title: LGE Gsx2 KO replicate 3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were aligned to mouse genome, mm10, using STAR aligner. Raw reads counts aligned to each genes were measured using FeatureCounts.
Genes within autosome were considered for analysis to avoid a bias from sex chromosome genes from the mixed samples.
Differential gene expression analysis was done using EdgeR.
BigWig files were generated in read-per-million scale in a strand-specific manner, i.e. plus- and minus-bigwig file per sample.
Genome_build: mm10
Supplementary_files_format_and_content: RPM-normalized bigWig files (a pair of files for plus and minus stranded per sample); an excel file containing differential analysis results and RPKM-normalized gene expression level for individual replicates

source_name: Mouse E12.5 LGE

extract_protocol:
Five hundred ng of total RNA was used to isolate polyA RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Samples were further enriched using SMARTer Apollo NGS library prep system (Takara Bio USA).
A dUTP-based stranded library was generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs). The library was indexed and amplified for 9 PCR cycles. Individually indexed libraries were proportionally pooled and sequenced at a depth of 25 million single-end 51bp reads using a HiSeq 1000 sequencer (Illumina, San Diego, CA).

treatment_protocol: E12.5 embryos were collected from Gsx2RA/+ x Gsx2EGFP/+ crosses in ice cold PBS and the LGE and a section of embryonic tail were dissected from each embryo. LGEs were stored in RNAlater (Ambion) and tails were used for genotyping.

value: Lateral ganglionic eminence (LGE)

tag: genotype


title: CSB_F_T24_R3

status: Public on Dec 04 2020

type: SRA

city: Bethesda

first: Susan

middle: T

last: Harbison

state: MD

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

country: USA

institute: National Heart Lung and Blood Institute

description:
ASA0012
Canton-S B, Female, CT24, Replicate 3

library_source: transcriptomic

data_processing:
Quality Control (QC) of FASTQ files were assessed using FastQC toolkit (v0.11.5) using default parameters (http://www.bioinformatics.babraham. ac.uk/projects/fastqc). Paired-end reads were aligned against the Drosophila melanogaster reference genome (dmel.r6.16) (dos Santos et al., 2015) using STAR (v2.5.3a) alignment software with the following parameters “--twopassMode basic --sjdbOverhang 75”(Dobin et al., 2013).We used featureCounts (v1.5.2) to compute gene-level read counts using only uniquely mapped reads with setting “-p -s 2” (paired-end, reverse- stranded) (Liao et al., 2013; Liao et al., 2014). We used the trimmed mean of M-values (TMM) normalization method to normalize raw read counts (Robinson and Oshlack, 2010).
Using the ERCC spike-in reads, we noted a bias in the data according to the date of the sequencing run. We removed this batch effect in our dataset from TMM-normalized reads using the ComBat function in the sva R package (Leek and Storey, 2007).
Genome_build: dmel.r6.16
Supplementary_files_format_and_content: There are two supplemental files. The first file (Circadian RNA-Seq raw read counts.csv) contains the raw read counts per gene for all 144 samples; the second file (Circadian RNA-Seq TMM normalized counts.csv contains the batch-corrected TMM-normalized read counts per gene for all 144 samples. Both files are in a .csv format.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were grown under standard culture (cornmeal-sucrose-agar medium, 25°C, 60-75% relative humidity) and lighting conditions (12-hour light: dark cycle) (LD). Five virgin males and five females of each line were used to set up w1118; Canton-S B and DGRP_892 cultures in an LD incubator. We collected 24-separate-sex vials with 150 virgin males and 150 virgin females in each vial per genotype/replicate.

extract_protocol:
Samples were randomized and extracted in groups of 12. For each RNA sample, 150 heads were placed in Omni-ruptor tubes (Omni International, Kennesaw, GA) with 4 RNase/DNase-free metal beads (Omni International, Kennesaw, GA) and homogenized in 1 ml TRIzol (Thermo Fisher Scientific, Grand Island, NY) using an Omni-bead ruptor with the following settings: Speed, 5.65 m/s; Time, 20 sec; Duration, 30 sec; Cycles, 2. Homogenates were incubated at room temperature for 5 minutes. 200 µl of chloroform (Mallinckrodt Baker, Center Valley, PA) were added to each tube; samples were then mixed by shaking for 15 seconds, incubated at room temperature for 3 minutes, and centrifuged at 4°C, 12,000 x g for 15 minutes. The 500-µl aqueous phase was transferred to new tubes and RNA was further purified using the PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA) with on-column DNase treatment, according to the manufacturer’s instructions. Purified total RNA was eluted in 60 µl of water and stored at -80°C. RNA was quantified by NanoDrop 8000 (Thermo Fisher Scientific, Grand Island, NY) and quality verified by BioAnalyzer 2100 using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA).
First, we added 0.02 µl ERCC Spike-In Control Mix 1 (Life Technologies, Carlsbad, CA) to 1 µg total RNA. Poly(A)-selected stranded mRNA libraries were constructed using Illumina TruSeq Stranded mRNA Sample Prep Kits (Illumina, San Diego, CA) per the manufacturer’s instructions except that PCR amplification was performed for 10 cycles rather than 15 to minimize the risk of over-amplification. Unique barcode adapters were applied to each library; dual indices were used. Libraries were pooled for sequencing and sequenced on multiple lanes of a HiSeq4000 using version 4 chemistry to achieve a minimum of 12 million 76-bp read pairs. Sequences were processed using RTA version 1.18.64 and CASAVA 1.8.2 (Illumina, San Diego, CA).

treatment_protocol: Half of the flies were light-entrained in an incubator with a 12:12 LD cycle for 3 days and the other half was entrained in an incubator with a reverse LD cycle for 3 days. Both groups of flies were then transferred to a common incubator kept in constant darkness (DD). After 3 days in DD, flies were flash-frozen on dry ice every 2 hours starting at circadian time (CT02/CT12). Flies were decapitated on dry ice for RNA extraction. We replicated this procedure three times to produce 144 RNA samples (3 biological replicates, 2 sexes, 2 genotypes and 12 time points).

tag: strain

tag: developmental stage

value: Adult

tag: Sex

value: Female

tag: tissue

value: Head

tag: timepoint

tag: replicate


title: polyArpb9mj261_rep3

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: polyA total RNA

data_processing:
ChIP-seq data mapping was done with BWA. RNA-seq data setes were mapped via STAR.
ChIP peak calling was done with MACS2 and linear enrichment was obtained with MACS2 bdgcmp function.
RNA-seq counting over genes and transposons was done with featureCounts.
Differential analysis of genes was performed via DEseq2 in Rstudio.
Log2 and Z-score transformation of ChIP-seq data was performed via custom scripts in Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: bw: big wigle format contains log2 or Z-score for ChIP-seq libraries per replicate.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: animals were grown at 20C, on HB101 E. coli seeded NGM plates.

extract_protocol:
All RNA samples were collected with Trizol and treated with Dnase I.
for polyA selected total RNA and ChIP-seq libraries, NEB-NEXT Ultra for Illumina was used. For, ribo-zero depleted total RNA libraries, NEB-NEXT Ultra II Directional for Illumina was used. For small-RNA-seq, Illumina TRU-SEQ was ued.

treatment_protocol: For ChIP, extracts were fixed with 1% FA.

