRNA transfection.

value: primary cultured keratinocyte

tag: knockdown

source_name: control siRNA transfected keratinocyte

value: control siRNA


title: Arabidopsis pistil_fresh_stage 9-10_rep 2

source_name: Arabidopsis pistils,removed stigma, stage 9-10,replicate 2

tag: developmental stage

value: Pistil removed stigma


title: Individual #5, 125D, rep1


title: Parental_total_RNA_rep2

value: parental


title: SL96961

tag: tissue


title: RNA_KMS27_Che-1_3

city: Rome

first: Maurizio

last: Fanciulli

address: via Chianesi

country: Italy

institute: IRCCS National Institute of Cancer Regina Elena

data_processing:
RNA-seq basic analysis was carried out with RAP (D'Antonio et al., 2015), a cloud Tuxedo-suite (Trapnell et al., 2009) based pipeline.
Raw reads we extracted using HTseq (Anders et al., 2015)  for NCBI’s RefSeq gene annotation and our custom spike-in annotation.
Gene-based differential expression was carried out using spike-in raw reads count as scaling factors with DEseq2 (Love et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: deseq2; cuffdiff output

growth_protocol: Kms27 cell line in Optimem supplemented 15% inactived serum , l-glutamine and gentamycin

extract_protocol:
transfected cells were extracted by TRizol (Thermofisher/Life Techn) and purified by Qiagen MIni Elute.
Library construction using Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA).

treatment_protocol: transfection by Lipofectamine 3000 with specific siRna for Che-1/AATF (ThermoFisher/Life tech.)

tag: genotype/variation

value: siChe

tag: spike in used


title: RNA_KMS27_Che-1_2

tag: cell line


title: rescue_Mut_WGBS_rep2

data_processing:
Raw reads were trimmed 10 bps off the 5’ end and 3’ end and then mapped to mm10 genome using bsmap (v 2.90) with the parameters “-p 10 -w 50 -v 0.1”.
Methylation ratio were calculated by methratio.py with the parameters “-t 2 -m 5 -z”.
Genome_build: mm10
Supplementary_files_format_and_content: methratio.py output files (.meth.txt) including methylation position and methylation ratio.

extract_protocol:
The bisulphite conversion was performed using the EZ DNA Methylation Gold kit from Zymo Research (#D5005).
Post-BS library preparation was performed using Accel-NGS® Methyl-Seq DNA Library Kit from Swift Biosciences (#36024).


title: RNA_KMS27_Che-1_1


title: Parental_total_RNA_rep1


title: rescue_WT_WGBS_rep2


title: RNA_KMS27_Control_3

value: control


title: SL96944

source_name: Female Rat age at OVX at 9 month, data collected as 10 month


title: SL96945


title: rescue_WT_WGBS_rep1


title: rescue_Mut_WGBS_rep1


title: RTBN-ko

city: Bethesda

first: Jianguo

last: Fan

state: MD

address: 6 Center Drive Rm 108A

institute: National Eye Institute

data_processing:
Differential mRNA expression between RTBDN knockout mice and age matched C57bl6/J control mice was quantified by RNA-seq data analysis using the Tuxedo package (i.e. the Tophat-Cufflinks pipeline) on the NIH Biowulf high performance computing platform.
Alignment was performed by use of Tophat version 2.1.1 (Bowtie2) and the mouse10 reference genome (NCBI) with standard parameters. Cufflinks version 2.2.1 was used to assemble the transcriptomes and CuffDiff was used to quantify the levels of gene expression in Reads Per Kilobase of transcript per Million mapped reads (RPKM).
False discovery rate (FDR) value of less than or equal to 0.1 was used as the criteria for “significant” differentially regulated genes.
Output files from Cuffdif was uploaded as the processed data files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene, "1" refers to wild type and "2" refers to RTBDN KO.

source_name: Retina

extract_protocol:
DNA-free total RNA was prepared from a pool of retinas from 5 RTBDN KO or age-matched C57bl6/J control mice, by use of PureLink RNA Mini Kit and TRIzol Reagent (Life Technologies) and on-column DNase treatment with PureLink Dnase (Life Technologies) according to manufacturer’s instructions.
RNA integrity was evaluated by 2100 Bioanalyzer (Agilent Technologies) with RIN no less than 7. RNA-seq was performed by NIH Intramural Sequencing Center (Bethesda, MD).
One paired end index library from each  polyA(+)-selected RNA samples was prepared. Six samples were pooled and loaded on 2 lane(s) of Illumina HiSeq 2000 Sequencer, and run as paired end index 100 base reads with a total of 40 million base read pairs per sample.

tag: strain

value: retina

tag: age

value: 3 month

value: RTBDN KO


title: METTL3_KO_total_RNA_rep1

tag: cell type

value: Embryonic stem cells


title: RNA_KMS27_Control_2


title: SL96943


title: METTL3_KO_WGBS_rep2


title: SL96960

source_name: Female Rat age at 9 month, acyclic menopause cycle


title: RNA_KMS27_Control_1


title: METTL3_KO_WGBS_rep1


title: SL96947


title: Input_KMS27

data_processing:
aligned to the reference genome using bowtie 2.3.4.2
The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools. V1.7
ChIP-seq peaks were called by using MACS2 v2.2.5  with parameters ‘-B --SPMR --broad --broad-cutoff 0.1’. Peaks with a –log10(q-value) lower than 2.0 were discarded.
Peaks in  bedGraph format (.bdg) were converted in bigWig (.bw) format using bedGraphToBigWig tool
All peaks matching blacklisted regions were discarded from further processing.
ChIP-seq samples including the Drosophila DNA were further processed for normalization according to the manufacturer guidelines
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and bed

extract_protocol:
Chipmentation protocol as described in Nat Methods. 2015;12(10):963-965. Schmidl C., et al;
Chipmentation library construction protocol as described in Nat Methods. 2015;12(10):963-965. Schmidl C., et al;

treatment_protocol: transfection by Lipofectamine 3000 with specific siRna for Che-1/AATF (ThermoFisher/Life techologies)


title: ATAC_KMS27_Control_2

data_processing:
aligned to the reference genome using bowtie 2.3.4.2
The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools. V1.7
ATAC-seq peaks were generated using MACS v2.2.5 with parameters ‘--nomodel --shift -100 --extsize 200 -B --SPMR --call-summits -q 0.01’.
Peaks in  bedGraph format (.bdg) were converted in bigWig (.bw) format using bedGraphToBigWig tool
All peaks matching blacklisted regions were discarded from further processing.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and bed

extract_protocol:
Extraction protocol as described in Nat Methods. 2013;10(12):1213-1218. (Buenrostro JD., et al;)
Library construction as described in Nat Methods. 2013;10(12):1213-1218. (Buenrostro JD:, et al;)


title: SL96946


title: SL96959


title: C57BL/6 treated with DEHP

city: Chiayi County

first: Mita

last: Tran

address: 168 University Road

department: Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

description: C57BL/6 mice model

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse (GRCm38/mm10) genomes using the Illumina Genome Analyzer Pipeline.
All reads mapping with two or fewer mismatches were retained and processed according to Rodriguez et al., BMC Genomics 2012
and PrEMeR-CG (Frankhouser et al., Bioinformatics 2014) for DMR identification
Genome_build: mm10

source_name: mice model

growth_protocol: C57BL/6 female and male mice, 6-8 weeks of age, were obtained from the National Laboratory Animal Center and maintained by the Animal Center of the Kaohsiung Medical University in a pathogen-free environment. All animal experiments were performed according to the guidelines of the Institutional Animal Care and Use Committee of the Kaohsiung Medical University (IACUC: 99032).

extract_protocol:
Genomic DNA was isolated by standard methods or by the QIAamp DNA Mini Kit (Qiagen) following the manufacturer's protocol. Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer's instructions. Briefly, one microgram of genomic DNA was sonicated and captured by MBD proteins. The methylated DNA was eluted in 1 M salt buffer. DNA in each eluted fraction was precipitated by glycogen, sodium acetate and ethanol, and was resuspended in TE buffer. Eluted DNA was used to generate libraries for sequencing following the standard protocols from Illumina. MBDCap-seq libraries were sequenced using the Illumina Genome Analyzer II as per manufacturer's instructions Illumina ChIP protocol.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6 mice are treated with DEHP (37μg/kg/day) or vehicle control for 10 days. These female mice were crossed with naïve male mice. F1 to F3 neonates from vehicle or DEHP-exposed mother were immunized with PBS or OVA. Splenic CD11c DC are then isolated for for global methylation analysis.

