title: FXS iPS Neurite D

source_name: iPS-derived motor neurons

value: Fragile X Syndrome


title: daf1_b1

status: Public on May 28 2020

type: SRA

city: Birmignham

first: Muhan

last: Hu

address: 1900 University BLVD

department: CDIB

country: USA

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 1.8.4 was used for basecalling
Fastq files were trimmed using Trim Galore! version 0.4.0 with parameters --paired --trim1
Trimmed fastq files were aligned to the reference genome using TopHat version 2.0.12 with parameters -r 150 --library-type fr-firststrand --keep-fasta-order
Transcript abundances were calculated from the alignments using Cufflinks version 2.21 with parameters --library-type fr-firststrand -g -L
Cuffmerge, Cuffquant and Cuffdiff were then used and differentially expressed genes were further analyzed
Genome_build: Ensembl WBcel235 ceWS240 Release 76
Supplementary_files_format_and_content: tab delimited Excel file containing the FPKM values for each gene for each sample

molecule: total RNA

organism: Caenorhabditis elegans

growth_protocol: Worms were synchronized at the L1 stage using the bleaching technique. L1 larva were grown on 15 cm NGM plates with extra NA 22 E. coli. Worms were grown at 16C until L4, and switched to 25C for 25hrs. Worms were washed with M9 buffer into 50mL tubes. The worms were washed with M9 until the supernatent is clear of bacteria.

extract_protocol: 250 mg of worms were extracted using Trizol

tag: tissue

value: whole worm


title: P8C

type: RNA

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent Technologies). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven and then washed at room temperature.

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies)

data_processing: Raw data were extracted using Agilent Feature Extraction Software (Agilent Technologies, v11.0.1.1). Background correction, averaging the expression values of duplicated probes and between-sample normalization of raw data were performed using limma35 and R 3.2.1（https://cran.r-project.org/）. Normalization was performed using quantile method.  All expression values for the probes was log2 transformed and normalized between groups using quantile method.

organism: Mus musculus

source_name: Young nasal mucosa in control group

label_protocol: RNA labeling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kits (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: RNA was prepared using TRIzol Reagent (Life Technologies) and RNeasy Mini Kits (QIAGEN) following the manufacturer's recommendations. RNA purity and integrity were confirmed based on its OD 260/280 ratio before analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies). Each total RNA sample pooled from 5 biological replicates (two experimental replicate).

treatment_protocol: Septal nasal mucosa were collected from young-adult or aged mice immediately after euthanization, and then snap-freezed with liquid nitrogen.

tag: strain

value: olfactory epithelium

tag: age

value: 8 weeks

tag: treatment

value: control


title: CAD FMR1KO Fmr1-RGG rescue Soma B

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt
Transcript abundances were calculated using salmon or kallisto against the mm10 or hg38 genomes
Gene abundances were calculated from transcript abundances using tximport
Reads were mapped to mouse genome (mm10 or hg38) using STAR
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: transcript abundances in txt format

molecule: polyA RNA

source_name: CAD cell line

extract_protocol:
RNA extraction was performed with Qiagen or Zymo Microprep Kits
Illumina TruSeq

tag: cell compartment

value: soma

tag: genotype

value: FMR1 KO, Fmr1-RGG rescue


title: N2_b3

source_name: N2 wild type


title: Sample 10, ILW muscle, mRNA

city: Bologna

first: Martina

last: Zappaterra

address: viale Fanin 46

department: Department of Agricultural and Food Science

country: Italy

institute: University of Bologna

description: low intramuscular fat

data_processing:
Raw reads were obtained in FASTQ format and were quality-assessed using FastQC program. The quality was measured according to sequence-read lengths and base-coverage, nucleotide contributions and base ambiguities, quality scores and over-represented sequences and all samples passed the QC parameters.
Terminal low quality bases and adaptor sequences were trimmed out using Trimmomatic utility
Clean reads were aligned against Ensembl reference genome Sus scrofa v. 11.1 using the splice-aware read mapper HiSat2.
BAM files obtained from read alignment were further processed with Stringtie in order to assemble known transcripts.
HTSeq was then used to quantify the reads and obtain the file with the gene counts.
The differential gene expression analysis was carried out in R environment with DESeq2 package.
In order to identify strongly co-expressed genes involved in IMF deposition, we employed a co-expression analysis approach using WGCNA package in R environment.
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: text file formatted as a matrix table of raw gene counts

organism: Sus scrofa

source_name: muscle

growth_protocol: All animals were housed in the same environment and fed the same diet.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer's instruction. Results of the extraction were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and the quality of the extracted RNA was assayed using an Agilent 2100 BioAnalyzer (Agilent Technologies).
Stranded total RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer's suggested protocol.
The libraries were tagged, and pairs of libraries were run on a single lane of an Illumina HiSeq2500 (Illumina). Paired-end reads of 100 bp were generated.

treatment_protocol: Semimembranosus muscle sample was collected in a commercial slaughterhouse. The sample was immediately frozen in liquid nitrogen and stored at -80C in a deep freezer until RNA isolation.

tag: breed

value: Italian Large White

tag: gender

value: female

value: Semimembranosus muscle

value: 239 days

tag: weight


title: FXS iPS Neurite C

organism: Homo sapiens

value: neurite


title: 24hr INCB059872 A input

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave.

institute: Vanderbilt University

library_source: genomic

data_processing:
Trimmomatic-0.32: trim adapter sequences
Bowtie2: read alignment to hg19+dm3
samtools: filter out low quality alignments and remove duplicate reads
samtools: divide hg19 reads and dm3 reads into separate files
MACS2: call peaks (q-value 0.001)
Genome_build: combined genome: hg19 + dm3
Supplementary_files_format_and_content: Processed data files are in bedgraph format with input signal subtracted from ChIP signal.

molecule: genomic DNA

source_name: THP-1 cell line

extract_protocol:
Cells were resuspended in Buffer 1 (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 0.2% aprotinin, 1 mM PMSF) and rocked at 4°C for 10 min. Samples were centrifuged and resuspended in Buffer 2 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.2% aprotinin, 1 mM PMSF) then rocked at 4°C for 5 min. Samples were centrifuged then resuspended in Buffer 3 (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% sarkosyl, 0.2% aprotinin, 1 mM PMSF, Complete mini protease inhibitor cocktail). Samples were sonicated using a Bioruptor (Diagenode) on high setting for 25 cycles (30 sec on, 30 sec off). Next, 1% Triton X-100 was added, and samples were vortexed for 10 sec. Debris was pelleted by centrifuging at 20,000 xg for 10 min, and cleared lysates were transferred to new tubes. At this point, aliquots of chromatin were removed to serve as input controls. One quarter of each sample volume (corresponding to ~10 million cells equivalent) was used for immunoprecipitation. Samples were incubated overnight with 10 μg anti-H3K27ac. Protein A and Protein G Dynabeads were mixed at 1:1 ratio and washed with equilibration buffer (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 1% Triton X-100). Samples were rotated at 4°C for 1 hour after adding 60 μl Dynabeads mix per sample. Beads were washed four times (once in each buffer) by rotating for 5 min at 4°C in the following buffers: low salt wash (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), high salt wash (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100), LiCl wash (10 mM Tris pH 8.0, 25 mM LiCl, 1 mM EDTA, 1% Triton X-100), TE. Beads were washed a second time in TE by rotating for 5 min at room temperature. Beads were resuspended in 50 μl elution buffer (TE with 0.1% SDS, 200 mM NaCl, 0.8 μg/μl Proteinase K).
Agencourt AMPure XP Beads were used at 1.8X volume according to manufacturer’s instructions for size selection. Libraries were preparing by following manufacturer’s instructions for NEBNext Ultra II DNA Library Prep Kit for Illumina.
Immediately prior to crosslinking, drosophila S2 cells were added to treated THP-1 cells to serve as spike-in control (~1:27 ratio of drosophila:human cells). Cells were crosslinked with 1% formaldehyde, quenched with glycine, and washed with cold PBS. See "ChIP protocol" column above for experiment-specific protocols.

tag: chip antibody


title: P8CT28

source_name: Young nasal mucosa in smoking group

value: cigarette smoke solution


title: Sample 12, ILW muscle, mRNA

description: low intramuscular fat

value: 229 days


title: P8A

source_name: Aged nasal mucosa in control group

value: 16 months


title: FXS iPS Neurite B


title: N2_b2


title: Sample 9, ILW muscle, mRNA

description: low intramuscular fat

value: 232 days


title: P8CT1


title: CAD FMR1KO GFP rescue Neurite C

value: FMR1 KO, GFP rescue


title: FXS iPS Neurite A

value: Fragile X Syndrome


title: N2_b1

value: whole worm


title: FXS iPS Soma D


title: Sample 11, ILW muscle, mRNA

description: low intramuscular fat

value: male

tag: status

value: castrated

value: 243 days


title: CAD FMR1KO GFP rescue Neurite B


title: CR 23

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

data_processing:
Raw data processing was performed according to the Drop-seqAlignmentCookbookv1.2Jan2016 McCarroll lab
R1 contains barcode (bases 1-12) and UMI (bases 13-20). R2 is the biological read.
Unmapped BAM reads were tagged with cell and molecular barcodes and 5' primer and 3' polyA sequences were trimmed
Fastq files were extracted and were aligned to hg19 and mm10 reference genomes using the STAR alignment software
Following alignment, digital gene expression (DGE) data was extracted from the aligned library using the Drop-seq program Digital Expression in order to generate a processed gene expression matrix used for all downstream analyses
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: .dge files text files

source_name: Normal mammary cells from reduction mammoplasty

growth_protocol: To estabalish CR cultures, normal mammary cells were co-cultured with irradiated J2 fibroblasts in F-media in a humidified incubator at 37˚C/5% CO2. Cells were allowed to grow up to 80% confluence. CR was performed according to the protocol by Liu et al 2017 doi: 10.1038/nprot.2016.174

extract_protocol: Drop-seq libraries were prepared according to Macosko et al 2015  doi: 10.1016/j.cell.2015.05.002

tag: cell type

value: mammary

value: Conditonally reprogrammed


title: Sample 7, ILW muscle, mRNA

description: low intramuscular fat

value: Italian Large White

value: 249 days


title: FXS iPS Soma C

value: soma


title: Sample 6, ILW muscle, mRNA

description: high intramuscular fat

value: Semimembranosus muscle


title: CR 15


title: FXS iPS Soma B


title: CAD FMR1KO GFP rescue Soma C


title: Sample 5, ILW muscle, mRNA

description: high intramuscular fat

value: 234 days


title: FXS iPS Soma A


title: CAD FMR1KO Fmr1-RGG rescue Soma A

value: FMR1 KO, Fmr1-RGG rescue


title: CR 11


title: CAD FMR1KO GFP rescue Soma A


title: Sample 3, ILW muscle, mRNA

description: high intramuscular fat

value: female

value: 244 days


title: NM 23

value: Normal


title: CAD FMR1KO GFP rescue Soma B

value: FMR1 KO, GFP rescue


title: Sample 4, ILW muscle, mRNA

description: high intramuscular fat

value: 235 days


title: NM 15


title: Unaffected iPS Neurite D

value: neurite

value: Unaffected


title: Sample 8, ILW muscle, mRNA

description: low intramuscular fat

value: male

value: castrated


title: Sample 2, ILW muscle, mRNA

description: high intramuscular fat


title: NM 11

value: mammary


title: Unaffected iPS Neurite B


title: Unaffected iPS Neurite C


title: Sample 1, ILW muscle, mRNA

description: high intramuscular fat

value: 243 days


title: wild-type S2 cells, TAF1 dsRNA knockdown, Replicate 3

city: Boulder

first: Dylan

middle: J

last: Taatjes

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

description:
nascent RNA
nascent RNA (PRO-seq) from S2 cells
counts_s2.txt

data_processing:
processing of all sequencing data was performed using the NascentFlow Pipeline (doi: 10.17605/OSF.IO/NDHJ2)
Genome_build: GRCh38 for HCT116 cells, DM6 for S2 cells

organism: Drosophila melanogaster

source_name: wild type S2

growth_protocol: HCT116 cells were grown in McCoy's media (Gibco, 16600082) with Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin and 10% fetal bovine serum (FBS) supplementation. Drosophila cell culture and RNAi. D. melanogaster Schneider line 2 (S2) cells were maintained at 25°C in Schneider‘s medium containing 10% (vol/vol) Fetalplex (Gemini), 100 units/mL penicillin, and 0.1 mg/mL streptomycin. RNAi was performed as described [Clemens, 2000] using 20-40 µg dsRNA. Cells were incubated with dsRNA for 2.5 d.