value: whole animal

tag: selection/treatment

value: polyA selection


title: LGE Gsx2 KO replicate 2

organism: Mus musculus


title: LGE Gsx2 KO replicate 1


title: polyArpb9mj261_rep2

description: polyA total RNA


title: LGE wild type replicate 4

value: Wild type mice


title: AFX.1

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Reads were quality-trimmed using TrimGalore!, and reads shorter than 15 nt were discarded. Reads were aligned to the mouse reference genome (mm10) using bowtie with parameters "-m1 -v1 --best --strata -X 2000 --trim3 1". Duplicates were removed using Picard tools. Moreover, reads shorter than one nucleosome length were discarded, and an offset of 4 nts was introduced.  Peaks were called with MACS2 and parameters "--nomodel --shift -55 --extsize 110 --broad -g mm --broad-cutoff 0.1".
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peaks

molecule: genomic DNA

source_name: EpiSC (AFX)1 p14

growth_protocol: ES cells were cultured in 2iL, FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX

extract_protocol:
50,000 cells were collected and washed with ice-cold PBS once then lysed in the buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). The nuclear pellets were collected and Tn5 tagmentation were performed with Illumina Nextera kit.  (FC-121-1030)
Library construction were performed with Illumina Nextera kit.  (FC-121-1030)

tag: culture condition

value: EpiSCs  cultured in AFX

tag: cell types

value: EpiSC

tag: passage


title: DGRP_892_F_T22_R2

description:
ASA0013
DGRP_892, Female, CT22, Replicate 2


title: AFX.2


title: CSB_F_T6_R2

description:
ASA0010
Canton-S B, Female, CT06, Replicate 2


title: polyArpb9mj261_rep1

description: polyA total RNA


title: LGE wild type replicate 3


title: DGRP_892_M_T22_R2

description:
ASA0011
DGRP_892, Male, CT22, Replicate 2

value: Male


title: AF.2

source_name: EpiSC(AF) p22

value: EpiSC cultured in AF


title: AF.3


title: polyAwt_rep2

description: polyA total RNA


title: AF.1


title: LGE wild type replicate 1


title: LGE wild type replicate 2


title: LGE Gsx2 KO replicate 4


title: DGRP_892_M_T4_R2

description:
ASA0014
DGRP_892, Male, CT04, Replicate 2


title: polyAwt_rep1

description: polyA total RNA


title: A3XR.3

source_name: FS2 p29

value: FS cells were cultured in A3XR

value: mouse Formative Stem cells


title: AFX.3


title: inputChIPseq_rpb9mj261_rep3

description: ChIP-seq

value: AMA-1 antibody


title: DS4_34pos

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

institute: University of Oxford

data_processing:
Quality and adapter trimming were performed using Trim Galore
were mapped to the human genome assembly hg19 using STAR software
The featureCounts function from the Subread package was used to quantify gene expression levels using standard parameters
Genome_build: hg19
Supplementary_files_format_and_content: txt counts table

organism: Homo sapiens

source_name: DS Human fetal CD34+ cells

extract_protocol:
CD34+ cells from feta liver were selected using magentic beads
SMART-Seq2 protocol

tag: disease state

value: DS

tag: cell type

value: DS primary fetal liver human CD34+


title: DGRP_892_F_T8_R1

description:
ASA0007
DGRP_892, Female, CT08, Replicate 1


title: CSB_M_T16_R2

description:
ASA0009
Canton-S B, Male, CT16, Replicate 2


title: polyAwt_rep3

description: polyA total RNA


title: inputChIPseq_rpb9mj261_rep2

description: ChIP-seq


title: A3XR.1


title: CSB_F_T6_R1

description:
ASA0005
Canton-S B, Female, CT06, Replicate 1


title: DS27_34pos


title: DGRP_892_F_T24_R2

description:
ASA0006
DGRP_892, Female, CT24, Replicate 2


title: A3XR.2


title: 5ar2.3

source_name: FS1 p21


title: DGRP_892_F_T12_R1

description:
ASA0003
DGRP_892, Female, CT12, Replicate 1


title: inputChIPseq_rpb9mj261_rep1

description: ChIP-seq


title: DGRP_892_F_T4_R2

description:
ASA0004
DGRP_892, Female, CT04, Replicate 2


title: NDS35L_34pos

source_name: Normal Human fetal CD34+ cells

value: Normal

value: Normal primary fetal liver human CD34+


title: DS22_34pos


title: NDS36L_34pos

value: Normal primary human CD34+


title: inputChIPseq_wt_rep2

description: ChIP-seq


title: DGRP_892_F_T4_R3

description:
ASA0008
DGRP_892, Female, CT04, Replicate 3

value: Adult

value: Female


title: 5ar2.1


title: CSB_M_T14_R1

description:
ASA0002
Canton-S B, Male, CT14, Replicate 1

value: Head


title: inputChIPseq_wt_rep1

description: ChIP-seq

value: whole animal


title: NDS34L_34pos


title: CSB_M_T18_R3

description:
ASA0001
Canton-S B, Male, CT18, Replicate 3


title: R820W_Male_1_week_EXERCISED 2

city: Raleigh

first: Mary

middle: Anna

last: Carbone

state: NC

address: 112 Derieux Place, Thomas Hall room 3543

department: Biological Sciences

institute: North Carolina State University

data_processing:
We demultiplexed the RNA sequences using the Illumina bcl2fastq program; assessed read quality using the FastQC program and pre-processed reads using Cutadapt to remove residual adapter sequences
Residual ribosomal RNA (rRNA) sequences were removed following alignment of sequencing reads to known rRNA sequences using TopHat
All remaining reads were processed using the CLC Genomics Workbench 11 (https://www.qiagenbioinformatics.com/) which is based on previously published methods
Reads were aligned to the D. melanogaster reference genome release 6.13 (Flybase.org).  Unaligned reads were mapped to the MYBPC3 transcript (NCBI Accession: NM_000256.3).
Genome_build: D. melanogaster reference genome release 6.13 (Flybase.org) and MYBPC3 transcript (NCBI Accession: NM_000256.3).
Supplementary_files_format_and_content: Read counts and differential expression analyses were assessed using the CLC Genomics Workbench 11.

source_name: whole body

growth_protocol: Flies were maintained in vials containing 10 ml cornmeal-molasses-agar medium (cornmeal, 65 g/L; molasses, 45 ml/L; yeast, 13 g/L) under a 12 h light-dark cycle.

extract_protocol:
Total RNA was extracted with QIAzol lysis reagent (Qiagen) and the the Quick-RNA MiniPrep Zymo Research Kit (Zymo Research).  Ribosomal RNA (rRNA) was depleted from 5 ug of total RNA using the Ribo-ZeroTM Gold Kit (Illumina, Inc). Depleted mRNA was fragmented and converted to first-strand cDNA using Superscript III reverse transcriptase (Invitrogen).  Second strand cDNA was synthesized using dUTP instead of dTTP to label the second strand cDNA.
cDNA from each sample was used to produce barcoded cDNA libraries using NEXTflexTM DNA barcodes (Bioo Scientific) with an Illumina TruSeq compatible protocol.  Briefly, each sample was subjected to end-repair (Enzymatics), adenylation of 3’-ends (Enzymatics), and ligation of indexed adapters (Enzymatics and Bioo Scientific). Each enzymatic reaction was purified using 1.8X Agencourt AMPure XP beads (Beckman-Coulter). Size selection of each library was performed using Agencourt AMPure XP beads (Beckman Coulter) to an approximate insert size of 130 bp and a total library size of approximately 250 bp. Second strand cDNA was digested with Uracil-DNA Glycosylase prior to PCR-enrichment to produce directional cDNA libraries.  PCR-enrichment of the purified barcoded DNA was carried out with KAPA HiFi Hot Start Mix (Kapa Biosystems) and NEXTflex Primer Mix (Bioo Scientific).