tag: treatment

value: DEHP (37μg/kg/day)


title: C57BL/6

description: C57BL/6 mice model

value: vehicle control


title: SL96958

value: Hippocampus

value: Female


title: Parental_WGBS_rep1

source_name: Embryonic stem cells


title: Parental_WGBS_rep2


title: anti HSC-C

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
RNA-seq data were mapped to mouse mm10 genome using STAR aligner
Mapped reads number of each gene were used to identify gene expression by feature Counts.
Gene expression counts were further normalized among samples based on the total numbers of all mapped reads, and subsequently log2-tranformed. Normalized data were further employed to identify differentially expressed genes with the cutoff values: 2 for the average fold change between the comparing two groups and 0.05 for the p value of t-test cross the replicated samples.
DAVID (https://david.ncifcrf.gov/) was used for GO pathway analysis of differentially expressed genes.
Hierarchical clustering with average linkage was performed for the normalized expression data cross different tissues, and subsequently, the heatmaps were generated from the clustering results.  Gene set enrichment analysis (GSEA) was performed based on the normalized data using GSEA v2.0 tool
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file for gene exprssion of RNA-seq

source_name: HSC a CD25

growth_protocol: not cultured, live sorted

extract_protocol:
Live Lin−Sca-1+c-Kit+Flt3-CD150+CD48− (long-term hematopoietic stem cells) were sorted from 10-12-week-old B6 mice treated with anti-CD25 and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 4 biological replicates per treatment condition.
RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 or 4 biological replicates per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122–2001, Illumina)

treatment_protocol: 10-12-week-old B6 mice treated with (0.5mg/ mouse) of InVivoMAb. anti-mouse CD25 (PC-61.5.3) was administered intraperitoneally weekly for 4 weeks before being euthanized for analysis.

value: Live Lin-Sca-1+c-Kit+Flt3-CD150+CD48- (long-term hematopoietic stem cells)

value: anti-mouse CD25


title: ATAC_KMS27_Control_1


title: SL96957


title: anti HSC-D


title: rescue_Mut_H33_ChIP

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5) with parameter “-k 1” to keep only one locus when a read mapped to multiple genomic regions.
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

treatment_protocol: mESCs were treated with 1μM Flavopiridol, or 1μM Triptolide directly to the culture media and incubating cells with the drug for 12hrs at 37ºC, or 10μM α-Amanitin for 24 hours at 37ºC.

value: METTL3 KO+Mut METTL3


title: ATAC_KMS27si_Che_2


title: SL96956


title: anti HSC-B


title: METTL3_KO_H33_ChIP

value: METTL3 KO


title: ATAC_KMS27si_Che_1


title: Chip_H3K27ac_siChe2

tag: chip antibody

value: anti-H3K27ac (Millipore, 07-360)


title: SL96955


title: anti HSC-A


title: RTBN-wt

tag: genotype

value: wild type


title: SL96954

source_name: Female Rat age at 9 month, irregular menopause cycle


title: WT HSC-D

source_name: HSC

extract_protocol:
Live Lin−Sca-1+c-Kit+Flt3-CD150+CD48− (long-term hematopoietic stem cells) were sorted from 10-12-week-old B6 mice treated with IgG1 and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 4 biological replicates per treatment condition.
RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 or 4 biological replicates per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122–2001, Illumina)

treatment_protocol: 10-12-week-old B6 mice treated with rat IgG1 isotype control (anti-horseradish peroxidase was administered intraperitoneally weekly for 4 weeks before being euthanized for analysis.

value: rat IgG1 isotype control


title: Chip_H3K27ac_siChe1

value: siChe


title: Parental_H33_ChIP

value: parental

tag: antibody


title: ES_Input_ChIP


title: SL96953


title: WT HSC-C


title: Chip_H3k27ac_CTRL1

value: control


title: SL96952


title: Chip_H3K27ac_CTRL2


title: WT HSC-B


title: SL96951


title: rescue_WT_H33_ChIP

value: METTL3 KO+WT METTL3


title: WT HSC-A


title: SL96950


title: S_A

source_name: Treg SPL

extract_protocol:
Live CD4+ CD8α− Foxp3+ NK-1.1− (Tregs) were sorted from spleen of 6-8-week-old Foxp3GFP mice and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 biological replicates per tissue.
RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 or 4 biological replicates per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122–2001, Illumina)

value: spleen

value: Live CD4+ CD8alpha- Foxp3+ NK-1.1- (Tregs)


title: Chip_HDAC_siChe

value: anti-HDAC1 (Sigma, H3284)


title: ES_H3K4me3_ChIP

value: Embryonic stem cells


title: Chip_HDAC_ctrl


title: METTL3_KO_TRIM28_ChIP_rep2


title: SL96949

value: Hippocampus


title: Parental_TRIM28_ChIP_rep2


title: Chip_BRD4_siChe

data_processing:
aligned to the reference genome using bowtie 2.3.4.2
The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools. V1.7
ChIP-seq peaks were called by using MACS2 v2.2.5 with parameters ‘-B --SPMR --broad --broad-cutoff 0.1’. Peaks with a –log10(q-value) lower than 2.0 were discarded.
Peaks in  bedGraph format (.bdg) were converted in bigWig (.bw) format using bedGraphToBigWig tool
All peaks matching blacklisted regions were discarded from further processing.
ChIP-seq samples including the Drosophila DNA were further processed for normalization according to the manufacturer guidelines
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and bed

value: anti-BRD4 (Bethyl, A301-985A-M)


title: S_B


title: SL96942

source_name: Female Rat age at 9 month, normal menopause cycle

value: Female


title: ChIP_BRD4_ctrl


title: S_C


title: METTL3_KO_SETDB1_ChIP_rep1

value: SETDB1 (Proteintech, #11231-1-AP)


title: SL96941


title: LN_A

source_name: Treg LN

extract_protocol:
Live CD4+ CD8α− Foxp3+ NK-1.1− (Tregs) were sorted from inguinal lymph node of 6-8-week-old Foxp3GFP mice and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 biological replicates per tissue.
RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 or 4 biological replicates per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122–2001, Illumina)

value: lymph nodes


title: ES_H3K27me3_ChIP


title: siEloA RNA-seq rep2

city: New York

first: Brian

middle: David

last: Dynlacht

address: 522 1st Ave, Smilow 1104

department: Dept. of Pathology and Cancer Center

institute: NYU School of Medicine

data_processing:
Peak calling: Bowtie2, MACS2
Mapping: STAR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: narrowPeak, bigWig

source_name: DLD1 colon cancer cell line

growth_protocol: DLD1 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was extracted with Trizol Reagent. Cells for ChIP or Cut&Run were fixed with 1% formaldehyde.
RNA-seq libraries were prepared with NEBNext® Small RNA Library Prep Set for Illumina or NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. ChIP-seq and Cut&Run libraries were made following standard protocol.

treatment_protocol: siRNA targeting Elongin A was purchased from Dharmacon Inc and transfected with RNAiMax at final concentration 50nM. Cells were harvested two days after transfection.

value: Colon cancer cell line

tag: sirna

value: Elongin A siRNA


title: SL96940


title: rescue_Mut_H3K9me3_ChIP_rep1

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: METTL3 KO+Mut METTL3

value: H3K9me3 (Active motif, #39161)


title: Parental_SETDB1_ChIP_rep1


title: control RNA-seq rep2

value: control siRNA


title: SL96939


title: rescue_WT_H3K9me3_ChIP_rep1


title: 384h_2.5F_rep3

description: 384 hours, 2.5 mM fructose, Replicate 3

data_processing: The scanned data was acquired in R using the package illiminaio. The non-normalized summarized bead-level data was then annotated with R package  illuminaHumanv4.db.

source_name: SGBS preadipocyte cells

extract_protocol: For RNA isolation, media was completely aspirated from cells and a total of 700 ul of QIAzol lysis reagent was added to the cells, and the lysed cells were scraped, collected in an Eppendorf vial, sheer disrupted by passing through a tuberculin syringe about 6 time, and the lysates flash frozen.