extract_protocol: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. http://doi.org/10.1093/bioinformatics/btq033) with the following modification. The final concentration of non-biotinylated CTP was raised from 0.25uM to 25uM, and the final library clean up and size selection was accomplished using 1X AMPure XP (Beckman).

treatment_protocol: The method used was adapted from [Clift/Schuh Cell 2017]. HCT116 cells cultured in McCoy’s 5A medium were grown to approximately 70% confluency. Media was aspirated off, and the cells were washed with PBS. 2ml of trypsin per plate were used to harvest adherent cells, after which an equal volume of Opti-MEM was added to each plate to neutralize the trypsin. Cells were combined in a 50ml centrifuge tube and spun down at 2,000xg for 5 minutes, then washed in PBS and spun down again at 2,000xg for 5 minutes. Cells were counted using a hemocytometer and diluted to 25 million cells/mL. 100 µl reactions were prepared, and cells were re-suspended in Buffer R and anti-TAF1 C413 antibody. A pulse only control was prepared, which consisted of cells suspended only in Buffer R. Transfections were performed using the Neon Transfection Kit (1530V, 1ms width, 1 pulse). Transfected cells were then pipetted into 1 mL of Opti-MEM in a 35mm dish and incubated at 37˚C for 1 hour. The Opti-Mem media (containing some suspended cells) was then pipetted off and saved. 500 µl of PBS was added to the cells on the plates, which were then harvested and centrifuged at 6,000xg for 5 minutes. Supernatant was aspirated off, and cell nuclei were subsequently isolated. For D. melanogaster Schneider line 2 (S2) cells RNAi was performed as described [Clemens, 2000] using 20-40 µg dsRNA. Cells were incubated with dsRNA for 2.5 d.

tag: cell line

value: wild type S2

value: late stage embryonic cells

value: TAF1 dsRNA knockdown


title: Biofilm_3

city: Santa Cruz

first: Sinem

last: Beyhan

state: CA

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

data_processing:
Illumina data were analyzed by UC Davis sequencing core with the newest available RTA and CASAVA software.
rRNA reads were filtered using riboPicker version 2.4.3 (PMID:22155869).
non-rRNA reads were mapped to V. cholerae O1 biovar El Tor str. N16961 (assembly GCA_000006745.1) transcripts using CLC-NGS Cell version 4.4.2 (Qiagen).
Significantly regulated genes were determined using EdgeR (PMID:19910308), fold change greater than 2.0 and false discovery rate less than 1% was used as a cutoff.
Genome_build: V. cholerae O1 biovar El Tor str. N16961 (assembly GCA_000006745.1)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.

organism: Vibrio cholerae

source_name: Biofilm

growth_protocol: Planktonic cultures were grown in 5 ml Lysogeny-Broth (LB) broth (1% tryptone, 0.5% yeast extract, 1% NaCl [pH 7.5]) at 30C for 16 hr 200 rpm. Biofilms cells were grown in 15cm silicon tube (ID 0.125/OD 0.250) with 2% LB (0.02% tryptone, 0.01% yeast extract, 1% NaCl [pH 7.5]), and grown at RT for 48 hr with a flow rate of 0.75 rpm

extract_protocol:
V. cholerae wild-type cells were grown in planktonic or biofilm mode as described. Cells were collected and supernatant removed after centrifugation. Pellets were immediately resuspended in 2 ml of TRIzol (Invitrogen, Carlsbad, CA) and stored at -80 C. Total RNA was isolated according to the manufacturer’s instructions. To remove contaminating DNA, total RNA was incubated with RNase-free DNase I (Ambion, Grand Island, NY), and an RNeasy mini kit (Qiagen, Valencia, CA) and ethanol precipitation was used to clean up RNA after DNase digestion. RNA concentration was calculated in a nanodrop and the quality was evaluated in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Three biological replicates were generated for each condition.
Five micrograms of total RNA was treated with a MICROBExpress Kit (Ambion, Grand Island, NY) to remove ribosomal RNA, and the efficiency was confirmed in a 2100 Bioanalyzer. Libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Twelve indexed samples were sequenced per single lane using the HiSeq4000 Illumina sequencing platform for 100 bp single reads (UC Davis Genome Center, UC Davis, CA).

value: A1552 smooth variant

tag: growth

value: biofilm

tag: molecule subtype

value: rRNA-depleted RNA


title: wild type S2 cells, LacI dsRNA control, Replicate 3

value: LacI dsRNA control


title: wild-type S2 cells, TAF1 dsRNA knockdown, Replicate 2


title: Unaffected iPS Neurite A


title: wild-type S2 cells, TAF1 dsRNA knockdown, Replicate 1


title: CAD FMR1KO GFP rescue Neurite A


title: wild type S2 cells, LacI dsRNA control, Replicate 2


title: Unaffected iPS Soma D

value: soma


title: Unaffected iPS Soma C


title: Planktonic_3

source_name: Planktonic

value: planktonic


title: Unaffected iPS Soma B


title: wild type S2 cells, LacI dsRNA control, Replicate 1


title: Biofilm_2


title: Biofilm_1


title: Unaffected iPS Soma A


title: Planktonic_2


title: CD_3D

city: Herts

first: Deborah

middle: Jane

last: Guest

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

country: United Kingdom

institute: Royal Veterinary College

data_processing:
RNA sequencing was performed on a NovaSeq6000 (Illumina) and HiSeq2500 both by external providers (Edinburgh Genomics, Edinburgh, UK & Otogenetics, Atlanta, USA respectivley).
20.2 – 23.8 million reads  of 100 base pair paired end data were generated per sample.
Resulting FASTQ files generated were then quality control (QC) checked using FASTQC and FASTQ Screen (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensemble version v95 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (Soneson et al 2015) was then used to import the quantified gene-level abundance data into R (v.3.5.2) and differential expression analysis conducted using R/Bioconductor DSeq2 (v.1.22.2) as described in Love et al., 2014, with batch correction applied.
Genes with adjusted pvalue of less than 0.01 and log2 fold change of ± 2 were considered as differentially expressed.
Genome_build: Ensemble version v95 EquCab 3.0
Supplementary_files_format_and_content: Comma Seperated Value (CSV) files include raw counts of sequencing reads for each sample in a matrix table

organism: Equus caballus

source_name: Tenocytes cultured in 3D

growth_protocol: Adult and Fetal cells were cultured in Dulbecco’s modified eagle medium (DMEM) high glucose, 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen, Renfrewshire, UK) and passaged using 0.25% trypsin-EDTA (Sigma-Aldrich) every 3-4 days. Undifferentiated ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts at 37°C, 5% CO2 in ESC medium (DMEM/F12 containing 15% fetal bovine serum, 2 mM L-glutamine, 1% non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol (all from Invitrogen) and 1000 units/ml leukaemia inhibitory factor (LIF) (Sigma-Aldrich). ESCs were passaged mechanically every 5-7 days in the presence of 2 μM thiazovivin (StemGent, Cambridge, USA). To differentiate the ESCs to tenocytes they were cultured in three-dimensional collagen gels in ESC media lacking LIF (Peprotech, London, UK) for 14 days.

extract_protocol:
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK) by an external provider (Cambridge Genomics, Cambridge, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK)

value: Adult tenocyte

tag: passage

value: 2-6 years


title: 320d_3D

value: Fetal tenocyte

value: 320 day gestatation


title: ES_PW_3D

value: ESC-derived tenocyte


title: ES_IG_3D


title: Knockout_Infected_rep1

city: Kuala Lumpur

first: Won

middle: Fen

last: Wong

address: Lembah Pantai

department: Department of Medical Microbiology,  Faculty of Medicine

country: Malaysia

institute: University of Malaya

description: RNA was hybridised overnight for 20 hours at 65ᵒC in a thermal cycler and subjected to nCounter MAX/FLEX. A total of 516 genes was detected following exclusion of 20 housekeeping genes and 234 genes which RNA count is below threshold 20.

hyb_protocol: Total of 100 ng RNA was hybridized in CodeSet mix carrying hybridization buffer, Reporter Code Set, Capture Probe Set at 65ᵒC for 20 hours following manufacturer protocols. Hybridized samples were subjected to nCounter PrepStation for samples for sample immobilization in a sample cartridge.

scan_protocol: The sample cartridge was processed for 2 hours using nCounter Digital Analyzer where images of the immobilized fluorescent reporters was taken with CCD camera through a microscope objective lens. 280 fields of view (FOV) were collected per cartridge lane which corresponds to the number of reporters counted.

data_processing: Raw data were normalization using an internally developed Pipeline Pilot Tool (NAPPA) which is publicly available. Two steps normalization was performed to account for firstly, the background using the spike in positive and negative controls, followed by input correction using housekeeping genes.

label: 6-spots of flourescence barcode

source_name: Pdpn knockout RAW264.7_SS1 infected_MOI10:1_24 hours

label_protocol: RNA was labelled with CodeSet that hybridized directly to the target where each probe pair consists of a color-coded Reporter and a Capture Probe to which a  target-specific sequence has been covalently attached.

growth_protocol: Cells were maintained using Dulbecco's Modified Eagle's medium (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco) at 37ᵒC in a humidified incubator with 5% CO2. Cell was passage every 3-4 days with medium change. H. pylori SS1 culture was maintained on chocolate agar plate supplemented with 7% laked horse blood (Oxoid, Basingstoke, UK) under microaerophilic conditions at 10% CO2, 37ᵒC in a humidified incubator and were subcultured every 3 days

extract_protocol: RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA) as described following manufacturer protocol. RNA integrity was checked using electrophoresis and quantified using Nanodrop.

treatment_protocol: Cells were seeded at concentration of 5 X 10^5 cells/mL in a 6-well plate overnight. H. pylori were grown for 3 days on chocolate agar plate supplemented with 7% laked horse blood at 10% CO2, 37ᵒC in a humidified incubator and harvested in brain heart infusion broth (Oxoid, UK). Bacteria was quantified using spectrophotometer and added into cells at MOI 10:1 for 24 hours. After 24 hours, cells are washed with 1X phosphate buffer saline and subjected to RNA extraction.

tag: genotype/variation

value: Pdpn knockout

tag: infection status

value: H. pylori SS1 infected

tag: infectious dose (multiplicity of infection, moi)

tag: cell seeding concentration

value: 5 X 10^5 cells/mL

tag: duration

value: 24 hours

tag: final rna concentration (ng)


title: Knockout_Infected_rep2


title: Wildtype_Infected_rep1

source_name: Wildtype RAW264.7_SS1 infected_MOI10:1_24 hours

value: Wildtype


title: Transgenic_Mock_rep2

source_name: Pdpn transgenic RAW264.7_Mock infected_24 hours

value: Pdpn overexpressing

value: Mock infected


title: Transgenic_Infected_rep1

source_name: Pdpn transgenic RAW264.7_SS1 infected_MOI10:1_24 hours


title: Planktonic_1

tag: strain

value: A1552 smooth variant


title: Transgenic_Infected_rep2


title: C. elegans Punc-119::ds-fzo-1 RNAi animals

city: Taipei City

first: Li-Tzu

last: Chen

address: No. 1, Sec. 1, Ren’ai Rd., Zhongzheng Dist.

department: Institute of Molecular Medicine

country: Taiwan

institute: National Taiwan University

data_processing:
Trimmomatics (Bioinformatics, 2014; 30(15): 2114–2120) was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks (Nat Protoc., 2012; 7(3):562-78) for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles. The reference genome and gene annotations were retrieved from Ensembl database. Initially, differentially expressed genes were defined as FKPM 0.3 with a fold change 2. We set a stringent criterion of FKPM larger than 1 with a fold change 1.5 or 0.5, resulting in 250 upregulated genes and 196 downregulated genes.
Genome_build: WBcel235 (GCA_000002985.3)/ Ensembl database
Supplementary_files_format_and_content: Microsoft excel file includes: 1. FPKM for each sample and the ratio of zcIs13; Punc-119::ds-fzo-1 RNAi FPKM/ zcIs13; WT FPKM as well as p and q value, 2. sorted data with FKPM no less than 0.3 and a fold change 2, 3. GO term, 4. KEGG PATHWAY

source_name: Whole-animal

growth_protocol: Strains were maintained at 25C as described (Brenner, 1974).