treatment_protocol: Larvae, females (1-week of age), exercised females (1-week of age), males (1-week of age), exercised males (1-week of age).

tag: sample id

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: driver line

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

tag: gene insertion

value: MyBPC3 (feline)

value: M

tag: age

tag: treatment

value: EXERCISED

tag: barcode

value: CCAACA

tag: lane number

tag: flow cell id


title: AMA1ChIPseq_rpb9mj261_rep3

description: ChIP-seq

tag: tissue


title: R820W_Male_1_week_EXERCISED 1

tag: strain

tag: developmental stage

tag: genotype

tag: Sex

value: CATGGC


title: B_SHAM_01_B06

city: Dresden

first: Vasiliki

last: Tsata

state: Saxony

address: Fetscherstrasse 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

country: Germany

institute: TU Dresden

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Reads were aligned to the zebrafish genome assembly (GRCz10) using GSNAP (2018-05-30; parameters:  --gunzip -A sam -t 14 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-87.ss.GRCz10.iit) with known splice sites from Ensembl (v87) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v87) were used for featureCounts (v1.6.2 parameters: -a EnsemblGene-87.GRCz10.TR.gtf -s 0 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx999.GRCz10.e87.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

organism: Danio rerio

source_name: OPCs

extract_protocol:
Adult fish were terminally anesthetized in 0.1 % w/vol Tricaine (Sigma Aldrich) in E3 solution with 10-5 % v/v methylene blue. The skin and musculature were removed dorsally until the spinal cord was exposed and carefully removed with fine forceps. Extracted tissue was placed on a microscope scale slide (# 474026, Carl Zeiss) and starting from the lesion site, a ~ 0.5 mm piece was cut from the rostral part with a scalpel. For sham control group, a ~ 0.5 mm tissue was dissected at the same area of the spinal cord along the rostral to caudal axis of the fish. 9 spinal cords (~ 0.5 mm pieces) were used per group and placed in 1ml of sterile Hanks’ Buffered Salt Solution (HBSS) (Gibco). Before tissue dissociation, spinal cords were kept constantly on ice to avoid cell degradation. Tissue dissociation, live cell staining and FACS sorting of cells was done with modifications using an unpublished protocol developed by the Brand lab (D. Freudenreich, A. Weber, M. Brand, unpublished, available on request from M.B. and (Lange et al., 2020)). Briefly, excised tissue was dissociated with the Neural Tissue Dissociation Kit (# 130-092-628, Miltenyi) by incubating for 15 min at 37 °C in dissociation buffer. Tissue digestion was stopped by the addition of 30 µL of Papain inhibitor, triturated with 10 strokes of a wide-tipped fire-polished Pasteur pipette and incubated at 37 °C for 10 min. After 2 more trituration steps with 10 strokes of a middle and small-tipped fire-polished Pasteur pipette, respectively, and incubation for 10 min at 37 °C, cell suspension was applied to a 20 µm cell strainer (BD Biosciences), mounted on a 15 ml falcon tube. After washing with 10 ml of sterile HBSS, cell suspension was pelleted by centrifugation at 300g for 10 min at room temperature. The supernatant was discarded and the pellet was re-suspended in 500 μl fresh, sterile HBSS. To stain for viable cells, 1 µl of 2 mM Calcein, AM, cell-permeant dye (C1429, Invitrogen) was added to the cell suspension. Cell suspension was protected from light and incubated for 10 min at room temperature until fluorescence activated cell sorting.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013). Briefly, 30 GFP+ cells from Tg(olig2:eGFP+) fish were FACsorted into single wells of a 96 well plate containing 2 μl of nuclease free water with 0.2 % (v/v) Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at ‑80 °C. After thawing the samples, 2 μl of a primer mix was added. RNA was then denatured for 3 minutes at 72 °C and the reverse transcription was performed at 42 °C for 90 min after filling up to 10 μl with reverse transcription buffer mix. The reverse transcriptase was inactivated at 70 °C for 15 min and the cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 μM UP-primer (UP-primer:AAGCAGTGGTATCAACGCAGAGT ). The amplified cDNA was then purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and DNA was eluted in 12 μl nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium). For library preparation, 700 pg cDNA in 2 μl were mixed with 0.5 μl Tagment DNA Enzyme, 2.5 μl Tagment DNA Buffer (Nextera, Illumina) and tagmented at 55 °C for 5 min. Subsequently, Illumina indices were added during PCR with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.7 μM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads.

treatment_protocol: Adult fish were anaesthetized by immersion in 0.25 % w/vol Tricaine (Sigma-Aldrich) and the spinal cord was transected under visual control 5 mm caudal to the brainstem-spinal cord junction, as previously described (Becker et al., 1997). Sham-lesioned fish were treated equally, except that the spinal cord was left intact.

value: adult

value: spinal cord

value: olig2:eGFP+ OPCs

value: sham control


title: B_SHAM_01_A03


title: 5ar2.2

tag: culture condition

value: FS cells were cultured in A3XR

tag: cell types

value: mouse Formative Stem cells


title: inputChIPseq_wt_rep3

description: ChIP-seq

tag: selection/treatment

value: AMA-1 antibody


title: AMA1ChIPseq_rpb9mj261_rep2

description: ChIP-seq


title: A31P_Male_1_week_EXERCISED 2

value: Adult

value: CACTCA

tag: replicate


title: Control+DON rep2

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

country: China

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample

source_name: gamadelta T cells

growth_protocol: Cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37°C and 5% CO2. Cells were plated in anti-CD3 and anti-CD28 pre-coated high binding plates.

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Mouse splenic gamadelta T cells were stimulated with IL-23 and IL-1β, together with or without DON for 3 days.

value: spleen

tag: agent

value: IL-23+IL1beta+DON stimulated


title: B_SHAM_01_A01

tag: cell type


title: AMA1ChIPseq_rpb9mj261_rep1

description: ChIP-seq

value: whole animal


title: Control rep3

value: IL-23+IL1beta stimulated


title: A31P_Male_1_week_EXERCISED 1

tag: sample id

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: driver line

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

tag: gene insertion

value: MyBPC3 (feline)

value: M

value: CAACTA


title: Control+DON rep1


title: B_SHAM_01_A04

tag: age

value: adult

value: spinal cord

tag: treatment


title: AMA1ChIPseq_wt_rep3

description: ChIP-seq


title: AMA1ChIPseq_wt_rep1

description: ChIP-seq


title: Attp2_Male_1_week_EXERCISED 2

value: Control (no insert)

value: EXERCISED

tag: barcode

value: GTAGAG

tag: lane number

tag: flow cell id


title: B_SHAM_01_A06

tag: tissue

value: olig2:eGFP+ OPCs

value: sham control


title: Control rep2

tag: strain


title: WT_Male_1_week_EXERCISED 2

tag: developmental stage

value: Adult

tag: genotype

value: WT

tag: Sex

value: CGTACG


title: B_SHAM_01_B03


title: AMA1ChIPseq_wt_rep2

description: ChIP-seq

value: whole animal

tag: selection/treatment

value: AMA-1 antibody


title: Control rep1

value: spleen

value: IL-23+IL1beta stimulated


title: WT_Male_1_week_EXERCISED 1

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: MyBPC3 (feline)

value: GTTTCG

tag: replicate


title: B_SHAM_01_A02

value: adult

value: spinal cord


title: Control+DON rep3

tag: agent

value: IL-23+IL1beta+DON stimulated


title: Attp2_Male_1_week_EXERCISED 1

value: Control (no insert)

value: M

value: EXERCISED

value: TTAGGC


title: B_SHAM_01_A05

tag: cell type

value: olig2:eGFP+ OPCs

value: sham control


title: R820W_Female_1_week_EXERCISED 2

tag: sample id

value: Adult

value: F

value: TCGGCA


title: R820W_Female_1_week_EXERCISED 1

tag: driver line

value: TCGAAG


title: B_SHAM_01_B05


title: A31P_Female_1_week_EXERCISED 2

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: gene insertion

value: TCCCGA


title: LINE1-AMO-1

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
Basecalls performed using CASAVA
Hi-C reads are processed using HiCPro version2.7.1b and replicates of same stage were pooled togethe
Compartment analysis are done as previously described. (Dixon et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: Raw Interaction matrix called by  HiCPro.