value: SGBS

tag: time

value: 384 hours

value: 2.5 mM  fructose


title: siEloA RNA-seq rep1


title: SL96938

tag: status


title: Bm_B

source_name: Treg BM

extract_protocol:
Live CD4+ CD8α− Foxp3+ NK-1.1− (Tregs) were sorted from these tissues (bone marrow) of 6-8-week-old Foxp3GFP mice and resuspended in Buffer RLT. RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 biological replicates per tissue.
RNA was extracted using RNAeasy micro kit (QIAGEN, Valencia, CA), with 3 or 4 biological replicates per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were prepared using the TruSeq RNA Library Preparation Kit v2 (catalog RS-122–2001, Illumina)

value: bone marrow


title: SL96937

tag: Sex


title: EB_METTL3_ChIP

source_name: Embryoid bodies

value: Embryoid bodies

value: parental

value: METTL3 (Bethyl, #A301-568A)


title: Elongin A Cut&Run (goat antibody) rep1

description: processed data file: eloa_g_peaks.narrowPeak

data_processing:
Library strategy: Cut&Run
Peak calling: Bowtie2, MACS2
Mapping: STAR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: narrowPeak, bigWig

value: wild type (no siRNA)


title: Bm_A

value: Live CD4+ CD8alpha- Foxp3+ NK-1.1- (Tregs)


title: SL96936

source_name: Female Rat age at 6 month

value: Hippocampus

value: Female


title: Bm_C


title: Parental_H3K9me3_ChIP_rep1

value: Embryonic stem cells


title: METTL3_KO_H3K9me3_ChIP_rep1

value: METTL3 KO


title: Elongin A ChIP

description: processed data file: wt_peaks.narrowPeak

value: Colon cancer cell line

value: Elongin A


title: ChIP-seq input


title: SL96935


title: SL96934


title: rescue_Mut_METTL3_ChIP_rep1

value: METTL3 KO+Mut METTL3

value: METTL3 (Bethyl, #A301-567A)


title: rescue_WT_METTL3_ChIP_rep1

value: METTL3 KO+WT METTL3


title: SX240_CUP_M60_R2

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 5 mM CuSO4, Replicate 2

data_processing:
Segemehl V0.18 used for mapping.
Read counts were calculated custom made perl script.
reads were normalised using LogNormalization from DESeq2 (v1.22.2) package in R.
Differential gene expression was calculated usingDESeq2 in R.
Mapped reads were transformed into graphical "GR" files for visualisation uding IGB
Genome_build: Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized (DESeq2) values for each Sample.

organism: Salmonella enterica

growth_protocol: Bacteria was grown to an OD600 of 0.15 (early log-phase growth) at 37 °C with agitation.

extract_protocol:
Cells were flash frozen and RNA was harvested using RNeasy mini kit (Qiagen). Illumina HiSeq 3000 RNA Sample Prep Kit was used with rRNA depleted for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Copper II Sulfate solution (CuSO4) (Sigma, St. Louis, MO) was added for final concentrations of 0 and 5 mM, and the cultures were incubated at 37 °C with agitation for 30 and 60 min.

value: Treated


title: SX240_CUP_M60_R3

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 5 mM CuSO4, Replicate 3


title: LN_B

value: lymph nodes


title: LN_C


title: SL96933

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Synovial sarcoma cell lines: Fusion knockdown scRNA-Seq (droplet-based)

city: Cambridge

first: Livnat

last: Jerby

address: 415 Main street

institute: Broad Institute of MIT and Harvard

data_processing:
Full-length RNAseq (SMART-Seq2)
Bowtie mapping to UCSC hg19 human transcriptome
RSEM v1.2.8
Droplet-based RNA-Seq (10x)
STAR
The README file contains further details.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (counts or TPM) for each gene (rows) in each cell (columns)

source_name: scRNA-Seq of synovial sarcoma cell lines following shRNA SSX knockdown

extract_protocol:
Dissociated individual cells from fresh tumor resections.
Full length RNAseq (SMART-Seq2) and a 3'-prime droplet-based approach (10x)

tag: tissue/cell type

value: Synovial sarcoma cell lines


title: Synovial sarcoma cell culture: Drug experiments scRNA-seq (SMART-Seq2)

source_name: scRNA-Seq of synovial sarcoma cell cultures following different treatments (TNF, IFN, abemaciclib, and panobinostat)

value: Synovial sarcoma cell cultures


title: SX240_CUP_M60_R1

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 5 mM CuSO4, Replicate 1


title: SL96932


title: METTL3_KO_METTL3_ChIP_rep1


title: Parental_METTL3_ChIP_rep1

value: parental


title: control RNA-seq rep1

value: control siRNA


title: SX240_CUP_M30_R3

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 5 mM CuSO4, Replicate 3


title: Synovial sarcoma tumors scRNA-seq (droplet-based)

source_name: scRNA-Seq of 3 human synovial sarcoma tumors

value: Synovial sarcoma tumor


title: SL96931


title: SX240_CUP_M30_R2

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 5 mM CuSO4, Replicate 2


title: Synovial sarcoma tumors scRNA-seq (SMART-Seq2)

source_name: scRNA-Seq of 12 human synovial sarcoma tumors


title: LncMyoD-KO clone 2 MyoD+LncMyoD Rep 1

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: MyoD adenovirus infection and LncMyoD plasmid transfection

data_processing:
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown

molecule: polyA RNA

source_name: embryo

growth_protocol: 10T1/2 fibroblasts were cultured in DMEM supplemented with 10%FBS and changed to DMEM supplmented with 2%HS after MyoD-induced transdifferentiation.

extract_protocol:
Medium was removed, and total RNA was isolated using NucleoSpin RNA XS (Macherey-Nagel).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The cDNA was then tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct RNA-seq library . The libraries were sequenced using DNBSEQ-G400 sequencer (BGI) (2 x 100)).

treatment_protocol: Cells were treated with MyoD adenovirus or LncMyoD-containing plasmid to induce transdifferentiation.

value: fibroblast

value: LncMyoD-KO


title: LncMyoD-KO clone 2 MyoD+LncMyoD Rep 2

value: MyoD adenovirus infection and LncMyoD plasmid transfection


title: SX240_CON_M60_R3

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 0 mM CuSO4, Replicate 3

value: Untreated


title: LncMyoD-KO clone 1 MyoD+LncMyoD Rep 2


title: SX240_CON_M60_R2

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 0 mM CuSO4, Replicate 2


title: LncMyoD-KO clone 1 MyoD+LncMyoD Rep 1


title: SX240_CON_M60_R1

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 60 minutes exposure of 0 mM CuSO4, Replicate 1


title: WT  MyoD+LncMyoD Rep 2

value: WT


title: SX240_CON_M30_R3

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 0 mM CuSO4, Replicate 3


title: WT  MyoD+LncMyoD Rep 1


title: SX240_CON_M30_R2

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 0 mM CuSO4, Replicate 2


title: LncMyoD-KO clone 2 LncMyoD Rep 2

description: LncMyoD plasmid transfection

value: LncMyoD plasmid transfection


title: SX240_CON_M30_R1

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 0 mM CuSO4, Replicate 1


title: SX240_CUP_M30_R1

description: Culture grown to an OD600 of 0.15 at 37 °C with agitation + 30 minutes exposure of 5 mM CuSO4, Replicate 1


title: UM-UC-3: AP-2α OE

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

description: cells infected with lentivirus expressing AP-2α cDNA.