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA). All procedures were carried out according to the manufacture’s protocol from Illumina.
Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform. The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate 30M (million reads or Gb) per sample.

tag: genotype

value: zcIs13; twnEx320[Punc-119::ds-fzo-1]

tag: developmental stage

value: L4 lavae

tag: growth temperature

value: 20 degree celsius


title: ES_HJ_3D

tag: age


title: TB130911_3D


title: Transgenic_Mock_rep1


title: C. elegnas control animals


title: Dithranol-treated ear mouse#39

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Clariom S Assay,  mouse (Cat No. 902919); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Data Pre-Processing (RStudio Version 1.2.1335: R Version 3.5.1  with MicroArrayPipeline v1.0 Shiny app based on limma Bioconductor package for differential expression analysis): includes RMA (background correction, quantile normalization across all chips in the experiment, log2  transformation, median polish summarization)

label: Biotin

source_name: Dithranol-treated ear mouse#39

label_protocol: 500ng for Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280)

growth_protocol: All animals were bred and housed in conventional housing

extract_protocol: miRNeasy Mini Kit inclusive DNase digest (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: Vehicle (Vaseline) or dithranol were applied for 6 days in increasing concentrations on ears

tag: treatment

value: dithranol-treated

tag: tissue

value: ear tissue

value: c-Jun/JunB knockout


title: Wildtype_Infected_rep2

tag: cell line


title: Knockout_Mock_rep1

source_name: Pdpn knockout RAW264.7_Mock infected_24 hours


title: Wildtype_Mock_rep2

source_name: Wildtype RAW264.7_Mock infected_24 hours


title: 319d_3D

tag: cell type

value: Fetal tenocyte

value: 319 day gestatation


title: TB250718B_3D

value: Adult tenocyte

value: 2-6 years


title: Vas-treated ear mouse#40

source_name: Vas-treated ear mouse#40

value: vaseline-treated


title: Dithranol-treated ear mouse#30

source_name: Dithranol-treated ear mouse#30


title: Knockout_Mock_rep2

value: Pdpn knockout

value: 5 X 10^5 cells/mL


title: Dithranol-treated ear mouse#25

source_name: Dithranol-treated ear mouse#25


title: Wildtype_Mock_rep1

value: Wildtype

value: 24 hours


title: Dithranol-treated ear mouse#31

source_name: Dithranol-treated ear mouse#31


title: THP-1 A5-KD 0hrs rep2

status: Public on May 27 2020

city: Zhengzhou

first: Jiazhen

last: Wang

address: 156 Jinshui East Road

country: China

institute: Henan University of Chinese Medicine

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole transcriptome using hisat v2.1.0 with default parameters
T>C conversion was calculated following slamdunk pipeline
Genome_build: hg38
Supplementary_files_format_and_content: .csv file was generated following slamdunk pipeline

growth_protocol: The human acute leukemia cell lines THP1 were maintained in Roswell Park Memorial Institute 1640 medium (RPMI-1640) with 10% FBS, 100 IU ml−1 penicillin and 100μg ml−1 streptomycin.

extract_protocol:
polyA RNA
Cells was labeled with 100μM 4sU (Sigma) for 1h and then washed twice with 1×PBS and incubated with standard medium supplemented with 10mM uridine (Sigma). Cell collected at indicated time points was extraction using TRIzol. NEBNext RNA Library Prep Kit (NEB, #E7760) was used for library preparation.


title: THP-1 control 4.5hrs rep2

value: wild type


title: THP-1 control 7.5hrs rep2


title: THP-1 A5-KD 1.5hrs rep2


title: Dithranol-treated ear mouse#15

source_name: Dithranol-treated ear mouse#15


title: Vas-treated ear mouse#21

source_name: Vas-treated ear mouse#21


title: MHH-cALL5 ruxolitinib 3

city: Loma Linda`

first: Christian

last: Hurtz

address: 11085 Campus Street

department: Basic Science

institute: Loma Linda University

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Clariom D Human Arrays  using the GeneChip Hybridization oven 645

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal

data_processing:
Affymetrix Command Console and Expression Console were used to quantitate probe intensities; default values provided by Affymetrix were applied to all analysis parameters.
Affymetrix Transcriptome Analysis Console (TAC) was used to run RMA to summarize and normalize probe intensity data

source_name: MHH-cALL5 ruxolitinib

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Expression Analysis Technical Manual

growth_protocol: MHH-cALL4 cells were cultured in vitro in RPMI supplemented with 20%FBS 1%Pen/Strep.

extract_protocol: RNA was extracted using the RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: MHH-cALL4 cells were treated either with DMSO or 1uM ruxolitinib for 12h.

value: human Ph-like ALL cell line

value: 1uM ruxolitinib for 12h


title: THP-1 control 1.5hrs rep2


title: THP-1 control 0hrs rep2


title: THP-1 A5-KD 7.5hrs rep2


title: THP-1 A5-KD 4.5hrs rep2


title: Vas-treated ear mouse#16

source_name: Vas-treated ear mouse#16


title: Vas-treated ear mouse#28

source_name: Vas-treated ear mouse#28


title: 271d_3D

source_name: Tenocytes cultured in 3D

value: 271 day gestatation


title: THP-1 A5-KD 4.5hrs rep1


title: THP-1 A5-KD 1.5hrs rep1


title: THP-1 A5-KD 7.5hrs rep1


title: THP-1 A5-KD 0hrs rep1


title: MHH-cALL5 ruxolitinib 1


title: MHH-cALL4 Control 3

source_name: MHH-cALL4 Control

value: vehicle (DMSO) for 12hr


title: MHH-cALL5 ruxolitinib 2


title: Vas-treated ear mouse#12

source_name: Vas-treated ear mouse#12


title: MHH-cALL4 Control 2


title: MHH-cALL4 Control 1


title: THP-1 A5-KD input rep2

data_processing:
Library strategy: Ribo-seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole transcriptome using hisat v2.1.0 with default parameters
Transcript abundance was calculated by kallisto.
Differential translational efficiency was called by Riborex
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx file was calculated by Riborex

extract_protocol:
total RNA
3 millions cells were lysed with 300μl lysis buffer (CaCl2 4 mM, MgCl 10 mM, K-HEPES pH 7.2 25 mM, KOAc 200 mM and NP-40 1%) for 5 min on ice and then centrifuged at 9000rpm for 5 min. Collect supernatant and 100 μl of lysate was mixed with TRIzol and saved as input. Adjust KOAc concentration of the lysate to 100 mM by 1:1 dilution with water and then incubated with 10μg/ml micrococcal nuclease for 30 min at 37°C. RNA was extracted with TRIzol. Followed by PNK treatment, ribosome-protected fragments (RPFs), 25 to 40 nucleotides long, was purified with 15% TBE-Urea Gel. Libraries were then prepared using the VAHTSTM Small RNA Library Prep Kit for Illumina® following manufacturer’s instructions.

tag: genotype/variaton


title: THP-1 control 7.5hrs rep1


title: THP-1 control 4.5hrs rep1


title: THP-1 control 1.5hrs rep1


title: THP1 shA5 rep-1 (RNA-seq)

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to hg38 whole transcriptome using kallisto v0.43.1 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values for each Sample

source_name: human AML cell line

extract_protocol:
Total RNA  were extracted with Trizol and mRNA were isolated with Oligo dT beads.
Libraries were prepared according to VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Part# NR601). Briefly, mRNA was interrupted  with metal ions in interrupted buffer ,  cDNA synthesis using random primers for reverse transcription of mRNA. The cDNA strands in the hybrid double strands were digested by RNaseH to synthesize cDNA complementary strands for cDNA second strand synthesis. Repair sticky ends were repaired to  blunt ends    add A-tail,and connection connector.After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: ALKBH5 knock-down


title: THP1 A5-res rep-2 (RNA-seq)

value: ALKBH5 rescue


title: THP-1 A5-KD ribo rep1


title: THP-1 control 0hrs rep1


title: THP-1 control input rep1

value: input


title: THP-1 A5-KD input rep1


title: THP-1 control ribo rep2

value: control


title: THP-1 control input rep2


title: THP1 shA5 rep-2 (RNA-seq)


title: THP1 A5-res rep-1 (RNA-seq)


title: THP-1 A5-KD ribo rep2


title: THP-1 control ribo rep1


title: THP1 shA5 rep-1 (m6A-seq)

description: THP1 shA5 rep-1 (m6A-seq)

data_processing:
Library strategy: m6A-seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole transcriptome using hisat v2.1.0 with default parameters
.bigWig files were generated using Deeptools v2.0 bamCoverage with parameters --binSize 5 --normalizeUsingRPKM
Genome_build: hg38
Supplementary_files_format_and_content: .bigWig files for each sample

extract_protocol:
RNA was harvested using Trizol reagent.mRNA are isolated，fragmented and m6A-specific antibodies are used to immunoprecipitate RNA. Specific m6a RNA is reverse-transcribed to cDNA through first strand synthesis and second strand synthesis
Illumina TruSeq DNA Sample Prep Kit (Cat#15026486) was used with DNA for the construction of sequencing libraries. Libraries were prepared for sequencing using Illumina protocols.