source_name: Mouse ESCs

growth_protocol: ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using in situ Hi-C developed by Rao et al. with some modification

treatment_protocol: mESCs were transfected by electroporation device, Nucleofector (Amaxa). Scramble AMO and L1 AMO were used at the concentration of 5 nmol/100 μl for ~2.5×106 cells. After transfection, cells were plated in mES media immediately, left to recover for 36 hours, and then harvested for downstream experiments and analysis. AMO tranfected mESCs were purified by FACS to enrich for successfully-nucleofected cells at 12h time-point after transfection.


title: LINE1-AMO-2


title: B_SHAM_01_B04

tag: age


title: A31P_Female_1_week_EXERCISED 1

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: MyBPC3 (feline)

tag: treatment

value: TCATTC


title: WT_Female_1_week_EXERCISED 2

value: WT

tag: barcode

value: ATTCCT


title: WT_Female_1_week_EXERCISED 1

value: ATGAGC

tag: lane number


title: Scramble-2

value: Scramble


title: B_SDPL_01_B10

value: adult

value: spinal cord

value: 7 dpl


title: B_SDPL_01_A11

value: olig2:eGFP+ OPCs


title: B_SDPL_01_A10


title: Crypt-H3K4me1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
Spiked-in ChIP-seq libraries (ChIP-Rx) were aligned to the mouse reference genome mm10 and fly reference dm6 using bowtie v1.1.2 (with parameters -k1 -I 10 -X 1000 --best. PCR duplicates were removed using samblaster. Unambiguous reads mapping to both mm10 and dm6 were discarded. For H3K27me3, H3K4me1, H3K4me3 and H3K9me3 peaks were called using MACS2 v2.1.1 with parameters -f BAMPE–keep-dup all -m 10 30 -p 1e-10. To normalize for differences in sample library size, a scaling factor for each sample was calculated as described in Orlando et al. 2014 and was applied during BigWig file generation with the parameter --scaleFactors from bamCompare (deeptools 3.1) with a bin size of 50. Deeptools 3.1 was also used to produce heatmaps with the functions computeMatrix and plotHeatmap. To create genome-wide scatter plots of ChIP-seq signal, the function multiBigwigSummary from deeptools 3.1 was used to create a matrix of 10kb non-overlapping bins for every sample, using the bigwig files obtained with the procedure explained above.
Genome_build: mm10
Supplementary_files_format_and_content: bed files from MACS2

source_name: intestinal mouse crypt

extract_protocol:
Total cell extracts were prepared in S300 buffer (20 mM Tris pH 8.0, 300 mM NaCl, 10%Glycerol, 0.2% Igepal). After 20 min incubation on ice, following centrifugation (13000 rpm,10 min, 4°C), pellets containing endogenous histones were lyzed in Urea Buffer (25 mM TrispH 6.8, 6 M Urea, 1 mM EDTA, 10% glycerol), sonicated and boiled immediately with SDSLaemmlisample buffer. Cytosolic and nuclear extracts were prepared with Nuclear PrepBuffer (10 mM Tris pH 8.0, 100 mM NaCl, 2 mM MgCl, 300 mM Sucrose, 0.2% Igepal) onice for 5 min. Nuclei were isolated by centrifugation (2500 rpm, 10 min, 4°C). Nuclei werewashed once in Nuclear Prep Buffer, lysed in S300 buffer, incubated on ice for 20 min andcentrifuged for 10 min at 13000 rpm at 4°C. Protease inhibitors were omitted when used forin vitro assays.
250 mg of chromatin supplemented with 5% spike-in of S2 Drosophila chromatin (prepared in thesame manner) and 5 mg of antibodies were used. The next day, chromatin lysates were incubated for 4 hours with protein-G Sepharose beads (GE Healthcare). Beads were washed 3 3 with low-salt buffer (150 mM NaCl, 20 mM Tris-HCl pH 8, 2 mM EDTA, 0.1%SDS, 1% Triton X-100) and 1 3 with high-salt buffer (500 mM NaCl, 20 mM Tris-HCl pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100),and then re-suspended in de-crosslinking solution (0.1 M NaHCO3, 1% SDS). DNA was purified with QIAquick PCR purification kite4 Molecular Cell 77, 840–856.e1–e5, February 20, 2020(QIAGEN) according to manufacturer’s instructions. DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol(Blecher-Gonen et al., 2013) by the IEO genomic facility and sequenced on an Illumina HiSeq 2000.

value: intestinal crypt

tag: antibody


title: Scramble-1


title: B_SDPL_01_A07

tag: tissue


title: B_SDPL_01_B09


title: Villi-H3K9me2

source_name: intestinal mouse villi

value: intestinal villi


title: Villi-H3K4me1


title: B_SDPL_01_A08


title: Attp2_Female_1_week_EXERCISED 2

tag: strain

value: Adult

value: Control (no insert)

value: F

value: EXERCISED

value: ATCACG

tag: flow cell id


title: WT_Larvae_non_exercised 2

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

tag: developmental stage

value: Larvae

value: MyBPC3 (feline)

tag: genotype

value: TAATCG


title: Attp2_Female_1_week_EXERCISED 1

tag: Sex

value: CTTGTA


title: WT_Larvae_non_exercised 1

value: WT

tag: replicate


title: R820W_Larvae_non_exercised 2

value: TATAAT


title: Crypt-H3K27me3


title: Crypt-H3K9me2


title: Crypt-Input


title: R820W_Larvae_non_exercised 1

value: ATTCCT


title: B_SDPL_01_A09

value: adult

value: spinal cord

value: olig2:eGFP+ OPCs

value: 7 dpl


title: B_SDPL_01_A12


title: B_SDPL_01_B11


title: B_SDPL_01_B12


title: E2J EGF 6h 3

type: RNA

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description:
replicate 3
E2J.6h.3

hyb_protocol: Genome wide expression analysis was performed on Illumina Human HT12 v4 BeadArray according to the manufacurers guidelines.

scan_protocol: Ilumina iScan and control software 1.3 10+ was used along with a Bead array reader and bead scan software 3.5.49

data_processing: Data were normilezed using quantile normalization with limma package in R

label: biotin

source_name: E2J EGF 6h 3

growth_protocol: Cells were cultured in RMPI media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. T47D cells transfected with C2GNT1 as described in Dalziel et al (27) were additionally cultured with 500 mg/ml G418

extract_protocol: RNA was isolated from cells using Rneasy Mini Kits from Qiagen. Contaminating DNA was used with a DNase-free kit (Ambion).

treatment_protocol: Cells were starved in RPMI media with 0.1% FCS for 24hours and simulated with EGF 100 μg/ml or not for the times indicated.