data_processing:
Illumina Casava1.6 software was used for basecalling.
Raw sequences were transformed into Clean Tags after removal of adaptor sequence, low-complexity sequence and low-quality sequence.
Clean Tags were mapped to GRCh37 whole genome using TopHat2 software.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a Cufflinks software.
Genome_build: GRCh37
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

source_name: bladder cells

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder cells

value: AP-2[alpha] OE


title: LncMyoD-KO clone 1 LncMyoD Rep 2

description: LncMyoD plasmid transfection


title: LncMyoD-KO clone 2 LncMyoD Rep 1

description: LncMyoD plasmid transfection


title: SV-HUC-1: AP-2α KD

description: cells infected with lentivirus expressing AP-2α shRNA

value: AP-2[alpha] KD


title: Low_glucose

city: Jining

first: Chunyu

last: bai

address: NO133，Hehua Road

institute: Jining Medical University

data_processing:
Sequence files (fastq) were mapped to the reference genome hg19 using Bowtie. Small RNA was classified by Unitas software.
Gene abundance was expressed as counts of exon model per million mapped  reads (CPM)
Differential expression analysis for miRNA was performed using DESeq  software. Differentially expressed miRNAs with |log2(FC)| value >1 and p value <0.05,  considered as significantly modulated, were retained for further analysis. This choice is  motivated by the decision to maximize the sensitivity of this analysis, in order to perform a  massive screening and identify candidate genes to be validated with a wider sample population  with real-time PCR analysis
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Evs derived from human beta cells

growth_protocol: human beta cells were cultured in DMEM medium supplement with 10% FBS

extract_protocol:
extracellular vesicles were isolated using SBI -- ExoQuick, and then RNA was extracted using the miRNeasy Serum/Plasma Kit(50) Qiagen#217184
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: human beta cells were washed with Krebs buffer, and incubated with high glucose (20 mM) or low glucose (2 mM) for 30 min respectively , the cell supernatant were selected to isolated extracellular vesicles using  XX methods

value: human beta cells

value: low glucose solution


title: LncMyoD-KO clone 1 LncMyoD Rep 1

description: LncMyoD plasmid transfection


title: SV-HUC-1: control

description: cells infected with lentivirus expressing scramle shRNA

value: control


title: WT  LncMyoD Rep 2

description: LncMyoD plasmid transfection


title: akt(-/-) 72

city: Wynnewood

first: Richard

middle: G

last: Pestell

state: Pennsylvania

address: 100 E Lancaster Ave LIMR R234

department: Pennsylvania Cancer and Regenerative Medicine Center

institute: Baruch S. Blumberg Institute

hyb_protocol: Affymetrix gene chips, mouse430_2 array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V11.5 software (Agilent, Palo Alto, CA, USA).

source_name: ErbB2 mammary tumor cells

label_protocol: Amplification and labeling was performed using the Ovation Pico WTA-system V2 RNA amplification system (NuGen Technologies, Inc.). Briefly, 50 ng of total RNA was reverse transcribed using a chimeric cDNA/mRNA primer, and a second complementary cDNA strand was synthesized. Purified cDNA was then amplified with ribo-SPIA enzyme and SPIA DNA/RNA primers (NuGEN Technologies, Inc.). Amplified DNA was purified with Qiagen MinElute reaction cleanup kit. The concentration of Purified ST-cDNA was measured using the Nanodrop. 2.5 µg ST-cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: ErbB2 mammary tumor cells isolated from spontaneously formed MMTV-ErbB2 induced mammary tumor. The mammary tumors were dissociated by chopping and then digested with 0.4 mg/ml collagenase in MEC culture media (Ham's F12 with 10% FBS, 1× MEM nonessential amino acids, 100 μg/ml penicillin and streptomycin, 50 μg/ml gentamicin, 4 μg/ml insulin, 1 μg/ml hydrocortisone, 10 ng/ml EGF, 10 ng/ml cholera toxin) in 5% CO2 at 37°C for 18 h. The digested material was homogenized by pipetting up and down and then was washed with PBS with 50 μg/ml gentamicin three times. The pellet was resuspended in MEC culture media in a 10-cm plate and then cultured for 4 h to remove fibroblasts. The suspension was keeping culture for 25 passages.

extract_protocol: Total RNA was extracted with Trizol from Invitrogen. DNA was removed by Dnase I digestion and then purified with Qiagen RNAeasy kit.


title: UM-UC-3: control

description: cells infected with lentivirus expressing empty vector


title: akt(+/+) 102


title: akt(-/-) 75


title: akt(-/-) 116


title: akt(+/+) 101


title: High_glucose

value: high glucose solution


title: WT  LncMyoD Rep 1

description: LncMyoD plasmid transfection


title: VV_rep5: RNAseq T cells

city: Pittsburgh

first: Daniel

middle: H

last: Kaplan

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

description: OT-I Trm developped with cognate antigen in skin

data_processing:
Single-end reads were aligned using Tophat2 to mm9 genome assmebly. Cufflinks was used to measure transcripts abundance and report it as RPKM values. Log2 transformed RPKM values were imported into R and a paired ttest was peroformed on log2(FPKM+1) values.
Bowtie2 (DNA reads aligner) version 2.2.3, Tophat2 (RNA reads aligner) version 2.0.13, Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq data as cufflink reported FPKM values

extract_protocol:
Single cell suspension of flank epidermis were prepared by digestion with 0.3% trypsin for 50-60 minutes.  LiveCD45+Thy1.2-Thy1.1+ OT-I Trm were double FACS sorted to ensure high purity and directly lysed using the Clontech SMART-Seq v.4 kit for complimentary DNA synthesis. 200-1000 OT-I cells were collected in 12.5 uL of the lysis buffer.
Illumina single and paired end libraries, RNA-seq and DNA-seq
Adapter ligation to fragements followed by pcr amplification using indexed primers for Illumnia HiSeq-2500

treatment_protocol: WT mice were adoptively transferred with 10^5 OT-I cells on day -1 then infected flank with  3 x10^6 pfu Vaccinia virus expressing SIINFEKL on day 0.  On day 5, mice were treated with 0.15% DNFB on the opposite flank to pull Trm into epidermis.  The mice were rested for 57-70 days after the infection.

value: Trm cells

value: Epidermal

tag: cell population


title: hUC-MSC-exosome-2

city: Guangzhou

last: Wang

state: Guangdong

address: number 600, Tianhe road

institute: Third affiliated hospital of sun yat-sen unversity

description: total RNA extracted from  none treated human umbilical cord mesenchymal stem cells

data_processing:
The original image data obtained from Illumina Novaseq sequencing was converted into sequence data by Base Calling (FASTQ format) to obtain the most original sequencing data file.The FASTQ format file records the base and mass fraction of the read segment tested.FASTQ format is stored as sequence reads and each read has four lines. The first and third lines are composed of sequence identifiers and read names (the first line starts with '@' and the third line starts with '+').In the third line, ID can be omitted, but "+" cannot be omitted), the second behavior base sequence, and the sequencing mass fraction of the corresponding position of the fourth behavior base.
Genome_build: mm 10
Supplementary_files_format_and_content: Excel table with raw small RNA readcounts and transcripts per million for every small RNA.

extract_protocol:
Exosomes were purified with total exosomes extraction kit for cell (introgen). The total RNA was extracted by seramir exosome RNA amplication kit (SBI).
The RNA libraries were prepared with Small RNA Sample Pre Kit.

tag: tissue

value: umbilical cord

value: mesenchymal stem cells

tag: cell compartment

value: exosome

value: non-treated


title: akt(+/+) 31


title: hUC-MSC-exosome-1

source_name: human umbilical cord mesenchymal stem cells


title: hUC-MSC-exosome-3


title: VV_rep4: RNAseq T cells


title: LncMyoD-KO clone 2 MyoD Rep 2

description: MyoD adenovirus infection

value: fibroblast

value: LncMyoD-KO

value: MyoD adenovirus infection


title: siEloA 4sU-seq DRB_25min rep2

data_processing:
Library strategy: 4sU-seq
Peak calling: Bowtie2, MACS2
Mapping: STAR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: narrowPeak, bigWig

value: Colon cancer cell line

value: Elongin A siRNA

tag: drb treatment


title: VV_rep3: RNAseq T cells


title: VV_rep2: RNAseq T cells


title: siEloA 4sU-seq DRB_15min rep2

tag: cell line


title: LncMyoD-KO clone 2 MyoD Rep 1

description: MyoD adenovirus infection

tag: strain


title: LncMyoD-KO clone 1 MyoD Rep 2

description: MyoD adenovirus infection


title: VV_rep1: RNAseq T cells


title: 24h_0F_rep2

type: genomic

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

institute: UMR1078 - Université de Bretagne Occidentale

description: 24 hours, 0 mM fructose, Replicate 3

hyb_protocol: The hybridization was performed according to the manufacturer’s recommendations.

data_processing: Preprocessing was performed with the function preprocessIllumina from the R package Minfi. This method was applied to reduce Infinium I/II type bias and correct for background. Absolute percentages of methylation (β-values) were then extracted and normalized with SWAN method. For each CpG site, averaged β-values across the cell triplicates were considered for the following analysis.