title: THP1 A5-res rep-2 (m6A-seq)

description: THP1 A5-res rep-2 (m6A-seq)


title: THP1 shCtrl rep-1 (RNA-seq)

value: wild-type


title: THP1 shCtrl rep-1 (m6A-seq)

description: THP1 shCtrl rep-1 (m6A-seq)


title: THP1 A5-res rep-1 (m6A-seq)

description: THP1 A5-res rep-1 (m6A-seq)


title: THP1 shCtrl rep-2 (m6A-seq)

description: THP1 shCtrl rep-2 (m6A-seq)


title: THP1 shCtrl rep-2 (RNA-seq)


title: ChIP-seq-IRI-JQ1-Pol2-rep1

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
The ChIP-seq analysis worklow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed the application of bowtie aligner (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and finally Homer software (Heinz et al., Mol. Cell, 2010) for the generation of bedGraph files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Kidney Cortex

extract_protocol:
Chip assays were performed as described previously (Shin et al., Nature Genetics, 2016). Briefly, snap-frozen kidney cortex (cortex plus outer medulla) from Sham or IRI mice (day 2) were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. After cell lysis and sonication, sheared chromatin was incubated with following antibodies: anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 17-614), anti-Brd4 (Behtyl Laboratory, A301-985A), and anti-RNA Polymerase II (Abcam, ab5408). Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on HiSeq 2000 machine (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Male C57bl6 mice, 10-12 weeks old, were randomly assigned to Sham and kidney ischemia reperfusion injury (IRI) surgery, kidney cortex were harvested 48 hours after surgery

value: kidney

tag: condition

value: 48h after IRI treated with JQ1

tag: chip-antibody

value: RNA Polymerase II (Abcam, ab5408)

tag: Sex

value: male

value: 10-12 weeks


title: ChIP-seq-IRI-STAT3-rep1

value: 48h after IRI

value: STAT3 (Santa Cruz, sc-482)


title: ChIP-seq-IRI-STAT5-rep2

value: STAT5 (Santa Cruz, sc-835)


title: ChIP-seq-IRI-STAT3-rep2


title: ChIP-seq-IRI-HNF4A-rep2

value: HNF4A (Abcam, ab41898)


title: ChIP-seq-IRI-STAT5-rep1


title: ChIP-seq-SHAM-JQ1-Pol2-rep1

value: Sham treated with JQ1


title: ChIP-seq-IRI-GR-rep2

value: GR (Thermo Scientific, PA1-511A)


title: ChIP-seq-IRI-HNF4A-rep1


title: 4 µM MEHP, 2 hr

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology (KIST)

description: Cell line treated by 4 µM mono-ethylhexyl phthalate for 2 hours

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
Transformed by logarithm and normalization using quantile method.

label: biotin

source_name: HeLa cell line treated with 4 µM mono-ethylhexyl phthalate for 2 hr

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin in humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: After the incubation time, the cells were PBS washed, trypsinized and centrifuged for 5 min at 1,200 rpm. The supernatant was discarded, and the remained cell pellet was resuspended in Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Each compounds (2, 20 and 100 µM) ware treated in the HeLa cells for different time points (2 and 24 hr). Final DMSO concentration was 0.1%.

value: HeLa

tag: agent

value: mono-ethylhexyl phthalate

tag: dose

value: 4 microM

tag: time (hours)


title: 100 µM MEHP, 2 hr

description: Cell line treated by 100 µM mono-ethylhexyl phthalate for 2 hours

source_name: HeLa cell line treated with 100 µM mono-ethylhexyl phthalate for 2 hr

value: 100 microM


title: 20 µM  BPS, 24 hr

description: Cell line treated by 20 µM bisphenol S for 24 hours

source_name: HeLa cell line treated with 20 µM bisphenol S for 24 hr

value: bisphenol S

value: 20 microM


title: 4 µM BPS, 2 hr

description: Cell line treated by 4 µM bisphenol S for 2 hours

source_name: HeLa cell line treated with 4 µM bisphenol S for 2 hr


title: Normal sample

description: non-treated HeLa cell (DMSO)

source_name: non-treated HeLa cell line


title: 100 µM  BPS, 24 hr

description: Cell line treated by 100 µM bisphenol S for 24 hours

source_name: HeLa cell line treated with 100 µM bisphenol S for 24 hr


title: 20 µM MEHP, 2 hr

description: Cell line treated by 20 µM mono-ethylhexyl phthalate for 2 hours

source_name: HeLa cell line treated with 20 µM mono-ethylhexyl phthalate for 2 hr


title: ChIP-seq-IRI-GR-rep1

value: kidney

value: wild-type


title: 100 µM MEHP, 24 hr

description: Cell line treated by 100 µM mono-ethylhexyl phthalate for 24 hours

source_name: HeLa cell line treated with 100 µM mono-ethylhexyl phthalate for 24 hr


title: 20 µM  BPS, 2 hr

description: Cell line treated by 20 µM bisphenol S for 2 hours

source_name: HeLa cell line treated with 20 µM bisphenol S for 2 hr


title: 20 µM MEHP, 24 hr

description: Cell line treated by 20 µM mono-ethylhexyl phthalate for 24 hours

source_name: HeLa cell line treated with 20 µM mono-ethylhexyl phthalate for 24 hr


title: 100 µM  BPS, 2 hr

description: Cell line treated by 100 µM bisphenol S for 2 hours

source_name: HeLa cell line treated with 100 µM bisphenol S for 2 hr


title: 4 µM MEHP, 24 hr

description: Cell line treated by 4 µM mono-ethylhexyl phthalate for 24 hours

source_name: HeLa cell line treated with 4 µM mono-ethylhexyl phthalate for 24 hr


title: ChIP-seq-IRI-Brd3-rep2

value: BRD3 (Bethyl Laboratories, A302-368A)


title: ChIP-seq-IRI-Brd3-rep1

value: male


title: ChIP-seq-IRI-Brd2-rep2

value: BRD2 (Bethyl Laboratories, A302-583A)

value: 10-12 weeks


title: ChIP-seq-IRI-Brd2-rep1

value: 48h after IRI


title: ChIP-seq-SHAM-STAT5-rep2

value: Sham

value: STAT5 (Santa Cruz, sc-835)


title: ChIP-seq-SHAM-STAT3-rep2

value: STAT3 (Santa Cruz, sc-482)


title: ChIP-seq-SHAM-HNF4A-rep2

value: HNF4A (Abcam, ab41898)


title: ChIP-seq-SHAM-STAT3-rep1


title: ChIP-seq-SHAM-HNF4A-rep1


title: 4 µM  BPS, 24 hr

description: Cell line treated by 4 µM bisphenol S for 24 hours

source_name: HeLa cell line treated with 4 µM bisphenol S for 24 hr

value: HeLa


title: PLum-AI cells, biological replicate 1

city: Beirut

first: Wassim

last: Abou-Kheir

address: Bliss St. DTS Bldg.

department: Department of Anatomy, Cell Biology, and Physiological Sciences

country: Lebanon

institute: American University of Beirut

hyb_protocol: The RNA samples were hybridized to the mouse Affymetrix Gene Chip 2.0 ST (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Applied Biosystems™ GeneChip Scanner 3000 (GCS 3000).

data_processing: The data was normalized using print-tip loess normalization and between arrays scale normalization using the LIMMA package (Smyth, G. K., Thorne, N. P., and Wettenhall, J. (2003). Limma: Linear Models for Microarray Data User’s Guide. Software manual available from http://www.bioconductor.org). The microarray data analysis was performed within the R statistical environment. Raw data was normalized using the Robust Multiarray Averaging (RMA) method (Irizarry et al., 2003; doi: 10.1093/biostatistics/4.2.249).

source_name: Androgen‑independent murine prostate cancer cell line

label_protocol: cDNA was synthesized using the QuantiTect Reverse Transcription Kit (Qiagen) according to the manufacturers’ protocol.

growth_protocol: Orthotopic tumors were previously generated from parental Prostate Luminal (PLum) cells under androgen‑dependent (PLum-AD) and androgen‑independent (PLum-AI) conditions in order to establish cellular models of prostate cancer progression (Abou-Kheir et al., 2011; doi: 10.1371/journal.pone.0026112). The tumors were taken and minced into small pieces to obtain PLum-AD and PLum-AI cells. PLum-AD and PLum-AI cells were cultured in the same media, PrEGM, in which the parental PLum cells were cultured and have been shown to select for their growth (Abou-Kheir et al., 2011; doi: 10.1371/journal.pone.0026112).

extract_protocol: PLum‑AD and PLum‑AI cells were grown up to 50–70% in confluency, and then RNeasy Micro Kit (Qiagen) was used to extract total RNA, according to the manufacturers’ protocol.

treatment_protocol: Unlike PLum-AD cells which grew well in serum-free PrEGM medium, PLum-AI cells grew better in 5% fetal bovine serum (FBS)-containing medium. PLum-AD cells were isolated from adenocarcinoma tumors in the presence of androgens, whereas PLum-AI cells were isolated from poorly differentiated sarcomatoid carcinoma in the absence of androgen (Daoud et al., 2016; doi: 10.18632/oncotarget.8436).

tag: tumor type

value: prostate cancer

tag: sample type

value: cell line (cultured in vitro)

tag: tumor stage represented

value: advanced (androgen-independent)


title: PLum-AI cells, biological replicate 2


title: PLum-AD cells, biological replicate 3

source_name: Androgen‑dependent murine prostate cancer cell line

value: primary (androgen-dependent)


title: PLum-AD cells, biological replicate 2


title: PLum-AD cells, biological replicate 1


title: ChIP-seq-SHAM-GR-rep1

tag: strain

tag: genotype

value: GR (Thermo Scientific, PA1-511A)


title: ChIP-seq-SHAM-Brd3-rep1

value: kidney

tag: age


title: ChIP-seq-SHAM-GR-rep2

value: wild-type


title: ChIP-seq-SHAM-Brd2-rep1


title: ChIP-seq-SHAM-Brd3-rep2

value: BRD3 (Bethyl Laboratories, A302-368A)


title: C57BL/6J.Tug1KO_Cast.WT_testes_0

first: Audrey

middle: Renee

last: Watson

state: Colorado

address: 3415 Colorado Avenue

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1127

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 genome using STAR, with the gene annotation obtained from GENCODE (vM16)
Uniquely-mapped reads were counted for genes by featureCounts
Transcripts per million was calculated
Differential expression was evaluated by using R package, DESeq2 and fdrtool.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated files and excel spreadsheet

extract_protocol:
Tissues were harvested immediately after euthanasia, snap frozen in liquid nitrogen and stored at -80˚C. Tissues were subsequently pulverized in liquid nitrogen and homogenized in TRIzol. Embryonic Mouse Fibroblasts (MEF, passage 2) and mouse embryonic stem cells (ESC) were cultured in 10cm dishes in normal conditions (37˚C, 5% CO2) and homogenized directly in Trizol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

value: testes

tag: background

tag: official strain name

value: Tug1_tm1.1Vlcg; CAST/EiJ

value: heterozygote

value: M


title: C57BL/6J.Tug1KO_Cast.WT_testes_2

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1129

tag: tissue


title: C57BL/6J.Tug1KO_Cast.WT_testes_1

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1128


title: C57BL/6J.WT_Cast.WT_testes_0

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1124

value: wild type


title: PLum-AI cells, biological replicate 3


title: Tug1-Rescue_34_G2_Testis

description:
Tug1_Tissues_without_Testes.csv
JR2219

value: Tug1_tm1.1Vlcg; tg(Tug1); CAGs-rtTA3;