tag: cell line

value: breast


title: T47D EGF 6h 3

description:
replicate 3
T47D.6h.3

source_name: T47D EGF 6h 3

label_protocol: Genome wide expression analysis was performed on Illumina Human HT12 v4 BeadArray according to the manufacurers guidelines.


title: E2J EGF 6h 1

description:
replicate 1
E2J.6h.1

source_name: E2J EGF 6h 1


title: Villi-Input

value: intestinal villi


title: T47D EGF 2h 2 rep2

description:
technical replicate
T47D.2h.2_Rpt

source_name: T47D EGF 2h 2 rep2


title: T47D EGF 6h 1

description:
replicate 1
T47D.6h.1

source_name: T47D EGF 6h 1


title: T47D EGF 6h 2

description:
replicate 2
T47D.6h.2

source_name: T47D EGF 6h 2


title: Crypt-H3K4me3

value: intestinal crypt


title: Villi-H3K27me3


title: SDPL.1X_01_D12

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Reads were aligned to the zebrafish genome assembly (GRCz10) using GSNAP (2018-05-30; parameters:  --gunzip -A sam -t 14 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-87.ss.GRCz10.iit) with known splice sites from Ensembl (v87) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v87) were used for featureCounts (v1.6.2 parameters: -a EnsemblGene-87.GRCz10.TR.gtf -s 0 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx1011.GRCz10.e87.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

source_name: OPC

extract_protocol:
Adult fish were terminally anesthetized in 0.1 % w/vol Tricaine (Sigma Aldrich) in E3 solution with 10-5 % v/v methylene blue. The skin and musculature were removed dorsally until the spinal cord was exposed and carefully removed with fine forceps. Extracted tissue was placed on a microscope scale slide (# 474026, Carl Zeiss) and starting from the lesion site, a ~ 0.5 mm piece was cut from the rostral part with a scalpel. For sham control group, a ~ 0.5 mm tissue was dissected at the same area of the spinal cord along the rostral to caudal axis of the fish. 9 spinal cords (~ 0.5 mm pieces) were used per group and placed in 1ml of sterile Hanks’ Buffered Salt Solution (HBSS) (Gibco). Before tissue dissociation, spinal cords were kept constantly on ice to avoid cell degradation. Tissue dissociation, live cell staining and FACS sorting of cells was done with modifications using an unpublished protocol developed by the Brand lab (D. Freudenreich, A. Weber, M. Brand, unpublished, available on request from M.B. and (Lange et al., 2020)). Briefly, excised tissue was dissociated with the Neural Tissue Dissociation Kit (# 130-092-628, Miltenyi) by incubating for 15 min at 37 °C in dissociation buffer. Tissue digestion was stopped by the addition of 30 µL of Papain inhibitor, triturated with 10 strokes of a wide-tipped fire-polished Pasteur pipette and incubated at 37 °C for 10 min. After 2 more trituration steps with 10 strokes of a middle and small-tipped fire-polished Pasteur pipette, respectively, and incubation for 10 min at 37 °C, cell suspension was applied to a 20 µm cell strainer (BD Biosciences), mounted on a 15 ml falcon tube. After washing with 10 ml of sterile HBSS, cell suspension was pelleted by centrifugation at 300g for 10 min at room temperature. The supernatant was discarded and the pellet was re-suspended in 500 μl fresh, sterile HBSS. To stain for viable cells, 1 µl of 2 mM Calcein, AM, cell-permeant dye (C1429, Invitrogen) was added to the cell suspension. Cell suspension was protected from light and incubated for 10 min at room temperature until fluorescence activated cell sorting.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013). Briefly, either cells from Tg(olig2:eGFP+) fish were FACsorted into single wells of a 96 well plate containing 2 μl of nuclease free water with 0.2 % (v/v) Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at ‑80 °C. After thawing the samples, 2 μl of a primer mix was added. RNA was then denatured for 3 minutes at 72 °C and the reverse transcription was performed at 42 °C for 90 min after filling up to 10 μl with reverse transcription buffer mix. The reverse transcriptase was inactivated at 70 °C for 15 min and the cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 μM UP-primer (UP-primer:AAGCAGTGGTATCAACGCAGAGT ). The amplified cDNA was then purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and DNA was eluted in 12 μl nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium). For library preparation, 700 pg cDNA in 2 μl were mixed with 0.5 μl Tagment DNA Enzyme, 2.5 μl Tagment DNA Buffer (Nextera, Illumina) and tagmented at 55 °C for 5 min. Subsequently, Illumina indices were added during PCR with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.7 μM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads.

treatment_protocol: Adult fish were anaesthetized by immersion in 0.25 % w/vol Tricaine (Sigma-Aldrich) and the spinal cord was transected under visual control 5 mm caudal to the brainstem-spinal cord junction, as previously described (Becker et al., 1997) . Sham-lesioned fish were treated equally, except that the spinal cord was left intact.

tag: cell type


title: T47D EGF 2h 3 rep2

description:
technical replicate
T47D.2h.3_Rpt

source_name: T47D EGF 2h 3 rep2


title: Crypt-H3K9me3


title: A31P_Larvae_non_exercised 2

tag: sample id

value: TACAGC


title: Attp2_Larvae_non_exercised 1

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: driver line

value: Control (no insert)


title: T47D EGF 2h 1 rep2

description:
technical replicate
T47D.2h.1_Rpt

source_name: T47D EGF 2h 1 rep2


title: Villi-H3K4me3


title: Attp2_Larvae_non_exercised 2

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: Larvae

tag: gene insertion

value: GCGCTA


title: Villi-H3K9me3


title: A31P_Larvae_non_exercised 1

value: MyBPC3 (feline)

tag: age

value: ATGAGC


title: SDPL.1X_01_H10

tag: treatment


title: T47D EGF 2h 3 rep1

description:
replicate 3
T47D.2h.3

source_name: T47D EGF 2h 3 rep1


title: E2J EGF 2h 3

description:
replicate 3
E2J.2h.3

source_name: E2J EGF 2h 3


title: E2J EGF 6h 2

description:
replicate 2
E2J.6h.2

source_name: E2J EGF 6h 2


title: E2J EGF 2h 2

description:
replicate 2
E2J.2h.2

source_name: E2J EGF 2h 2


title: E2J EGF 2h 1

description:
replicate 1
E2J.2h.1

source_name: E2J EGF 2h 1


title: WT_Male_1_week_non_exercised 2

source_name: whole body

value: Adult

value: WT

value: M

tag: barcode

value: GTGAAA


title: SDPL.1X_01_C11

value: adult

value: spinal cord

value: olig2:eGFP+ OPCs


title: SDPL.1X_01_E11

value: 7 dpl


title: SDPL.1X_01_G10


title: SDPL.1X_01_F10


title: WT_Female_1_week_non_exercised 2

value: F

value: CAAAAG

tag: lane number


title: T47D Not treated 1 rep2

description:
technical replicate
T47D.NT.1_Rpt

source_name: T47D Not treated 1 rep2

value: breast


title: CtrlT_e

city: Huntington

first: Jiang

last: Tian

state: WV

address: 1 John Marshall Dr

department: Biomedical Sciences

institute: Marshall University

data_processing:
Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with  FPKM values and raw genes counts for every gene and every sample

source_name: Mouse Embryonic Fibroblasts(MEF)

growth_protocol: Mouse Embryonic Fibroblasts (MEF) were obtained from American Type Culture Collection and maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 μg/ml streptomycin in 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from cell lysates using miRNeasy Mini Kit (Qiagen Inc., Cat No.: 217004).
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: MEF cells grown on 12-well plates were transfected with CMV-miR-29b or col1a1-miR-29b vector using Lipofectamine 3000 reagent (ThermoFisher Scientific, Cat.No.: L3000008) according to the manufacturer's protocol. Empty pcDNA3 vector transfected cells were used as control. At 6 hours after transfection, MEF cells were treated with TGF-β (R&D systems, Cat.No.: 240-B) for an additional 24h. Cells without TGF-β treatment were used as non-treatment control.