label: Cy3 and Cy5

source_name: SGBS preadipocytes cells

label_protocol: The labeling  was performed according to the manufacturer’s recommendations.

extract_protocol: For obtaining samples for DNA isolation, media was removed and cells were washed with PBS and aspirated to remove all PBS. The cells were gently scraped in the presence of a total of 400 ul of PBS, collected using a pipette fitted with a wide mouth tip, transferred to an eppendorf vial, and flash frozen.

treatment_protocol: Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation. differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr). Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation.

value: SGBS

tag: time post-induction

value: 24 hours

value: 0 mM fructose


title: 192h_2.5F_rep2

description: 192 hours, 2.5 mM fructose, Replicate 2

value: 192 hours

value: 2.5 mM fructose


title: LncMyoD-KO clone 1 MyoD Rep 1

description: MyoD adenovirus infection

tag: cell type


title: DNFB_rep5: RNAseq T cells

description: OT-I Trm developped without cognate antigen in skin


title: WT  MyoD Rep 2

description: MyoD adenovirus infection

value: WT

tag: treatment


title: DNFB_rep4: RNAseq T cells

value: Trm cells


title: control 4sU-seq DRB_15min rep2

value: control siRNA


title: 24h_0F_rep1

description: 24 hours, 0 mM fructose, Replicate 1


title: siEloA 4sU-seq no DRB rep2


title: 48h_0F_rep3

description: 48 hours, 0 mM fructose, Replicate 3

value: 48 hours


title: 96h_0F_rep1

description: 96 hours, 0 mM fructose, Replicate 1

value: 96 hours


title: 384h_5G_rep2

description: 384 hours, 5 mM Glucose, Replicate 2

value: 384 hours

value: 5 mM Glucose


title: siEloA 4sU-seq DRB_5min rep2


title: 192h_5G_rep1

description: 192 hours, 5 mM Glucose, Replicate 1


title: 384h_5G_rep3

description: 384 hours, 5 mM Glucose, Replicate 3


title: control 4sU-seq DRB_5min rep2


title: LncMyoD-KO clone 2 no treatment Rep 2

description: no treatment

value: fibroblast

value: no treatment


title: 192h_2.5F_rep3

description: 192 hours, 2.5 mM fructose, Replicate 3


title: DNFB_rep3: RNAseq T cells

value: Epidermal


title: 384h_2.5F_rep3

description: 384 hours, 2.5 mM fructose, Replicate 3


title: 384h_5F_rep1

description: 384 hours, 5 mM fructose, Replicate 1

value: 5 mM fructose


title: DNFB_rep2: RNAseq T cells


title: 192h_5G_rep2

description: 192 hours, 5 mM Glucose, Replicate 2


title: control 4sU-seq no DRB rep2

value: Colon cancer cell line


title: DNFB_rep1: RNAseq T cells


title: LncMyoD-KO clone 1 no treatment Rep 2

description: no treatment

value: LncMyoD-KO


title: siEloA 4sU-seq DRB_25min rep1

value: Elongin A siRNA


title: A10

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

institute: National Institute for Environmental Studies

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
Adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in coverage and ≥10% methylation differences between control groups and arsenite groups using the logistic regression method. DMRs were detected for regions containing ≥3 CpG sites and at least one DMC and with ≥10% absolute mean CpG methylation difference by using an eDMR package on R
TSS distance of DMRs were calculated by using bedtools 2.25.0.
Genome_build: mm10

source_name: Sperm

extract_protocol:
Sperm was lysed in lysis buffer (7.3 mM Tris-HCl (pH 7.5), 7.3 mM NaCl, 18.2 mM EDTA, 1.8% SDS, 1.8% 2-ME, 1.4 mg/ml proteinase K) and DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in 10 mM Tris (pH7.4).
RRBS libraries were prepared as previously described (Matsushita et al.,BMC cancer 18: 317, 2018; Okamura et al. Cancer Sci 110:2629, 2019) with some modifications. Briefly, 100 ng of genomic DNA was sonicated for one second by a Focused-ultrasonicator (Covaris) before restriction enzyme reaction.

value: sperm

tag: dam treatment group

value: arsenic

tag: generation

tag: age

value: 15-17 weeks


title: siEloA 4sU-seq DRB_15min rep1

tag: sirna


title: 192h_0F_rep1

description: 192 hours, 0 mM fructose, Replicate 1

value: SGBS

value: 192 hours

value: 0 mM fructose


title: LncMyoD-KO clone 1 no treatment Rep 1

description: no treatment

tag: genotype


title: LncMyoD-KO clone 2 no treatment Rep 1

description: no treatment


title: A9


title: WT  no treatment Rep 2

description: no treatment

value: WT


title: 192h_0F_rep2

description: 192 hours, 0 mM fructose, Replicate 2


title: 384h_0F_rep2

description: 384 hours, 0 mM fructose, Replicate 2


title: A8


title: siEloA 4sU-seq DRB_5min rep1


title: 0h_0F_rep6

description: 0 hours, 0 mM fructose, Replicate 6

value: 0 hours


title: A6


title: 384h_0F_rep3

description: 384 hours, 0 mM fructose, Replicate 3

value: 384 hours


title: 192h_10F_rep1

description: 192 hours, 10 mM fructose, Replicate 1

value: 10 mM fructose


title: WT  no treatment Rep 1

description: no treatment

value: fibroblast


title: LncMyoD_Input Rep 2

data_processing:
Library strategy: ChIRP-seq
Reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with default parameters.
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings. Unmapped and duplicate reads were removed.
Reads that appear in both the odd and even probe pools were kept for downstream peakcalling.
Peaks were called with MACS2 v2.1.1 (Zhang et al., 2008) using the following parameters: -g mm -p 1e-2 –nomodel –shift 0 –keep-dup all -B –SPMR.
Fold-change signals were generated with the bdgcmp command in MACS2 v2.1.1 (Zhang et al., 2008) and then converted to BigWig format using the UCSC bedGraphToBigWig v332 tool.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files containing consensus peak calls of pooled samples; BigWig treatment over control fold change tracks

source_name: Skeletal muscle

growth_protocol: Primary myoblasts were cultured in 2% HS in DMEM for 2 days before harvest

extract_protocol:
Lysates were clarified from sonicated nuclei and LncMyoD-DNA complexes were isolated with biotin-labeled DNA probes.
Library was constructed using ChIRP-seq protocol from Chu et al., (2012). Briefly, LncMyoD-bound DNA was tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct ChIP-seq library. Library was then sequenced using DNBSEQ-G400 sequencer (BGI) (2 x 100).

value: Differentiated myotubes

tag: target

value: none (input)


title: control 4sU-seq DRB_25min rep1

source_name: DLD1 colon cancer cell line

value: control siRNA


title: A4


title: control 4sU-seq DRB_15min rep1

value: Colon cancer cell line


title: LncMyoD_even Rep 2

value: LncMyoD binding sites


title: C9

value: control


title: 0h_0F_rep4

description: 0 hours, 0 mM fructose, Replicate 4


title: LncMyoD_odd Rep 2


title: control 4sU-seq DRB_5min rep1


title: LncMyoD_Input Rep 1


title: C6

value: sperm


title: control 4sU-seq no DRB rep1


title: C8


title: C5


title: 384h_10F_rep2

description: 384 hours, 10 mM fructose, Replicate 2


title: 192h_5F_rep3

description: 192 hours, 5 mM fructose, Replicate 3

value: 5 mM fructose


title: LncMyoD_even Rep 1


title: siEloA PolI ChIP-seq

value: Elongin A siRNA

tag: chip antibody

value: PolI


title: 384h_10F_rep1

description: 384 hours, 10 mM fructose, Replicate 1

value: SGBS


title: LncMyoD_odd Rep 1


title: control PolI ChIP-seq


title: LncMyoD-KD MyoD Rep 2 Input

data_processing:
Reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with default parameters.
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings. Unmapped and duplicate reads as well as read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1540 -q 10 -b’.
Reads from sample replicates were pooled together into a single file using samtools v1.3 (Li et al., 2009).
For each individual sample replicate as well as pooled replicates, the predominant fragment length was estimated for use during peak calling using phantompeakqualtools v1.2 (Kharchenko, Tolstorukov & Park, 2008).
Relaxed narrow and broad peak calling to determine enriched regions was performed on individual sample replicates as well as pooled replicates using MACS2 v2.1.1 (Zhang et al., 2008) with treatment and control as input files and parameters ‘-g mm -p 1e-2 --nomodel --shift 0 --extsize {estimated fragment length from last step} -B --SPMR’.
Peaks called in the pooled replicates were kept and considered a consensus peak if they had at least a 50% overlap with peaks called in the individual replicates. This was done using intersect in bedtools v2.26.0 (Quinlan, Hall, 2010).
Fold-change signals were generated with the bdgcmp command in MACS2 v2.1.1 (Zhang et al., 2008) and then converted to BigWig format using the UCSC bedGraphToBigWig v332 tool.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files containing consensus peak calls of pooled samples; BigWig treatment over control fold change tracks

growth_protocol: Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was constructed using ChIPmentation protocol from Schmidl et al., (2015). Briefly, antibody-bound DNA was tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct ChIP-seq library. Library was then sequenced using DNBSEQ-G400 sequencer (BGI) (2 x 100).