value: rescue


title: Tug1-Rescue_88_G3_Testis

description:
Tug1_Tissues_without_Testes.csv
JR2220


title: Tug1-KO_L14-65_Testis

description:
Tug1_Tissues_without_Testes.csv
JR2218

value: Tug1 knockout


title: C57BL/6J.WT_Cast.WT_testes_2

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1126


title: C57BL/6J.WT_Cast.WT_testes_1

description:
Tug1_Testes_AlleleSpecific_Data.xlsx
JR1125


title: Tug1-WT_L15-73_Testis

description:
Tug1_Tissues_without_Testes.csv
JR2217


title: KO-1_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1990


title: WT-L233-65_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1989


title: KO-9_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1988


title: R-8_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1986


title: ko_prostate_1

description:
Tug1_Tissues_Testes.csv
JR1108

value: prostate


title: KO-63_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1985


title: wt_prostate_1

description:
Tug1_Tissues_Testes.csv
JR1110


title: wt_prostate_2

description:
Tug1_Tissues_Testes.csv
JR1111


title: WT-L223-61_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1984


title: ko_prostate_0

description:
Tug1_Tissues_Testes.csv
JR1106


title: wt_eye_0

description:
Tug1_Tissues_Testes.csv
JR1105

value: eye


title: ko_eye_1

description:
Tug1_Tissues_Testes.csv
JR1103


title: ko_eye_2

description:
Tug1_Tissues_Testes.csv
JR1100


title: wt_spleen_0

description:
Tug1_Tissues_Testes.csv
JR1099

value: spleen


title: wt_spleen_2

description:
Tug1_Tissues_Testes.csv
JR1098


title: ko_eye_0

description:
Tug1_Tissues_Testes.csv
JR1102


title: ko_spleen_1

description:
Tug1_Tissues_Testes.csv
JR1097


title: ko_liver_2

description:
Tug1_Tissues_Testes.csv
JR1093

value: liver


title: wt_spleen_1

description:
Tug1_Tissues_Testes.csv
JR1095


title: wt_liver_2

description:
Tug1_Tissues_Testes.csv
JR1092


title: ko_spleen_2

description:
Tug1_Tissues_Testes.csv
JR1094


title: wt_eye_2

description:
Tug1_Tissues_Testes.csv
JR1104


title: ko_spleen_0

description:
Tug1_Tissues_Testes.csv
JR1096


title: WT-L233-47_Testis

description:
Tug1_Tissues_without_Testes.csv
JR1987


title: ko_liver_0

description:
Tug1_Tissues_Testes.csv
JR1090


title: ko_liver_1

description:
Tug1_Tissues_Testes.csv
JR1091


title: wt_prostate_0

description:
Tug1_Tissues_Testes.csv
JR1109


title: ko_heart_1

description:
Tug1_Tissues_Testes.csv
JR1084

value: heart


title: wt_heart_2

description:
Tug1_Tissues_Testes.csv
JR1086


title: wt_heart_0

description:
Tug1_Tissues_Testes.csv
JR1087


title: wt_eye_1

description:
Tug1_Tissues_Testes.csv
JR1101


title: wt_heart_1

description:
Tug1_Tissues_Testes.csv
JR1083


title: ko_heart_0

description:
Tug1_Tissues_Testes.csv
JR1082


title: ko_heart_2

description:
Tug1_Tissues_Testes.csv
JR1085


title: Sample_kidney_IRI48h_JQ1_rep1

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

extract_protocol:
Total RNA was isolated from kidney cortex samples with the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018A), Libraries for next generation sequencing were prepared with TruSeq Stranded RNA LT Kit (Illumina, 15032611).
Libraries for sequencing were prepared using standard Illumina protocols.

value: 48h after IRI treated with JQ1

value: male

value: 10-12 weeks


title: Sample_kidney_IRI48h_JQ1_rep2

value: kidney

value: wild-type


title: Sample_kidney_IRI48h_rep3

value: 48h after IRI


title: Sample_kidney_IRI48h_JQ1_rep3


title: Sample_kidney_IRI48h_rep4


title: Sample_kidney_SHAM_rep4

value: Sham


title: Sample_kidney_IRI48h_rep1


title: Sample_kidney_SHAM_rep3


title: Sample_kidney_SHAM_rep1


title: ChIP-seq-IRI-Pol2-rep1

value: RNA Polymerase II (Abcam, ab5408)


title: ChIP-seq-IRI-Pol2-rep2


title: wt_liver_0

description:
Tug1_Tissues_Testes.csv
JR1088

value: wild type

value: M


title: Sample_kidney_SHAM_rep2


title: ChIP-seq-IRI-H3K4me3-rep1

value: H3K4me3 (Millipore, 17-614)


title: ChIP-seq-IRI-H3K4me3-rep2


title: ChIP-seq-IRI-H3K27ac-rep1

value: H3K27ac (Abcam, ab4729)


title: Sample_kidney_IRI48h_JQ1_rep4


title: wt_liver_1

description:
Tug1_Tissues_Testes.csv
JR1089


title: ChIP-seq-IRI-Brd4-rep1

value: BRD4 (Bethyl Laboratory, A301-985A)


title: ChIP-seq-SHAM-H3K4me3-rep2


title: ChIP-seq-SHAM-Pol2-rep2


title: Sample_kidney_IRI48h_rep2


title: ChIP-seq-SHAM-H3K4me3-rep1


title: ChIP-seq-SHAM-H3K27ac-rep2


title: ChIP-seq-SHAM-Pol2-rep1


title: ChIP-seq-SHAM-Brd4-rep1


title: ChIP-seq-SHAM-Brd4-rep2


title: ChIP-seq-SHAM-H3K27ac-rep1


title: EpiLC_Dppa4KO_EMseq

city: Monterotondo

first: Kristjan

middle: Holm

last: Gretarsson

state: Roma

address: Via Ercole Ramarini, 32

institute: EMBL Rome

description:
H75VKBGXC_8_D4KOc3_Epi_BS_19s003305-1-1_Gretarsson_lane119s003305
H75VKBGXC_7_D4KOc2_Epi_BS_19s003304-1-1_Gretarsson_lane119s003304
EM-seq of Dppa4 KO EpiLC

data_processing:
library strategy: EnzymaticMethyl-seq (EMseq)
Raw fastQ sequences were quality trimmed using Trim Galore
reads aligned to mm10 using Bismark (0.20.0)
Mapped reads were analysed using the Seqmonk software. The genome was binned into tiles containing 50 CpGs and tiles with different DNA methylation status (Logistic regression p<0.05 and binomial p<0.01 with minimal reads of 10 per probe) were identified as differentially methylated regions (DMRs).
Using bins over all refseq promoters (+800bp downstream) and at the 5’ end of LINE1 elements > 5kb (+/- 500bp) differentially methylated promoters (DMPs) and differentially methylated LINE1s (DMLs) were identified (Logistic regression p<0.05 and binomial p<0.01 with minimal reads of 10 per probe).
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx files listing DNA methylation (as percentage) over [1] all DM Line1 for WT, Dppa2 KO and Dppa4 KO in ESC and EpiLC [2] all DM promoters for WT, Dppa2 KO and Dppa4 KO in ESC and EpiLC.

source_name: Epiblast-Like cells

growth_protocol:
3.5e4 naïve ESC per cm2 were seeded on fibronectin coated wells in EpiLC media (NDIFF 227 supplemented with knockout serum replacement (1%) (KSR), Activin-A (20 ng/ml), bFGF (12.5 ng/ml) and penicillin/streptomycin) for 44 hours
2i/L ESC: 2i/L culture media: NDIFF 227 supplemented with PD0325901 (1µM), CHIR99021 (3μM), LIF (1000 U/ml), FBS (1%), and penicillin/streptomycin cultured on gelatin

extract_protocol:
genomic DNA was isolated from cells using the Zymo Microprep DNA kit
To generate high quality base resolution DNA methylation libraries we used the NEBnext EnzymaticMethyl-seq (EMseq) kit following the manufacturers instructions

tag: strain background

value: mixed 129:B6

tag: genotype/variation

tag: cell type

value: Epiblast-Like cells


title: eRGMc1_2iL_day12_GFPlow

data_processing:
Sequence reads were trimmed and quality control checked using cutadapt (v1.15) (cutadapt -g TTGTGGAAAGGACGAAACACCG) and FastQC
Counting and statistical analysis of sgRNA frequency was performed with the Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK, version 0.5.9) tool
The normalized gRNA counts (MAGeCK -count -norm-method total) from the sorted and unsorted control samples were compared using the -test command in MAGeCK. Resulting in a list of enriched genes in the sorting population compared to the unsorted control
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx files, MAGeCK test command output; listing all gene knocked out and their log fold enrichment of corresponding gRNA counts in the GFPlow samples compared to the unsorted control along with statistical analysis (RRA, p value, FDR and gene ranking)

source_name: eRGM line #1 stably infected with Mouse CRISPR Knockout Pooled Library in 2iL for 12 days. FACS of the lowest (1%) GFP expressing cells

growth_protocol: 2i/L ESC: 2i/L culture media: NDIFF 227 supplemented with PD0325901 (1µM), CHIR99021 (3μM), LIF (1000 U/ml), FBS (1%), and penicillin/streptomycin cultured on gelatin

extract_protocol:
Genomic DNA was isolated from isolated populations using the Quick-DNA microprep plus kit (Zymo Research, #D3020) or a DNeasy blood and tissue kit (Qiagen, #69504)
gRNAs from each population were amplified from genomic DNA using custom primers with the P7 flow cell overhangs: 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTACTATTCTTTCCCCTGCACTGT-3’ (8bp Barcode) and P5 overhang: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTTGTGGAAAGGACGAAACACCG-3’ using Q5 Hot Start High-Fidelity polymerase (NEB, #M0494S) for 21-24 cycles. sgRNA amplicons were purified with SPRI beads (Beckman Coulter, #B23318)
PCR with Illumina primers

treatment_protocol: Briefly, eRGM lines #1 and #2 were stably infected with Mouse CRISPR Knockout Pooled Library (Brie, addgene #73633) followed by puromycin selection and transition to hypomethylated state in 2iL for 12 days. GFPlow cells were collected (lowest 1%) by FACS along with unsorted cell population (control)

tag: cell line

value: eRGM line #1

value: Embryonic Stem Cell

tag: culture

value: 2i/L culture media

tag: treatment

value: gRNA library transduced

tag: sorting

value: GFP negative lowest 1%


title: eRGMc2_2iL_day12_unsortedControl

source_name: eRGM line #2 stably infected with Mouse CRISPR Knockout Pooled Library in 2iL for 12 days. Unsorted cell population (control)

value: eRGM line #2

value: Unsorted


title: eRGMc1_2iL_day12_unsortedControl

source_name: eRGM line #1 stably infected with Mouse CRISPR Knockout Pooled Library in 2iL for 12 days. Unsorted cell population (control)


title: ESC_Dppa4KO_EMseq

description:
H75VKBGXC_6_D4KOc3_2i_BS_19s003303-1-1_Gretarsson_lane119s003303
H75VKBGXC_5_D4KOc2_2i_BS_19s003302-1-1_Gretarsson_lane119s003302
EM-seq of Dppa4 KO ESC

source_name: Embryonic Stem Cell

growth_protocol:
2i/L ESC: 2i/L culture media: NDIFF 227 supplemented with PD0325901 (1µM), CHIR99021 (3μM), LIF (1000 U/ml), FBS (1%), and penicillin/streptomycin cultured on gelatin
2i/L ESC: 2i/L culture media: NDIFF 227 supplemented with PD0325901 (1µM), CHIR99021 (3μM), LIF (1000 U/ml), FBS (1%), and penicillin/streptomycin cultured on gelatin


title: eRGMc2_2iL_day12_GFPlow

source_name: eRGM line #2 stably infected with Mouse CRISPR Knockout Pooled Library in 2iL for 12 days. FACS of the lowest (1%) GFP expressing cells


title: ChIP-seq-IRI-H3K27ac-rep2

source_name: Kidney Cortex

value: kidney

tag: condition

value: 48h after IRI

value: wild-type

tag: chip-antibody

tag: Sex

value: male

value: 10-12 weeks


title: EpiLC_Dppa2KO_EMseq

description:
H2H3MBGXC_4_D2KOc2_Epi_BS_19s003301-1-1_Gretarsson_lane119s003301
H2H3MBGXC_3_D2KOc1_Epi_BS_19s003300-1-1_Gretarsson_lane119s003300
EM-seq of Dppa2 KO EpiLC


title: ESC_WT_EMseq

description:
H37W5BGXC_10_CtrlC3_2iL_BS_19s003307-1-1_Gretarsson_lane119s003307
H37W5BGXC_9_CtrlC1_2iL_BS_19s003306-1-1_Gretarsson_lane119s003306
EM-seq of WT ESC