tag: plasmid

value: Control

value: TGF-β


title: T47D EGF 2h 2 rep1

description:
replicate 2
T47D.2h.2

source_name: T47D EGF 2h 2 rep1

tag: tissue


title: CtrlT_c


title: T47D Not treated 3 rep2

description:
technical replicate
T47D.NT.3_Rpt

source_name: T47D Not treated 3 rep2


title: Ctrl_e

description: Ctrl

value: No Treatment


title: WT_Female_1_week_non_exercised 1

tag: strain

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: CTAGCT


title: T47D EGF 2h 1 rep1

description:
replicate 1
T47D.2h.1

source_name: T47D EGF 2h 1 rep1


title: R820W_Male_1_week_non_exercised 2

value: Adult

value: MyBPC3 (feline)

value: GAGTGG

tag: flow cell id


title: R820W_Female_1_week_non_exercised 2

tag: developmental stage

value: CACGAT


title: R820W_Male_1_week_non_exercised 1

tag: genotype

value: M

value: TCGGCA


title: CtrlT_d


title: SDPL.1X_01_E09

value: adult

value: spinal cord

value: olig2:eGFP+ OPCs


title: Ctrl_c

description: Ctrl


title: Δgrr replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Product of the deleted gene: Gallocin response regulator (Grr) a response regulator that activates the transcription of gallocin genes likely after being activated by Ghk
15-3

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11 . Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (NC_013798.1, from NCBI).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g locus_tag -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the WT, 13, 14 and 15 biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Streptococcus gallolyticus UCN34 (NC_013798.1, from NCBI)
Supplementary_files_format_and_content: Output file from DESzq2

organism: Streptococcus gallolyticus UCN34

source_name: Sgg UCN34 Δgrr

growth_protocol: The WT strain and the three regulatory mutants Δgsp, Δghk and Δgrr were inoculated at DO=0,1 in liquid THY (10mL) from fresh agar plates and incubated without agitation at 37°C.

extract_protocol:
At DO(600)=0,5, RNA were extracted with the MP Biomedicals™ FastRNA™ Pro Blue Kit and treated with DNase (Invitrogen™ Ambion™ TURBO DNA-free Kit) to remove residual DNA. DNase was inactivated with the DNase inactivation reagent present in the kit.
rRNA were depleted from 0,5 μg of total RNA using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. Sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit (20020595) following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher).  Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.

tag: deleted gene

value: gallo_rs10350 (grr)


title: SDPL.1X_01_H08

value: 7 dpl


title: WT_Male_1_week_non_exercised 1

value: WT

tag: Sex

value: TCCCGA

tag: replicate


title: SDPL.1X_01_D09

tag: cell type


title: ColT_e

value: TGF-β


title: T47D Not treated 2 rep2

description:
technical replicate
T47D.NT.2_Rpt

source_name: T47D Not treated 2 rep2

tag: cell line

value: breast


title: E2J Not treated 2

description:
replicate 2
E2J.NT.2

source_name: E2J Not treated 2


title: R820W_Female_1_week_non_exercised 1

tag: sample id

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: driver line

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: F

value: CTCAGA


title: Δgrr replicate 2

description:
Product of the deleted gene: Gallocin response regulator (Grr) a response regulator that activates the transcription of gallocin genes likely after being activated by Ghk
15-2


title: E2J Not treated 3

description:
replicate 3
E2J.NT.3

source_name: E2J Not treated 3


title: Attp2_Male_1_week_non_exercised 2

value: Adult

tag: gene insertion

value: Control (no insert)

tag: age

value: CCGTCC


title: T47D Not treated 3 rep1

description:
replicate 3
T47D.NT.3

source_name: T47D Not treated 3 rep1


title: SDPL.1X_01_G08

source_name: OPC

tag: treatment


title: E2J Not treated 1

description:
replicate 1
E2J.NT.1

source_name: E2J Not treated 1


title: ColT_d


title: T47D Not treated 2 rep1

description:
replicate 2
T47D.NT.2

source_name: T47D Not treated 2 rep1


title: SDPL.1X_01_F08


title: Ctrl_d

description: Ctrl

value: Control

value: No Treatment


title: SDPL.1X_01_D10

value: adult

value: spinal cord


title: Attp2_Male_1_week_non_exercised 1

value: M

tag: barcode

value: TCATTC

tag: lane number


title: T47D Not treated 1 rep1

description:
replicate 1
T47D.NT.1

source_name: T47D Not treated 1 rep1

tag: tissue


title: Col_e

tag: plasmid


title: Δghk replicate 3

description:
Product of the deleted gene: Gallocin histidine kinase (Ghk), a putative histidine kinase that likely respond to GSP concentration by activating Grr
14-3

source_name: Sgg UCN34 Δghk

value: gallo_rs10345 (ghk)


title: Attp2_Female_1_week_non_exercised 2

tag: strain

value: GGTAGC

tag: flow cell id


title: Δghk replicate 2

description:
Product of the deleted gene: Gallocin histidine kinase (Ghk), a putative histidine kinase that likely respond to GSP concentration by activating Grr
14-2


title: SDPL.1X_01_G07

tag: genotype

value: olig2:eGFP+ OPCs

value: 7 dpl


title: Col_d


title: Attp2_Female_1_week_non_exercised 1

value: y,w/P[int, y+];Chr2/Chr2;P[attP2, y+]

tag: developmental stage

value: CGGAAT


title: SDPL.1X_01_F07


title: A31P_Male_1_week_non_exercised 2

value: yw; +/+; TinCΔ4-Gal4/TinCΔ4-Gal4

value: MyBPC3 (feline)

tag: Sex

value: GTGGCC


title: Col_c


title: Δgsp replicate 3

description:
Product of the deleted gene: Gallocin stimulating peptide (GSP), a secreted peptide that activates gallocin transcription
13-3

source_name: Sgg UCN34 Δgsp

tag: deleted gene

value: gallo_rs10340 (gsp)


title: A31P_Male_1_week_non_exercised 1

source_name: whole body

value: Adult

value: TCGAAG

tag: replicate


title: CMVT_e

value: TGF-β


title: Δghk replicate 1

description:
Product of the deleted gene: Gallocin histidine kinase (Ghk), a putative histidine kinase that likely respond to GSP concentration by activating Grr
14-1


title: SHAM.1X_01_C03

value: adult

tag: cell type

value: sham control


title: SDPL.1X_01_G11

value: spinal cord


title: CMVT_d


title: A31P_Female_1_week_non_exercised 2

tag: sample id

value: F

value: CACCGG


title: Δgsp replicate 2

description:
Product of the deleted gene: Gallocin stimulating peptide (GSP), a secreted peptide that activates gallocin transcription
13-2


title: Δgrr replicate 1

description:
Product of the deleted gene: Gallocin response regulator (Grr) a response regulator that activates the transcription of gallocin genes likely after being activated by Ghk
15-1

value: gallo_rs10350 (grr)