treatment_protocol: Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest

value: Muscle stem cells

value: LncMyoD-KD


title: siEloA Pol_II_ser5p ChIP-seq rep2

extract_protocol:
RNA was extracted with Trizol Reagent. Cells for ChIP or Cut&Run were fixed with 1% formaldehyde.
RNA-seq libraries were prepared with NEBNext® Small RNA Library Prep Set for Illumina or NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. ChIP-seq and Cut&Run libraries were made following standard protocol.

value: Pol II-ser5p


title: Nhe1 Astro-KO Ipsilateral [300_IL]

first: Gulnaz

last: Begum

address: 3501 5th Ave

department: Neurology

data_processing:
CLC genomics Workbench 10.1.1 was used for data processing
Single-end RNA-Seq reads, obtained in FASTQ format, were subjected to sequence quality checks using QC for Sequencing Reads” tool. The reads were mapped against the mouse reference genome mm10 using default parameters of “RNA-Seq Analysis” tool.
Diferentially expressed genes (DEGs) were identified by comparing normalized gene reads between wild-type and Nhe1 Astro-KO ischemic (ipsilateral) astrocyte samples using “Differential Expressions in Two Group” tool. The tool uses a multifactorial statistics based on a negative binomial Generalized Linear Model. Genes with FDR corrected P-value ≤ 0.05 and Log2 fold change ≥ 1.2 or ≤ -1.2 were considered as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with gene expression data for each Sample.
Supplementary_files_format_and_content: Expression value      "TPM"   "RPKM"

source_name: Astrocytes

extract_protocol:
Single cell suspension of astrocytes from the ipsilateral and contralateral hemispheres from wild-type and Nhe1 Astro-KO brains after 24 h tMCAO (transient middle cerebral artery occlusion) were prepared using Adult Brain Dissociation Kit (Miltenyi Biotec, Germany) following manufacturers protocol. RNA from ACSA-2+ astrocytes was extracted on the QIAsymphony SP (Qiagen Corporation, Germany) using the QIAsymphony RNA Kit
RNA libraries were prepared for sequencing using Illumina HiSeq 2500

value: Brain

value: Post natal day 90-120

value: Gfap-CreERT2+/-;Nhe1f/f (Nhe1 Astro-KO)

tag: agent

value: Tamoxifen


title: C3

value: 15-17 weeks


title: Nhe1 Astro-KO Contralateral [300_CL]


title: control Pol_II_ser5p ChIP-seq rep2

data_processing:
Peak calling: Bowtie2, MACS2
Mapping: STAR
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: narrowPeak, bigWig

value: control siRNA


title: LncMyoD-KD MyoD Rep 2

value: MyoD-ChIP


title: siEloA Pol_II_ser2p ChIP-seq rep2

value: Colon cancer cell line

value: Pol II-ser2p


title: Nhe1 Astro-KO Ipsilateral [298_IL]


title: LncMyoD-KD MyoD Rep 1


title: control Pol_II_ser2p ChIP-seq rep2


title: 0h_0F_rep5

description: 0 hours, 0 mM fructose, Replicate 5

value: 0 hours

value: 0 mM fructose


title: 24h_0F_rep3

description: 24 hours, 0 mM fructose, Replicate 3

value: 24 hours


title: 96h_0F_rep3

description: 96 hours, 0 mM fructose, Replicate 3

value: 96 hours


title: Nhe1 Astro-KO Contralateral [298_CL]


title: control 4sU-seq DRB_25min rep2


title: Ctrl MyoD Rep 2 Input

value: control


title: 0h_0F_rep1

description: 0 hours, 0 mM fructose, Replicate 1

value: SGBS


title: WT  MyoD Rep 1

description: MyoD adenovirus infection

value: fibroblast

value: WT

value: MyoD adenovirus infection


title: siEloA ChIP-seq input rep2

value: Elongin A siRNA


title: Nhe1 Astro-KO Ipsilateral [295_IL]

value: Brain

value: Post natal day 90-120

value: Gfap-CreERT2+/-;Nhe1f/f (Nhe1 Astro-KO)


title: LncMyoD-KD MyoD Rep 1 Input

value: Muscle stem cells

value: LncMyoD-KD


title: control ChIP-seq input rep2

value: Colon cancer cell line

value: control siRNA


title: Nhe1 Astro-KO Contralateral [295_CL]

value: Tamoxifen


title: Ctrl MyoD Rep 2

value: MyoD-ChIP


title: 96h_0F_rep2

description: 96 hours, 0 mM fructose, Replicate 2

value: 0 mM fructose


title: Ctrl MyoD Rep 1 Input


title: siEloA ChIP-seq input rep1


title: Wild-type Ipsilateral [474_IL]

value: Gfap-CreERT2+/-;Nhe1f/f (wild-type)

value: Corn oil


title: Ctrl MyoD Rep 1

value: control


title: 384h_0F_rep1

description: 384 hours, 0 mM fructose, Replicate 1

value: SGBS

value: 384 hours


title: Wild-type Contralateral [474_CL]


title: siEloA 4sU-seq no DRB rep1


title: control ChIP-seq input rep1


title: LncMyoD-KD H3K27ac Rep 2 Input


title: control Pol_II_ser5p ChIP-seq rep1

value: Pol II-ser5p


title: Wild-type Contralateral [297_CL]


title: 384h_5F_rep2

description: 384 hours, 5 mM fructose, Replicate 2

value: 5 mM fructose


title: siEloA Pol_II_ser2p ChIP-seq rep1

value: Elongin A siRNA

value: Pol II-ser2p


title: Wild-type Ipsilateral [296_IL]

value: Brain

value: Post natal day 90-120


title: LncMyoD-KD H3K27ac Rep 1 Input

value: Muscle stem cells

value: LncMyoD-KD


title: Wild-type Ipsilateral [297_IL]


title: LncMyoD-KD H3K27ac Rep 2


title: Wild-type Contralateral [296_CL]


title: 192h_5F_rep2

description: 192 hours, 5 mM fructose, Replicate 2

value: 192 hours


title: 192h_5F_rep1

description: 192 hours, 5 mM fructose, Replicate 1


title: siEloA Pol_II_ser5p ChIP-seq rep1

value: Colon cancer cell line


title: 0h_0F_rep2

description: 0 hours, 0 mM fructose, Replicate 2

value: 0 hours


title: 192h_5G_rep3

description: 192 hours, 5 mM Glucose, Replicate 3

value: 5 mM Glucose


title: 384h_5F_rep3

description: 384 hours, 5 mM fructose, Replicate 3


title: mouse IgG Cut&Run control

description: processed data file: eloa_m_peaks.narrowPeak

value: wild type (no siRNA)


title: LncMyoD-KD H3K27ac Rep 1


title: 0h_0F_rep3

description: 0 hours, 0 mM fructose, Replicate 3

value: 0 mM fructose


title: 48h_0F_rep1

description: 48 hours, 0 mM fructose, Replicate 1

value: 48 hours


title: Ctrl H3K27ac Rep 2 Input

value: control


title: Elongin A Cut&Run (mouse antibody)