value: Wild Type


title: ESC_Cop1KO_2iL_RNA-seq [Cop1KO_c6_ESC]

description:
processed data file:
Gene expression (RPM) of selected pluripotency genes, DNA methylation regulators and signaling related genes.xlsx

data_processing:
Raw RNAseq reads were quality trimmed using TrimGalore
mapped to the mouse mm10 genome assembly using RNA Star (2.5.2b-0, default parameters except for --outFilterMultimapNmax 1000)
Mapped reads were imported into seqmonk (Primary alignment only, MAPQ > 20). The data was quantified using the RNA-seq quantification pipeline in Seqmonk normalised per reads per million (RPM) or for transcript size and library size (RPKM) after batch Normalisation (ESC and EpiLC seperate)
Differentially expressed genes were determined using DEseq2: p<0.05 and absolute log FC>1
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx file with list of all differentially expressed genes and their expression values from Dppa2 and Dppa4 KO in ESC and EpiLC
Supplementary_files_format_and_content: .xlsx file with list of all DM promoter associated gene expression values (RPKM) in WT, Dppa2 and Dppa4 KO in ESC and EpiLC
Supplementary_files_format_and_content: .xlsx file with gene expression values (RPM) of selected pluripotency, DNA methylation regulation and signalling pathway related genes in SerumLif, t2iL, 2iL, Cop1 KO and Dusp6 KO ESC

extract_protocol:
Total RNA isolated using Rnase easy (Qiagen)
mRNA was enriched using the NEBNext Poly(A) mRNA magnetic isolation module and prepped into stranded libraries using the NEBnext Ultra II directional RNA library prep kit following all manufactures guidelines


title: ESC_Dusp6KO_2iL_RNA-seq [Dusp6KO_c6_ESC]


title: ESC_Cop1KO_2iL_RNA-seq [Cop1KO_c22]


title: ESC_Dppa2KO_EMseq

description:
H2H3MBGXC_2_D2KOc2_2i_BS_19s003299-1-1_Gretarsson_lane119s003299
H2H3MBGXC_1_D2KOc1_2i_BS_19s003298-1-1_Gretarsson_lane119s003298
EM-seq of Dppa2 KO ESC


title: THP1 shA5 rep-2 (m6A-seq)

description: THP1 shA5 rep-2 (m6A-seq)

source_name: human AML cell line

value: ALKBH5 rescue


title: ESC_Dusp6KO_2iL_RNA-seq [Dusp6KO_c4_ESC]


title: ChIP-seq-IRI-Brd4-rep2

value: BRD4 (Bethyl Laboratory, A301-985A)


title: EpiLC_WT_DNMT1KO_RNA-seq

description:
processed data file:
DM Promoters Associated Gene expression RPKM.xlsx

value: mixed 129:B6

value: Tamoxifen (800nM) to induce Dnmt1KO


title: ESC_Dppa2KO_DNMT1KO_2iL_RNA-seq

value: Dppa2 and Dnmt1


title: ESC_WT_DNMT1KO_2iL_RNA-seq

value: Embryonic Stem Cell


title: ESC_WT_SerumL_RNA-seq [WT_SerumLif_r2]


title: EpiLC_Dppa2KO_DNMT1KO_RNA-seq

value: Epiblast-Like cells


title: ESC_WT_SerumL_RNA-seq [WT_SerumLif_r1]


title: EpiLC_Dppa2KO_RNA-seq

description:
processed data file:
DEG_Dppa2-4_ESC-EpiLC.xlsx
DM Promoters Associated Gene expression RPKM.xlsx


title: EpiLC_DKO_RNA-seq

description:
processed data file:
DEG_Dppa2-4_ESC-EpiLC.xlsx

value: Dppa2 and Dppa4


title: EpiLC_Dppa4KO_RNA-seq


title: EpiLC_WT_EMseq

description:
H37W5BGXC_12_CtrlC3_Epi_BS_19s003309-1-1_Gretarsson_lane119s003309
H37W5BGXC_11_CtrlC1_Epi_BS_19s003308-1-1_Gretarsson_lane119s003308
EM-seq of WT EpiLC


title: EpiLC_WT_RNA-seq


title: ESC_WT_2iL_RNA-seq [CtrlC3_2iL_ESC]


title: ESC_Dppa4KO_2iL_RNA-seq


title: ESC_DKO_2iL_RNA-seq


title: ESC_WT_2iL_RNA-seq [CtrlC1_2iL_ESC]

description:
processed data file:
DEG_Dppa2-4_ESC-EpiLC.xlsx
DM Promoters Associated Gene expression RPKM.xlsx
Gene expression (RPM) of selected pluripotency genes, DNA methylation regulators and signaling related genes.xlsx


title: ESC_WT_t2iL_RNA-seq [ControlC1_t2iL_ESC]


title: ESC_WT_t2iL_RNA-seq [ControlC3_t2iL_ESC]


title: ESC_WT_t2iL_RNA-seq [ControlC2_t2iL_ESC]


title: EpiLC_Dppa4KO_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane117Dppa4c4EpiLCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane114Dppa4c3EpiLCDNMT1K4me3

data_processing:
library strategy: Cut&Run
Raw Fastq sequences were quality trimmed with TrimGalore (0.4.3.1)
aligned to the mouse mm10 genome using Bowtie2 (2.3.4.2,) with the following parameteres -I 50 -X 800 --fr -N 0 -L 22 -i 'S,1,1.15' --n-ceil 'L,0,0.15' --dpad 15 --gbar 4  --end-to-end --score-min 'L,-0.6,-0.6'
Mapped sequences were analysed using Seqmonk and reads over genomic regions of interest were quantified, normalised to the largest Datastore and log transformed, giving Tag density values
For Dppa2 Cut and Run peaks were identified using MACS2 (p<1e-5)
Tag density for H3K4me3, H3K27me3 and H3K9me3 in ESC and in EpiLC was calculated over all DM promoters and all DM L1s
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx files with tag denisty values listed from Cut and Run of H3K4me3, H3K27me3 and H3K9me3 in WT, Dppa2KO and Dppa4KO in ESC and in EpiLC over all DM promoters or over all DM L1s

growth_protocol: 3.5e4 naïve ESC per cm2 were seeded on fibronectin coated wells in EpiLC media (NDIFF 227 supplemented with knockout serum replacement (1%) (KSR), Activin-A (20 ng/ml), bFGF (12.5 ng/ml) and penicillin/streptomycin) for 44 hours

extract_protocol:
Cells were immobalised to concavalin beads, permeabilised with digitonin and incubated with antibody. After washing, the cells are incubated with A-Mnase protein which is then activated to digest around the protein bound DNA. DNA-protein complexes diffuse out of the cells and the DNA is eventually collected and size selected with SPRI beads.
5-10ng DNA input for library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645S, NEB)

tag: cnr antibody

value: Anti-H3K4me3 (Diagenode - C15410003-50)


title: ChIP-seq-SHAM-Brd2-rep2

tag: strain

value: Sham

value: BRD2 (Bethyl Laboratories, A302-583A)


title: ESC_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane19Control1ESCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane112Control2ESCDNMT1K4me3


title: EpiLC_Dppa2KO_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane116Dppa2c4EpiLCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane113Dppa2c2EpiLCDNMT1K4me3


title: EpiLC_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane118Control2EpiLCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane115Control1EpiLCDNMT1K4me3


title: ESC_Dppa2KO_2iL_RNA-seq


title: ESC_Dppa4KO_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane18Dppa4c3ESCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane111Dppa4c4ESCDNMT1K4me3


title: EpiLC_WT_Dppa2

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane140EpiLCControl2Dppa2
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane139EpiLCControl1Dppa2

value: Anti-Dppa2 (Millipore Sigma, MAB4356)


title: ESC_Dppa2KO_DNMT1KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane17Dppa2c2ESCDNMT1K4me3
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane110Dppa2c4ESCDNMT1K4me3


title: ESC_WT_Dppa2

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1200ESC0Control20Dppa2
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1190ESC0Control10Dppa2


title: EpiLC_Dppa2KO_K9me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane124EpiLCDppa2c4K9me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane121EpiLCDppa2c2K9me3

value: Anti-H3K9me3 (Abcam 8898)


title: EpiLC_Dppa4KO_K9me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane125EpiLCDppa4c4K9me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane122EpiLCDppa4c3K9me3


title: ESC_WT_K9me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane160ESC0Control20K9me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane130ESC0Control10K9me3


title: EpiLC_WT_K9me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane126EpiLCControl2K9me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane123EpiLCControl1K9me3


title: ESC_Dppa2KO_K9me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane140ESC0Dppa2c40K9me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane110ESC0Dppa2c20K9me3


title: ESC_WT_2iL_RNA-seq [CtrlC2_2iL_ESC]

description:
processed data file:
Gene expression (RPM) of selected pluripotency genes, DNA methylation regulators and signaling related genes.xlsx


title: EpiLC_Dppa4KO_K27me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane131EpiLCDppa4c4K27me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane128EpiLCDppa4c3K27me3

value: Anti-H3K27me3 (Millipore 07-449)


title: ESC_Dppa4KO_K9me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane150ESC0Dppa4c40K9me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane120ESC0Dppa4c30K9me3


title: EpiLC_WT_K27me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane132EpiLCControl2K27me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane129EpiLCControl1K27me3


title: ESC_Dppa4KO_K27me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane180ESC0Dppa4c30K27me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1110ESC0Dppa4c40K27me3


title: ESC_Dppa2KO_K27me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane170ESC0Dppa2c20K27me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1100ESC0Dppa2c40K27me3


title: EpiLC_Dppa2KO_K27me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane130EpiLCDppa2c4K27me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane127EpiLCDppa2c2K27me3


title: ESC_WT_K27me3

description:
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane190ESC0Control10K27me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1120ESC0Control20K27me3


title: EpiLC_WT_K4me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane138EpiLCControl2K4me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane135EpiLCControl1K4me3

value: Anti-H3K4me3 (Active Motif 39060)


title: EpiLC_Dppa2KO_K4me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane136EpiLCDppa2c4K4me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane133EpiLCDppa2c2K4me3


title: ESC_Dppa2KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane11Dppa2c1_ESCK4me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1160ESC0Dppa2c40K4me3


title: ESC_Dppa4KO_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane15Dppa4c3_ESCK4me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1170ESC0Dppa4c40K4me3


title: ChIP-seq-SHAM-STAT5-rep1

value: kidney

tag: genotype

value: wild-type

value: STAT5 (Santa Cruz, sc-835)

value: male

value: 10-12 weeks


title: KLE cells

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

data_processing:
Whole cell RNAs were purified using the mirVana RNA isolation kit. Yield and purity were assessed with an Agilent Model 2100 DNA Analyzer and a Trinean DropSense 16 spectrophotometer
Genomic DNA (gDNA) was purified using the DNeasy kit. Yield and purity were determined using a NanoDrop 2000 spectrophotometer and horizontal gel electrophoresis (1% agarose in 1X TBE)
Transcription profiling was performed starting with 500 ng of total cellular RNA, which was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded total RNA library preparation kit. Sequencing was performed using Illumina HiSeq 4000 genome sequencer using a 150 bp paired-end SBS chemistry.
RNAseq output BAM files were aligned against Build 38 (GRCh38) of the human genome. Genomic variation was annotated with ANNOVAR software. DNA base calling differences between each cell line and the reference genome was then tabulated for each of the cell lines.
Genome_build: hg38
Supplementary_files_format_and_content: TXT format. Annotated genomic variation.  Gene expression data were not used in the manuscript, only somatic mutations.