title: Δgsp replicate 1

description:
Product of the deleted gene: Gallocin stimulating peptide (GSP), a secreted peptide that activates gallocin transcription
13-1


title: ColT_c


title: A31P_Female_1_week_non_exercised 1

tag: driver line

value: CTATAC


title: SDPL.1X_01_B08

value: olig2:eGFP+ OPCs

value: 7 dpl


title: SDPL.1X_01_C12


title: CMVT_c


title: WT replicate 2

source_name: Sgg UCN34


title: WT replicate 1


title: CMV_d

description: CMV

source_name: Mouse Embryonic Fibroblasts(MEF)

value: No Treatment


title: SDPL.1X_01_G12


title: shortRNA_chr_rpb9mj261_rep2

description: nuclear fractionation chromatin

source_name: whole animal

value: whole animal

tag: selection/treatment

value: nuclear fractionation capped RNA-seq


title: WT replicate 3


title: SDPL.1X_01_E12

tag: age


title: CMV_c

description: CMV

tag: treatment


title: SDPL.1X_01_H11


title: SDPL.1X_01_D11


title: CMV_e

description: CMV


title: SDPL.1X_01_E10


title: shortRNA_chr_wt_rep2

description: nuclear fractionation chromatin


title: H358 BRM Knockout 1

city: Chapel Hill

first: Vinh

last: Nguyen

address: 450 West Drive

department: Toxicology

institute: UNC- Chapel Hill

data_processing:
aligned to hg38 with star
transcript counts with salmon
tximport into Rstudio
Differntial expression DEseq2
GSEA
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

growth_protocol: Gibco RPMI+10% FBS

extract_protocol:
Zymo RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BRM/SMARCA2 CRISPR Knockout

tag: cell line


title: H358 BRM Knockout 2


title: shortRNA_chr_wt_rep1

description: nuclear fractionation chromatin


title: shortRNA_NP_rescue_rep2

description: nuclear fractionation nucleoplasmic


title: shortRNA_chr_rescue_rep2

description: nuclear fractionation chromatin


title: FATKO_T1_EP35

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: .tsv / normalized gene expression

source_name: Skin SCC derived primary cell line

extract_protocol:
RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.
Bulk RNA-seq

tag: background

value: Mixed


title: SDPL.1X_01_C10

tag: tissue


title: FATKOTAZKO_T1


title: FATKOTAZKO_T2


title: SDPL.1X_01_F09


title: H358 BRG1 Knockout 3

value: BRG1/SMARCA4 CRISPR Knockout


title: SDPL.1X_01_C09


title: H358 BRG1 Knockout 2


title: EP16-TI-Sox


title: shortRNA_NP_rescue_rep1

description: nuclear fractionation nucleoplasmic


title: H358 BRM Knockout 3


title: EP11-TI-Sox


title: shortRNA_chr_rpb9mj261_rep1

description: nuclear fractionation chromatin


title: shortRNA_NP_rpb9mj261_rep2

description: nuclear fractionation nucleoplasmic


title: H358 BRG1 Knockout 1


title: shortRNA_NP_rpb9mj261_rep1

description: nuclear fractionation nucleoplasmic


title: SDPL.1X_01_C08


title: SDPL.1X_01_H07


title: H358 Parent 2

value: Parental


title: shortRNA_NP_wt_rep2

description: nuclear fractionation nucleoplasmic


title: FATKO_T1_EP36


title: EP36-TI_2


title: H358 Parent 3


title: EP35-TI_1


title: shortRNA_NP_wt_rep1

description: nuclear fractionation nucleoplasmic


title: SDPL.1X_01_E07


title: AdCRE-CTRL-3-Epp

source_name: Lung cancer


title: H358 Parent 1


title: SHAM.1X_01_C05


title: HN8P2 lcWGS

data_processing:
Adaptors sequences were removed with TrimmomaticSE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”
The mouse-contaminated sequence reads were filtered out with bbsplit.sh which belongs to BBMap, with parameters “ambiguous=best ambiguous2=toss maxindel=900000 qtrim=f untrim=f minratio=0.65”
The filtered reads were mapped to human reference genome hg19, with Burrows-Wheeler Alignment Tool, under mem mode.
The read group information of aligned reads was  substituted by picard AddOrReplaceReadGroups and sorted with picard SortSam.
The duplicated reads were marked and excluded with picard MarkDuplicates algorithm.
The chromosomal aberration is quantified by QDNAseq (version 1.22.0), with a size of non-overlapping bin was 30kb, and copy number was quantified under the human reference genome hg19
Genome_build: Grch37/hg19
Supplementary_files_format_and_content: .txt format / quantified copy number by qDNAseq

source_name: Head and Neck SCC

extract_protocol:
DNA extraction from FACS isolated tumor cells was performed using DNA extraction kit (QIAGEN) following manufacturer recommendations.
DNA libraries were created with the KAPA Hyper prep kit (Roche) V2 according to the manufacturer's instructions
Low Coverage Whole Genome Sequencing

tag: tissue origin

value: Head and Neck

tag: cancer type

value: Squamous cell carcinoma

tag: fat1 genotype

value: Mutated


title: L119P2 lcWGS

source_name: Lung SCC

value: Lung


title: ribozerorpb9mj261_rep2

description: ribo-zero total RNA

value: ribo-zero depletion


title: AdCRE-FAT-KO-2-Epp

tag: genotype


title: HN6P2 lcWGS


title: SHAM.1X_01_F04

value: adult

value: spinal cord

value: sham control


title: SDPL.1X_01_C07

value: olig2:eGFP+ OPCs


title: AdCRE-FAT-KO-1-Epp


title: SL14P1 lcWGS

source_name: Skin SCC

value: Skin


title: ribozerowt_rep3

description: ribo-zero total RNA


title: SHAM.1X_01_F03


title: SCS6P2 lcWGS


title: AdCRE-FAT-KO-2-Epm


title: SDPL.1X_01_D07

value: 7 dpl


title: ribozerorpb9mj261_rep3

description: ribo-zero total RNA

value: whole animal


title: ribozerowt_rep2

description: ribo-zero total RNA


title: SHAM.1X_01_G03


title: AdCRE-FAT-KO-1-Epm


title: P1P3 lcWGS


title: S159P2 lcWGS


title: F3E13-14-Epp-Fat1KO_S19


title: AdCRE-CTRL-4-Epp


title: SHAM.1X_01_E03


title: F3E13-14-Epp-Fat1KO_S23


title: SHAM.1X_01_B01


title: ribozerowt_rep1

description: ribo-zero total RNA


title: RNA-seq of Homo sapiens: tumor H9_Tumor

city: Guangzhou

first: Changxi

last: Wang

state: Guangdong

address: No.74, Zhongshan second road

institute: Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2.
Read count for each gene was calculated using Salmon software. Then transcript per million (TPM ) were calculated using Tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Osteosarcoma

extract_protocol:
Sarcoma specimens including tumor, adjacent normal tissues and paired blood samples were obtained from osteosarcoma patients.RNA was extracted using Trizol reagent.
RNA libraries were construncted for sequencing using standard Illumina protocols