title: 192h_2.5F_rep1

description: 192 hours, 2.5 mM fructose, Replicate 1

value: SGBS

value: 2.5 mM fructose


title: Elongin A Cut&Run (goat antibody) rep2

description: processed data file: eloa_g_peaks.narrowPeak


title: MCF7 AP-2α ChIP replicate 3

description: ChIP-chip using AP-2α antibody in MCF7 cells

hyb_protocol: The labeled DNAs were hybridized using Hybridization System (NimbleGen, Cat. # 00895/00896) and NimbleChip X1 Mixer (NimbleGen, Cat. # 00800) per manufacturer's protocol.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.
GFF files: scaled, log2 (ChIP/Input) ratio

source_name: AP-2α ChIP DNA from MCF7 cells

label_protocol: “ChIP” and “Input”  DNA samples were directly labeled by Klenow Fragment (New England Biolabs) and Cy3/Cy5 dye-labeled random primer (TriLink Biotechnologies) per manufacturer's protocol.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. 4. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer with protease inhibitors. The crosslinked chromatin was sheared to an average size of 500 bp using a Biorupter sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. 555μl of dilution buffer containing protease inhibitor cocktail was added to each ChIP sample (final volume is 850ul), then mixed with 50μl of magnetic beads coupled Rabbit IgG for 30min at 4°C by end-over-end rotation. After the incubation, beads was removed by Magnetic Separation Rack for 2 minutes at 4°C. The supernatant (400 ul) was incubated with AP-2α antibody (Santa Cruz) overnight at 4°C with by end-over-end rotation. Then, 50μl of magnetic beads were added and mixed for 1h by end-over-end rotation at 4°C. The magnetic beads were harvested by Magnetic Separation Rack for 2 minutes at 4°C and washed with 500ul of each buffer t 4°C for 5min with rotation  in the following order : low salt, high salt, LiCl and TE. The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinase K to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input  (1/10 of the material used for ChIP) by phenol extraction and ethanol precipitation.

value: MCF7 cells

source_name: Input DNA from MCF7 cells

value: none, input DNA


title: Ctrl H3K27ac Rep 1


title: MCF7 AP-2α ChIP replicate 2


title: MCF7 AP-2α ChIP replicate 1


title: Ctrl H3K27ac Rep 2


title: N2 + 50% ev + 50% cco-1 RNAi,1

status: Public on Dec 07 2020

city: Lausanne

first: Terytty Yang

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, FastQC was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
Alignment was performed against C. elegans genome (WBcel235 ce11 top-level and Ensembl release 89 annotation) following the bowtie2 (version 2.3.5) manual guidelines with default parameters.
SAMtools (version 1.4.1) was used to sort, filter and index the obtained alignments. Peak calling was then performed using MACS2 (version 2.1.2) between samples of interest.
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with peak counts identified for each group

organism: Caenorhabditis elegans

growth_protocol: Worms were synchronized by bleaching. Synchronized worm eggs were plated in NGM plates under the described conditions and raised at 20 ̊C.

extract_protocol:
Worms were harvested and washed with M9 buffer for three times. Worms were then fixed with 1% formaldehyde in PBS for 30 min, and quenched by glycine. Immunoprecipitaion were carried by using the antibodies against H3K18Ac (Cat. 07-354, Merck) or H3K27Ac (Ab4729, abcam).
Libraries were prepared for sequencing using standard BGISeq500 protocol

treatment_protocol: RNAi treatment was started from the egg phase and treated until worms reached L4/young adult phase and then collected in 15 mL tubes

tag: RNAi clone

value: E. coli HT115, cco-1 RNAi

value: Wild-type

tag: stage at harvesting

value: L4/young adult

tag: antibody

value: IP with H3K18Ac antibody


title: N2 + ev, 2

source_name: N2 + ev

value: E. coli HT115

value: IP with H3K27Ac antibody


title: Input_cco-1

description: Input sample

data_processing:
After sequencing on the BGIseq-500 platform, FastQC was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
Alignment was performed against C. elegans genome (WBcel235 ce11 top-level and Ensembl release 89 annotation) following the bowtie2 (version 2.3.5) manual guidelines with default parameters.
SAMtools (version 1.4.1) was used to sort, filter and index the obtained alignments.Peak calling was performed using MACS2 (version 2.1.2) against default Poisson distribution to generate raw counts for each sample, or between samples of interest for comparison.
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with peak counts identified for each group

source_name: input

value: Wild-type N2


title: N2 + 50% ev + 50% cco-1 RNAi,2


title: 192h_10F_rep3

description: 192 hours, 10 mM fructose, Replicate 3

growth_protocol: SGBS preadipocytes were plated at 2x105 cells in 100 mm dishes, supplemented with 10 ml growth medium, grown to confluence and initiated to differentiate as per. All media used for the growth, differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr).

value: 192 hours

value: 10 mM fructose


title: Gak-KO-1

city: New Haven

first: Xuefei

last: Tian

state: CT

address: 300 Cedar Street

department: Nephrology/Internal Medicine

institute: Yale University School of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: The scanner is a 16-bit sophisticated opto-mechanical confocal scanner which measures fluorescence intensity emitted by the labeled cRNA/cDNA bound to the probe arrays. The scanner uses a high-quality, solid state 532nm Diode-Pumped, Frequency Doubled Nd:YAG (Neodymium-doped Yttrium Aluminum Garnet) Green Laser. The scanner optics are designed to condition the laser beam to deliver an excitation spot size of 3.5.

data_processing: Background correction was done individually for each data using RMA algorithm in limma package. Probes were mapped to gene symbols using the annotation file downloaded from Affymetrix website where probes with no annotation were discarded. The expression values with biological replicates were averaged. Z score for each gene was calculated following the method published by Cheadle et al. (2003). When comparing two samples, Z ratio of each gene was calculated.

source_name: Mice kidney glomeruli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Glomeruli were isolated from the kidney cortical tissue in the control mice and Gak KO mice at 3 weeks of age using Dynabeads (Invitrogen) perfusion and Percoll density gradient centrifugation (GE Healthcare) .The glomerular RNA was extracted using an RNeasy Plus Mini kit (Qiagen), and that was sent to the Yale Center for Genome Analysis for microarray analysis on the Affymetrix mouse genome 430 2.0 platform

treatment_protocol: Control mice and Gak-KO mice at 3 weeks of age

tag: gender

value: Male

tag: tissue

value: kidney glomeruli

tag: genotype/variation

value: Gak-KO


title: Input_ev

description: Input sample

tag: strain


title: 192h_10F_rep2

description: 192 hours, 10 mM fructose, Replicate 2

tag: cell line

tag: time post-induction


title: 384h_10F_rep3

description: 384 hours, 10 mM fructose, Replicate 3

value: 384 hours

tag: treatment


title: Control-2

value: Female

value: control


title: 384h_5G_rep1

description: 384 hours, 10 mM glucose, Replicate 1

value: SGBS

value: 5 mM Glucose


title: Gak-KO-2


title: Ctrl H3K27ac Rep 1 Input

tag: cell type

value: Muscle stem cells


title: N2 + 50% mrps-5 RNAi + 50% atfs-1 RNAi_ rep2

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the WBcel235 assembly of the worm genome using ensembl release 89 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with counts per gene per sample

growth_protocol: Worms were synchronized by bleaching. Synchronized worm eggs were plated in NGM plates under the described conditions and raised at 20 ̊C. Worms were harvested after 2 days (at L4/young adult stage) and washed with M9 buffer for three times to remove the bacteria, then snap frozen in liquid nitrogen.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. The samples were then frozen and thawed quickly 8 times in liquid nitrogen to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocol with polyA enrichment

treatment_protocol: RNAi treatment was started from the egg phase and treated until worms reached L4/young adult phase and then collected in 1.5 mL tubes