source_name: Human endometrial cancer

growth_protocol: Optimal growth media for each cell line

extract_protocol:
mirVana RNA kit; QIAGEN gDNA kit
Illumina TruSeq stranded total RNA; Illumina Library Quantifiction Kit; 150bp paired end SBS chemistry on a HiSeq 4000 platform

tag: cancer type

value: Adenocarcinoma

value: KLE


title: ECC-1 cells


title: Ishikawa cells

value: Ishikawa


title: Hec50co cells


title: HeLa cells, TDCPP, 100uM-2hr

data_processing:
FastQC v0.11.7 was used to see the average base quality per cycle. Phred quality score of 20 (99%) or higher was considered as acceptable.
Before entering the analysis, the adapter sequence is removed through the Trimmomatic 0.38 program. Bases less than base quality 3 from the ends of the reads are removed and bases are removed if the window size equals to 4 and mean quality equals to 15 are not satisfied by the sliding window trim technique. After that, trimmed data was generated by removing reads shorter than min length (36 bp).
Pre-processed trimmed reads are mapped to known reference genomes. HISAT2 program (version 2.1.0) was used to process spliced read mapping through Bowtie2 2.3.4.1 aligner. A genomic DNA reference (UCSC hg19) was used to map the cDNA fragments obtained through RNA-seq experiments.
After Read mapping, transcript assembly was performed through the StringTie program, version 1.3.4d. As a result, the expression profile value for each sample was obtained for the known transcript, and the read count and Fragment per Kilobase of transcript per Million mapped reads (FPKM) values were summarized based on the transcript/gene. For the sample’s raw signal, normalized counts calculated as transformed logarithm and normalization using the quantile method.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: xlsx file with indicated normalized counts, FPKM and read counts for each of 7 samples.

source_name: HeLa cell line treated with 100 µM tris(1,3-dichloro-2-propyl)phosphate for 2 hr

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin in humidified atmosphere containing 5% CO2 at 37 0C.

extract_protocol:
After the incubation time, the cells were PBS washed, trypsinized and centrifuged for 5 min at 1,200 rpm. The supernatant was discarded, and the remained cell pellet was resuspended in Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

treatment_protocol: Tris(1,3-dichloro-2-propyl)phosphate (2, 20 and 100 µM) ware treated in the HeLa cells for different time points (2 and 24 hr). Final DMSO concentration was 0.1%.

value: HeLa


title: HeLa cells, TDCPP, 20uM-2hr

source_name: HeLa cell line treated with 20 µM tris(1,3-dichloro-2-propyl)phosphate for 2 hr


title: HeLa cells, TDCPP, 4uM-1day

source_name: HeLa cell line treated with 4 µM tris(1,3-dichloro-2-propyl)phosphate for 24 hr


title: HeLa cells, TDCPP, 4uM-2hr

source_name: HeLa cell line treated with 4 µM tris(1,3-dichloro-2-propyl)phosphate for 2 hr


title: HeLa cells, TDCPP, 20uM-1day

source_name: HeLa cell line treated with 20 µM tris(1,3-dichloro-2-propyl)phosphate for 24 hr


title: HeLa cells, TDCPP, 100uM-1day

source_name: HeLa cell line treated with 100 µM tris(1,3-dichloro-2-propyl)phosphate for 24 hr


title: 24hr_HS_Oligo_None_3

city: Boston

first: Eran

last: Mick

state: MA

address: 185 Cambridge st

institute: Massachusetts General Hospital

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq (v. 2.20.0.422)
Transcript quantification was performed using kallisto (v. 0.44) against Ensembl v. 93 transcript annotations.
Transcript-level abundance estimates were aggregated to the gene level and combined across 2 sequencing runs using tximport (v. 1.10.1) in R.
Genome_build: mm10
Supplementary_files_format_and_content: Gene level counts in each sample obtained as described above and not normalized. Mouse genes are listed by Ensembl gene ID and overexpressed transgenes are listed by name

source_name: C2C12 cells

growth_protocol: C2C12 cells were cultured in T175 flasks in DMEM containing 10mM glucose, 4mM glutamine and no sodium pyruvate. Cells were seeded for experiments in 24-well plates. 1. Myoblast media was supplemented to 10% dialyzed fetal bovine serum when cells were not intended for differentiation. Expression of transgenes (Luciferase control, LbNOX, mitoLbNOX or NDI1) was induced by addition of 300ng/ml doxycycline 24 hours prior to the start of treatment. 2. Myoblast media was supplemented to 20% dialyzed fetal bovine serum when cells were intended for differentiation. Differentiation was induced after cells became confluent by switching to media supplemented to 2% dialyzed horse serum. Cells were considered largely post-mitotic 24 hours after the switch to low serum media. If protein expression was required, the cells were transduced with adenovirus expressing GFP, LbNOX or mitoLbNOX 48 hours after the switch to low serum media. Cells were considered differentiated myotubes 4 days after the switch to low serum media.

extract_protocol:
Cells were lysed in buffer RLT and RNA isolated with the Qiagen RNeasy kit
Smart-seq2; polyA selected

treatment_protocol: Treatments with mitochondrial inhibitors lasted for 10 hours, except chloramphenicol treatment which extended to 48 hours.

value: C2C12 cells

tag: cell state

value: 24hrs in differentiation media

tag: protein expression

value: Oligomycin


title: 24hr_HS_DMSO_None_1

value: DMSO


title: EpiLC_Dppa4KO_K4me3

description:
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane137EpiLCDppa4c4K4me3
HLMTVBGXC_K64_CnR_EpiLC_19s004605-1-1_Gretarsson_lane134EpiLCDppa4c3K4me3

value: mixed 129:B6

value: Epiblast-Like cells


title: HeLa cells, NT

source_name: non-treated HeLa cell line

value: non-treated


title: RL95-2 cells

value: Adenosquamous carcinoma


title: affl2_HS_rep2

city: Emerald Hills

first: Sophie

middle: Jean

last: Walton

address: 346 Lakeview Way

department: Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
Base calls were performed with RTA 1.13.48.0
Conversion to FASTQ with bcl2fastq 1.8.4.
RNA-seq quantification was performed using Kallisto (Bray et al., 2016) with 200 bootstraps in sigle-end mode with average length of 300 bp and standard deviation of 20 bp.
Genome_build: WBcel235
Supplementary_files_format_and_content: Tab-delimited text files with TPM values for each transcript (output from Kallisto quantification)

growth_protocol: For each condition in each replicate we picked 250 L4s onto plates freshly seeded with OP50.

extract_protocol:
Worms were lysed using a motor and pedestal, and RNA was extracted using Qiagen’s RNeasy kit.
RNA integrity was assessed using RNA 6000 Pico Kit for Bioanalyzer (Agilent Technologies #5067-1513) and mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following manufacturer’s instructions. Briefly, mRNA isolated from ~200 ng - 1 μg of total RNA was fragmented to the average size of 200 nt by incubating at 94 °C for 15 min in first strand buffer, cDNA was synthesized using random primers and ProtoScript II Reverse Transcriptase followed by second strand synthesis using NEB Second Strand Synthesis Enzyme Mix. Resulting DNA fragments were end-repaired, dA tailed and ligated to NEBNext hairpin adaptors (NEB #E7335). After ligation, adaptors were converted to the ‘Y’ shape by treating with USER enzyme and DNA fragments were size selected using Agencourt AMPure XP beads (Beckman Coulter #A63880) to generate fragment sizes between 250 and 350 bp. Adaptor-ligated DNA was PCR amplified followed by AMPure XP bead clean up. Libraries were quantified with Qubit dsDNA HS Kit (ThermoFisher Scientific #Q32854) and the size distribution was confirmed with High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies #5067- 4626). Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt to the depth of 20 million reads per sample following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4.

treatment_protocol: To heat shock worms, we covered each plate with parafilm and placed them in a preheated water bath at 33 °C for 30 minutes. For the non heat shock condition, we covered each plate with parafilm and left them at room temperature (20 °C) for 30 minutes.

tag: developmental stage/tissue

value: Whole animal L4 stage

value: heat shock


title: affl2_HS_rep3


title: N2_HS_rep1

value: WT


title: affl2_NoHS_rep1

value: non-heat-shock


title: affl2_HS_rep1


title: N2_HS_rep2


title: affl2_NoHS_rep2


title: N2_HS_rep3


title: affl2_NoHS_rep3


title: N2_NoHS_rep3


title: Tubes_BAM15_None_3

value: Differentiated myotubes


title: N2_NoHS_rep2


title: N2_NoHS_rep1


title: Tubes_Oligo_None_2


title: Tubes_Hyp_Oligo_None_3


title: ESC_WT_K4me3

description:
HY52FBGXC_K65_K4me3_CutRun_19s005118-1-1_Gretarsson_lane16Controlc3_ESCK4me3
HNVF3BGXC_K64_CnR_ESC_19s004604-1-1_Gretarsson_lane1180ESC0Control20K4me3

tag: strain background

value: Wild Type

value: Embryonic Stem Cell

value: Anti-H3K4me3 (Diagenode - C15410003-50)


title: Blasts_DMSO48_Luc_2

value: Proliferating myoblasts

value: Luciferase


title: Blasts_DMSO_NDI1_2

value: C2C12 cells


title: Tubes_Pier_GFP_2

value: GFP

value: Piericidin


title: Blasts_Oligo_Luc_1

value: Oligomycin


title: Tubes_Oligo_None_3


title: Tubes_Hyp_DMSO_None_3


title: Tubes_Oligo_Lb_3

value: LbNOX


title: Tubes_Pier_Lb_1


title: Blasts_Pier_Luc_2


title: 24hr_HS_Pier_None_3

value: 24hrs in differentiation media


title: Tubes_Anti_None_2

value: Antimycin


title: Tubes_Anti_None_1


title: Blasts_Anti_Lb_1


title: Blasts_DMSO48_Lb_1


title: 14-15 daf abi3-5 seeds +1 day on moist blotter rep 1

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

hyb_protocol: 150 ng of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Normalized expression values were calculated from probe level data (CEL file) using the function of Robust Multi-Array expression measure

organism: Arabidopsis thaliana

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix

growth_protocol: 16 hours light, 20 C; 8 hours dark 18 C in a growth chamber

extract_protocol: RNA was extracted following the protocol of Chang et al., (1993), Plant Molecular Biology Reporter, 11, 113-116, and then further cleaned using a Qiagen Plant Rneasy minikit column.

treatment_protocol: Flowers were tagged the day they opened and developing seeds collected 15-16 daf and frozen directly. Another set of seeds were collected at 14-15 daf and placed on moist blotter for one day prior to freezing.

tag: tissue

value: seeds


title: 14-15 daf Ler seeds +1 day on moist blotter rep 2

value: Ler


title: 15-16 daf abi3-5 seeds rep 2

description: 15-16 daf abi3-5 seeds

source_name: 15-16 daf abi3-5 seeds


title: 14-15 daf abi3-5 seeds +1 day on moist blotter rep 3


title: 15-16 daf abi3-5 seeds rep1

description: 15-16 daf abi3-5 seeds


title: S10

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used

Supplementary_files_format_and_content: gene analysis, glm using EdgeR Bioconductor Package

organism: Rattus norvegicus

source_name: thyroarytenoid muscle

extract_protocol:
Muscles were removed, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long Evans

value: muscle

tag: age

value: 8 months

value: WT


title: S12


title: 15-16 daf Ler seeds rep 2

description: 15-16 daf Ler seeds

source_name: 15-16 daf Ler seeds


title: Blasts_Anti_mLb_3

tag: cell line

value: mitoLbNOX


title: Blasts_Anti_Luc_1


title: 14-15 daf abi3-5 seeds +1 day on moist blotter rep 2


title: 15-16 daf Ler seeds rep 1

description: 15-16 daf Ler seeds


title: 14-15 daf Ler seeds +1 day on moist blotter rep 3


title: 15-16 daf abi3-5 seeds rep 3

description: 15-16 daf abi3-5 seeds


title: 14-15 daf Ler seeds +1 day on moist blotter rep1


title: S8


title: Tubes_Pier_None_1

value: Differentiated myotubes


title: S6


title: S3


title: Tubes_Oligo_Lb_2


title: S2


title: Blasts_Pier_NDI1_1

value: Proliferating myoblasts


title: 24hr_HS_DMSO_None_3

value: DMSO


title: S1


title: Blasts_DMSO_mLb_2

value: C2C12 cells


title: Tubes_Pier_GFP_1

value: GFP


title: 15-16 daf Ler seeds rep 3

description: 15-16 daf Ler seeds


title: S11


title: Monosomy_7 16730

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

state: NY

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Alignment: Sequencing reads were aligned against the hg19 ensemble reference transcriptome using the STAR/2.5 aligner
Gene counting: Gene counting for each sample was performed using featureCounts/1.5.3.
Differential gene expression between euploid and aneuploid, euploid and mosaic, and aneuploid and mosaic embryos was calculated using DES-seq2/3.5 (R Bioconductor Package).
Pathway analysis: EnrichR was used to perform pathway enrichment analysis on the 60 most DEGs across all mosaic embryos compared to normal embryos.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized counts from DESeq2

source_name: Blastocyst Cells

growth_protocol: Cryopreserved human embryos which had undergone trophectoderm biopsy followed by PGT-A with NGS which had been donated for research were considered for the study.

extract_protocol:
Amplified complementary DNA from the samples was created using the SMATer v4 Ultra Low Kit with 12 polymerase chain reaction (PCR) cycles (Clontech, cat #634890).
RNA-seq library preparation was performed using the Low Input Library Prep (Clontech, cat #6348900) followed by amplification of the library with 5 PCR cycles.
RNA-seq: Sequencing on the Illumina HiSeq 2500 with 50 nucleotide length paired end reads was then performed.

treatment_protocol: Selected embryos were first thawed using standard protocols (Irving Scientific Vit Kit®-Thaw, Santa Anna, CA), washed three times in 50 uL of phosphate-buffered saline (PBS), and then placed into individual microcentrifuge tubes with 9.5 uL of PBS. Tubes were immediately frozen at -23 degrees Celsius and then transported on ice for processing with RNA-seq.

tag: sample type

value: Monosomy


title: Tubes_Hyp_Oligo_None_2

tag: treatment


title: Tubes_Anti_None_3


title: Tubes_DMSO_None_1


title: Trisomy_7 16732

value: Trisomy


title: Tubes_Pier_None_2

value: Piericidin


title: Trisomy_19 16478


title: Blasts_DMSO48_Luc_1

value: Luciferase


title: Blasts_Anti_Lb_3

value: LbNOX

value: Antimycin


title: Blasts_Pier_mLb_3


title: Trisomy_15 15094


title: Blasts_DMSO_Lb_2


title: Trisomy_15 15092


title: Trisomy_15 15091


title: 24hr_HS_Oligo_None_2

value: 24hrs in differentiation media

value: Oligomycin


title: Trisomy_15 15093


title: Mosaic Trisomy 15 18014

description: Mosaic Trisomy 15

value: Mosaic Trisomy 15


title: Tubes_Pier_None_3


title: Tubes_Oligo_GFP_2


title: Mosaic Partial Trisomy 7pter-p14.3 18002

description: Mosaic Partial Trisomy 7pter-p14.3

value: Mosaic Partial Trisomy 7pter-p14.3


title: Tubes_DMSO_None_2


title: Tubes_DMSO_Lb_3


title: Mosaic Partial Monosomy 9q21.13-qter_2 18016

description: Mosaic Partial Monosomy 9q21.13-qter_2

value: Mosaic Partial Monosomy 9q21.13-qter


title: Mosaic Partial Monosomy 9q21.11-qter_1 18015

description: Mosaic Partial Monosomy 9q21.11-qter_1

value: Mosaic Partial Monosomy 9q21.11-qter


title: Monosomy_7 16726


title: Tubes_Hyp_DMSO_None_2

value: Differentiated myotubes


title: Sample_kidney_SHAM_JQ1_d2_rep4

extract_protocol:
Total RNA was isolated from kidney cortex samples with the PureLink RNA Mini Kit (Thermo Fisher Scientific, 12183018A), Libraries for next generation sequencing were prepared with Kit, TruSeq RNA SMP Prep Kit-v2 (Illumina, RS-122-2001) and sequenced on HiSeq 3000 machine (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Male C57bl/6 mice, 10-12 weeks old, were randomly assigned to vehicle and JQ1 treatment before SHAM surgery, kidney cortex were harvested 48 hours after surgery

tag: agent

value: Sham treated with JQ1

value: wild-type

value: Kidney Cortex


title: Blasts_CAP_Lb_2

value: C2C12 cells

value: Proliferating myoblasts

value: Chloramphenicol


title: Sample_kidney_SHAM_JQ1_d2_rep1


title: Trisomy_7 16477

value: Trisomy


title: Trisomy_19 16791


title: Blasts_Oligo_Lb_3


title: Sample_kidney_SHAM_JQ1_d2_rep3


title: Mosaic Partial Monosomy 1q21.1-qter_1_1 18003

description: Mosaic Partial Monosomy 1q21.1-qter_1_1

value: Mosaic Partial Monosomy 1q21.1-qter


title: Mosaic Partial Monosomy 1q21.2-qter_1_2 11

description: Mosaic Partial Monosomy 1q21.2-qter_1_2

value: Mosaic Partial Monosomy 1q21.2-qter


title: Sample_kidney_SHAM_veh_d2_rep4

value: Sham


title: Blasts_Anti_Luc_3

value: Luciferase

value: Antimycin


title: Blasts_Pier_mLb_1

value: mitoLbNOX

value: Piericidin


title: Mosaic Partial Monosomy 10q23.1-qter 15

description: Mosaic Partial Monosomy 10q23.1-qter

value: Mosaic Partial Monosomy 10q23.1-qter


title: Mosaic Trisomy 19 18018

description: Mosaic Trisomy 19

value: Mosaic Trisomy 19


title: Trisomy_15 15090


title: Blasts_Pier_Lb_3

value: LbNOX


title: Sample_kidney_SHAM_veh_d2_rep2


title: Sample_kidney_SHAM_veh_d2_rep1


title: Blasts_Pier_Lb_1


title: Mosaic Monosomy X 18004

description: Mosaic Monosomy X

value: Mosaic Monosomy X


title: Sample_95B8

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

data_processing:
Tophat was used to align the sequence to the  mouse genome mm10
samtools was used to sort the bam files
samtools was used to convert bam files to sam files
HTSeq was used to count the read number of genes
Filtered out genes with reads count less than 10 in all the samples
DESeq was used to normalize the data and to the Variance Stabilizing Transformation
Genome_build: mm10
Supplementary_files_format_and_content: tex file were generated containing reads count

source_name: blood CD8+ cells

extract_protocol: Rneasy Plus Micro kit following the protocol provided, https://www.qiagen.com/it/resources/resourcedetail?id=59b921cd-b65f-42d5-9a0b-1da673d7c01b&lang=en

tag: cell type

value: blood CD8+ cells

value: 9 weeks after birth

value: KC blood


title: Sample_43B8

value: 4 weeks after birth


title: Mosaic Monosomy 7 13

description: Mosaic Monosomy 7

value: Mosaic Monosomy 7


title: Sample_W3B8

value: 30 weeks after birth

value: WT blood


title: Blasts_DMSO_Luc_2

value: C2C12 cells

value: Proliferating myoblasts

value: DMSO


title: Mosaic Monosomy 4_2 12

description: Mosaic Monosomy 4_2

value: Mosaic Monosomy 4


title: Sample_42B8


title: Sample_kidney_SHAM_JQ1_d2_rep2

value: Sham treated with JQ1

value: wild-type

value: Kidney Cortex


title: Sample_303B8


title: Mosaic Monosomy 4_1 18005

description: Mosaic Monosomy 4_1


title: Sample_302B8


title: Sample_205B8

value: 20 weeks after birth


title: Mosaic Monosomy 19 18017

description: Mosaic Monosomy 19

value: Mosaic Monosomy 19


title: Sample_kidney_SHAM_veh_d2_rep3

value: Sham


title: Tubes_Oligo_Lb_1

value: Differentiated myotubes

value: LbNOX

value: Oligomycin


title: Sample_132B8

value: blood CD8+ cells

value: 13 weeks after birth

value: KC blood


title: Sample_133B8


title: Tubes_DMSO_Lb_2


title: Tubes_Hyp_Oligo_None_1


title: Sample_W3P8

source_name: pancreatic cd8+ cells

value: pancreatic cd8+ cells

value: 30 weeks after birth

value: WT pancreas


title: Mosaic Monosomy 15 18001

description: Mosaic Monosomy 15

value: Mosaic Monosomy 15


title: Sample_95P8

value: 9 weeks after birth

value: KC pancreas


title: Tubes_DMSO_None_3

value: C2C12 cells

value: DMSO


title: Sample_W1P8


title: Tubes_Oligo_Pier_None_1


title: Sample_43P8

value: 4 weeks after birth


title: Monosomy_XO 16145

value: Monosomy


title: 24hr_HS_Pier_None_2

value: 24hrs in differentiation media

value: Piericidin


title: Monosomy_XO 16146


title: Sample_42P8


title: Sample_41P8


title: Monosomy_9 16775


title: Sample_303P8


title: Sample_302P8


title: Sample_205P8

value: 20 weeks after birth


title: Blasts_Oligo_Luc_3

value: Proliferating myoblasts

value: Luciferase

value: Oligomycin


title: Sample_133P8

value: 13 weeks after birth


title: Sample_132P8

value: pancreatic cd8+ cells


title: Sample_131B8

value: blood CD8+ cells

value: KC blood


title: Sample_131P8


title: Blasts_Anti_mLb_2

value: mitoLbNOX

value: Antimycin


title: Monosomy_4 16742


title: Blasts_Pier_Luc_3


title: ko_mef_2

city: Boulder

institute: University of Colorado Boulder

description:
Tug1_Tissues_Testes.csv
JR1259

value: mef

tag: background

tag: official strain name

value: Tug1 knockout

value: M


title: Sample_94P8

value: 9 weeks after birth

value: KC pancreas


title: ko_mef_1

description:
Tug1_Tissues_Testes.csv
JR1258

tag: Sex


title: Mosaic Monosomy 10 14

description: Mosaic Monosomy 10

value: Mosaic Monosomy 10


title: Blasts_Pier_Luc_1

value: C2C12 cells

value: Piericidin


title: Monosomy_19 16729

value: Monosomy


title: ko_mef_0

description:
Tug1_Tissues_Testes.csv
JR1257


title: Monosomy_4 16794


title: wt_mef_2

description:
Tug1_Tissues_Testes.csv
JR1256

value: wild type


title: wt_mef_1

description:
Tug1_Tissues_Testes.csv
JR1255


title: Monosomy_19 16769


title: Monosomy_15 16728


title: 24hr_HS_DMSO_None_2

value: 24hrs in differentiation media

value: DMSO


title: wt_mef_0

description:
Tug1_Tissues_Testes.csv
JR1254


title: Monosomy_9 16754


title: Blasts_DMSO_NDI1_1

value: Proliferating myoblasts


title: Monosomy_15 16614


title: Monosomy_10 16797