value: E. coli HT115, mrps-5 RNAi, atfs-1 RNAi

value: Wild-type


title: N2 + 50% mrps-5 RNAi + 50% atfs-1 RNAi_ rep3

value: L4/young adult


title: N2 + 50% mrps-5 RNAi + 50% atfs-1 RNAi_ rep1


title: Control-1


title: N2 + ev, 1

value: E. coli HT115

value: IP with H3K18Ac antibody


title: N2 + 50% mrps-5 RNAi + 25%cbp-1  RNAi + 25% ev_rep3

value: E. coli HT115, mrps-5 RNAi, cbp-1 RNAi


title: 192h_0F_rep3

description: 192 hours, 0 mM fructose, Replicate 3

value: 192 hours

value: 0 mM fructose


title: 48h_0F_rep2

description: 48 hours, 0 mM fructose, Replicate 2

value: 48 hours


title: N2 + 50% mrps-5 RNAi + 25%cbp-1  RNAi + 25% ev_rep1


title: N2 + 50% mrps-5 RNAi + 50% ev_ rep3

source_name: N2 + 50% mrps-5 RNAi + 50% ev_ rep3

value: E. coli HT115, mrps-5 RNAi


title: N2 + 50% mrps-5 RNAi + 25%cbp-1  RNAi + 25% ev_rep2


title: N2 + 50% mrps-5 RNAi + 50% ev_ rep2

source_name: N2 + 50% mrps-5 RNAi + 50% ev_ rep2


title: N2 + 50% cco-1 RNAi + 50% atfs-1 RNAi_ rep2

value: E. coli HT115, cco-1 RNAi, atfs-1-1 RNAi


title: N2 + 50% mrps-5 RNAi + 50% ev_ rep1

source_name: N2 + 50% mrps-5 RNAi + 50% ev_ rep1


title: 384h_2.5F_rep2

description: 384 hours, 2.5 mM fructose, Replicate 2

value: 384 hours

value: 2.5 mM fructose


title: N2 + 50% cco-1 RNAi + 50% atfs-1 RNAi_ rep1


title: N2 + 50% cco-1 RNAi + 25% cbp-1  RNAi + 25% ev_rep3

value: E. coli HT115, cco-1 RNAi, cbp-1 RNAi


title: N2 + 50% cco-1 RNAi + 25% cbp-1 RNAi + 25% ev_rep1


title: N2 + 50% ev + 50% cco-1 RNAi_rep3

source_name: N2 + 50% ev + 50% cco-1 RNAi_rep3

value: E. coli HT115, cco-1 RNAi


title: N2 + 50% ev + 50% cco-1 RNAi_rep2

source_name: N2 + 50% ev + 50% cco-1 RNAi_rep2


title: N2 + 50% cco-1 RNAi + 25% cbp-1  RNAi + 25% ev_rep2


title: N2 + atfs-1 RNAi_rep3

source_name: N2 + atfs-1 RNAi_rep3

value: E. coli HT115, atfs-1 RNAi


title: N2 + atfs-1 RNAi_rep1

source_name: N2 + atfs-1 RNAi_rep1


title: N2 + 50% ev + 50% cco-1 RNAi_rep1

source_name: N2 + 50% ev + 50% cco-1 RNAi_rep1


title: 384h_2.5F_rep1

description: 384 hours, 2.5 mM fructose, Replicate 1

source_name: SGBS preadipocytes cells

value: SGBS


title: N2 + cbp-1 RNAi_rep2

source_name: N2 + cbp-1 RNAi_rep2

value: E. coli HT115, cbp-1 RNAi


title: N2 + atfs-1 RNAi_rep2

source_name: N2 + atfs-1 RNAi_rep2

value: Wild-type


title: N2 + cbp-1 RNAi_rep1

source_name: N2 + cbp-1 RNAi_rep1

value: L4/young adult


title: N2 + cbp-1 RNAi_rep3

source_name: N2 + cbp-1 RNAi_rep3


title: N2 + ev_rep3

source_name: N2 + ev_rep3

value: E. coli HT115


title: N2 + ev_rep2

source_name: N2 + ev_rep2


title: N2 + 50% cco-1 RNAi + 50% atfs-1 RNAi_ rep3


title: control Pol_II_ser2p ChIP-seq rep1

source_name: DLD1 colon cancer cell line

value: Colon cancer cell line

value: control siRNA

value: Pol II-ser2p


title: N2 + ev_rep1

source_name: N2 + ev_rep1


title: neonatal pancreatic islets, S35178_a

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

data_processing:
The data was processed with the RNA-Seq nf-core (v18.10.1) workflow, which can be found at https://github.com/nf-core/rnaseq.
Quality control was done with FASTQC (v0.11.8) and adapter trimming was performed by Trim Galore! (v0.5)
STAR (v2.6.1) was used for aligning the reads to the pig reference genome Ensembl release 94.
dupRadar (v1.10.0) was used for scanning RNA-Seq data for PCR clonal artifacts and the discovered duplicates were highlighted with Picard MarkDuplicates (v2.18.15).
Read counting on features (e.g. genes) was performed with featureCounts (v1.6.2).
For the differential expression analysis the raw read count table resulting from featureCounts was used and fed into the R package DESeq2 (v1.22.1).
Genome_build: Pig genome Ensembl release 94.
Supplementary_files_format_and_content: The tab-delimited text file that includes the raw read counts.

organism: Sus scrofa

source_name: Pancreas

extract_protocol:
Total cellular RNA was extracted from  porcine islets using a commercial kit for RNA isolation (Macherey Nagel RNA isolation kit).
The mRNA was isolated from 0.2 ug total RNA with an integrity number of ≥ 9 by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module in accordance with the manufacturer’s instructions. Final elution was done in 15 µl 2x first strand cDNA synthesis buffer (NEBnext, NEB). Samples were then directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB). Following ligation, adapters were depleted by a 1X XP bead purification (Beckman Coulter). Indexing was carried out during the following PCR enrichment (15 cycles, 65 °C).Following two further bead based purifications (1X XP beads) libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen), equimolarly pooled and used for 75bp single read sequencing on Illumina NextSeq 500 resulting in an average 28 Mio sequenced fragments per sample.

value: neonatal pancreatic islets

value: HSA + SB

tag: timepoint of culture

value: day 10

tag: tissue status

value: maturated


title: neonatal pancreatic islets, S35171_b

value: Fet-A


title: neonatal pancreatic islets, S35177


title: neonatal pancreatic islets, S35176_a

value: HSA


title: neonatal pancreatic islets, S35183


title: neonatal pancreatic islets, S35172_a


title: neonatal pancreatic islets, S35172_b


title: neonatal pancreatic islets, S35185

value: HSA + LDN


title: neonatal pancreatic islets, S35171_a


title: neonatal pancreatic islets, S35178_b


title: neonatal pancreatic islets, S35174

value: HSA + SB + LDN


title: neonatal pancreatic islets, S35181

value: day 6

value: immature


title: neonatal pancreatic islets, S35179


title: neonatal pancreatic islets, S35173


title: neonatal pancreatic islets, S35186


title: neonatal pancreatic islets, S35175


title: neonatal pancreatic islets, S35184


title: cFLIP

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from epidermis isolated from epidermal cFLIPKO animals.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: epidermis isolated from cFLIPKO animals

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice epilated back skin was treated with Tamoxifen in order to induce Cre expression for 3 consecutive days.

extract_protocol: RNA from isolated epidermis was purified according to the manufacturer's instructions.

treatment_protocol: Epidermis/Dermis separation was performed by heating of the isolated skin at 60°C, after ON incubation in RNAlater stabilization solution.

value: cFLIPKO

value: Epidermis

tag: pool id

value: Pool 1


title: neonatal pancreatic islets, S35182


title: neonatal pancreatic islets, S35170_b


title: neonatal pancreatic islets, S35169_b


title: neonatal pancreatic islets, S35169_a


title: neonatal pancreatic islets, S35167


title: neonatal pancreatic islets, S35176_b


title: neonatal pancreatic islets, S35168


title: neonatal pancreatic islets, S35180


title: neonatal pancreatic islets, S35170_a


title: cTNFKO/TNFKO  epidermal

description: Gene expression data from epidermis isolated from epidermal cFLIPKO/TNF KO animals.

source_name: epidermis isolated from cFLIPKO/TNFKO animals

value: cFLIPKO/TNFKO

value: Pool 3


title: TNFKO

description: Gene expression data from epidermis isolated from TNF KO animals.

source_name: epidermis isolated from TNFKO animals

value: TNFKO

value: Pool 2


title: neonatal pancreatic islets, S35165

value: neonatal pancreatic islets


title: neonatal pancreatic islets, S35164


title: neonatal pancreatic islets, S35163


title: vehicle-3

city: Wenzhou

first: Jianlou

last: Niu

state: Zhejiang

address: Chashan Town

institute: Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: liver tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: vehicle


title: vehicle-2


title: vehicle-1


title: neonatal pancreatic islets, S35166

value: HSA + SB

value: day 10

value: maturated


title: FGF19WT-3


title: FGF19ΔKLB-2


title: FGF19ΔKLB-1


title: FGF19WT-2