value: tumor

tag: gender

value: male

tag: kshv infection

value: positive


title: SDPL.1X_01_F11


title: Fat1KO.EPP.F3E5n12

value: Mixed


title: ribozerorpb9mj261_rep1

description: ribo-zero total RNA


title: SHAM.1X_01_E05


title: FATKO.EPM.F3E3n16


title: RNA-seq of Homo sapiens: tumor H2_Tumor

value: female


title: S142P1 lcWGS

value: Wildtype


title: HN62P1 lcWGS

value: Head and Neck

value: Squamous cell carcinoma


title: iS6FRp18-7

data_processing:
Reads were quality-trimmed with TrimGalore! and the “--paired -q 30” option. Trimmed reads were aligned to the human reference genome hg38 using Tophat2. Gene counts were obtained using featureCounts (ENSEMBL genes).
aligned to the hg38 genome using tophat2 v2.1.0
Genes quantified using Featurecounts v1.5.0 and ensembl release 87
Genome_build: Hg38
Supplementary_files_format_and_content: Gene count matrix

source_name: hFS cells

growth_protocol: hFS cells are cultured in A3X or A3XR medium

extract_protocol:
Cells were lysed in Trizol and total RNAs are prepared by PureLink RNA Mini Kit
NEXTflex Rapid Directional RNA-seq Kit were used

value: hNaive PSC derived hFS cells

tag: culture condition


title: SHAM.1X_01_D05

source_name: OPC


title: F3E13-14-Epm-Fat1KO_S24


title: L6P2 lcWGS

value: Lung


title: RNA-seq of Homo sapiens: normal H2_Normal

value: normal

value: negative


title: SHAM.1X_01_H04

value: adult

value: spinal cord

value: sham control


title: L35P2 lcWGS

source_name: Lung PC

value: Pleomorphic carcinoma

value: Mutated


title: SHAM.1X_01_G06

value: olig2:eGFP+ OPCs


title: L75P1 lcWGS

source_name: Lung ADC

value: Adenocarcinoma


title: L30P2 lcWGS


title: iS6FR_p15-4


title: F3E13-14-Epm-Fat1KO_S20


title: RYFP2-YFPp_Control-R1


title: SHAM.1X_01_F06


title: E54P1 lcWGS


title: RNA-seq of Homo sapiens: normal H9_Normal

value: male


title: iS6FR_p14-3


title: iS6F_p18


title: SHAM.1X_01_G04


title: F3E1122-Control-Epcam

value: Mixed


title: E49P2 lcWGS

source_name: Esophagus ADC

value: Esophagus


title: F3E124-Control-Epcam


title: SHAM.1X_01_F05


title: SHAM.1X_01_E06


title: E48P1 lcWGS

source_name: Esophagus SCC

value: Wildtype


title: iS6F_p14


title: F3E13-14-FatKO-Epm

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “HEADCROP:10 CROP:70 ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60”
ATAC-seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very-sensitive --no-discordant --no-unal --no-mixed –non-deterministic”.
Mitochondrial reads, reads from unmapped or random contigs and reads with a mapping quality less than 20 were removed using samtools.
Duplicate reads were removed by Picard tools.
Peak calling was performed on each individual sample by macs2 (version 2.1.0.20151222) using options “-f BAMPE -g mm -q 0.05 --nomodel --call-summits -B –SPMR”
Genome_build: Grcm38/mm10
Supplementary_files_format_and_content: .txt / quantified peak intensity, .bdg / display of continuous-valued data in track format

extract_protocol:
For ATAC sequencing 100000 sorted cells from different tumor subpopulations were collected in 1mL of PBS supplemented with 3% FBS at 4oC. Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4oC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37oC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.
DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from 200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations


title: F3E13-14-FatKO-Epp


title: iH9FR_p22-12


title: iS6F_p15


title: SDPL.1X_01_H09

value: 7 dpl


title: SHAM.1X_01_C06


title: MCD_MoKCs 7

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

institute: UPMC

data_processing:
RNA-Seq analysis was completed using the Eoulsan pipeline. The STAR index was used to map raw reads to the genome and data normalization was performed with Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file counts

source_name: Kupffer Cells

extract_protocol:
Liver were digested with collagenase D. Kupffer cells subsets were sorted on a BDFACSAria. mRNA were extracted using the QIAGEN micro kit. MRNA were amplified using Smartseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Liver

value: Kupffer Cells

tag: cell subset

value: MoKCs

tag: Sex

value: Female

tag: diet

value: MCD


title: SHAM.1X_01_H05

value: adult

tag: cell type


title: iH9FR_p14-3

value: hNaive PSC derived hFS cells


title: MCD_MoKCs 6


title: SHAM.1X_01_G05

tag: age

value: spinal cord

value: sham control


title: SL14P1

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
The mouse-contaminated sequence regions which are mapped to mouse reference genome mm10 and the reads which are not mapped to human reference genome hg38 were filtered out with bbsplit.sh which belongs to BBMap, with a set of parameters “ambiguous=best ambiguous2=toss maxindel=900000 qtrim=f untrim=f minratio=0.65”.
Paired-end reads were then aligned with Burrows-Wheeler Alignment Tool 15, under aln mode, with human reference genome hg38.
With Picard tools, the reads were sorted and duplicated reads were removed.
The local realignment process were done with The Genome Analysis Toolkit (GATK) and all mate-pair information between each read and its mate pair was verified by picard tools.
Coverage of regions was calculated by Picard CalculateHsMetrics and the regions with a mean coverage at least 10 were used for mutation calling.
The base quality scores of selected regions were recalibrated with GATK and the variants for tumor and normal were called with GATK, HaplotypeCaller function.
To get the somatic mutation, the variants from normal were filtered out from those from tumor by bedtools (Version 2.27.0) intersect.
The somatic variants were annotated by ANNOVAR (v2013Jun21), the program called annotate_variation.pl and table_annovar.pl, using corresponding reference genome.
Genome_build: Grch38/hg38
Supplementary_files_format_and_content: .vcf / Detected somatic variants

extract_protocol:
DNA extraction from FACS isolated tumor cells or from the blood was performed using DNA extraction kit (QIAGEN) following manufacturer recommendations.
Whole-genome DNA libraries were created with the KAPA Hyper prep kit (Roche) V2 according to the manufacturer's instructions
Whole Exome Sequencing

value: Skin

value: Squamous cell carcinoma

value: Mutated


title: iH9F_p22


title: HN8P2

value: Head and Neck


title: SHAM.1X_01_D04

value: olig2:eGFP+ OPCs

tag: treatment


title: MCD_MoKCs 5


title: HN6P2


title: iH9F_p21


title: SCS6P2


title: MCD_MoKCs 4


title: SHAM.1X_01_E04


title: MCD_MoKCs 3


title: iH9F_p14


title: SHAM.1X_01_D06


title: P1P3


title: RYFPIIcar2YFP-Epp

value: Mixed


title: SHAM.1X_01_H03


title: L119P2

value: Lung


title: HNES1FR_p7


title: MCD_MoKCs 2


title: L35P2

value: Pleomorphic carcinoma


title: SHAM.1X_01_G02


title: HNES1FR_p1


title: HN62P1

value: Wildtype


title: MCD_MoKCs 1

value: Liver

value: Kupffer Cells


title: SHAM.1X_01_D01


title: SHAM.1X_01_E02


title: iH9FR_p21-11


title: S142P2


title: MCD_EmKCs 6

value: EmKCs

value: Female


title: HNES1F_p7


title: L6P2


title: SHAM.1X_01_C02

value: adult


title: MCD_EmKCs 5

value: MCD


title: MCD_EmKCs 4


title: HNES1F_p4

value: hNaive PSC derived hFS cells


title: SHAM.1X_01_H01

value: spinal cord

value: sham control


title: L30P2

value: Squamous cell carcinoma


title: MCD_EmKCs 3


title: S159P2

value: Skin

value: Mutated


title: SHAM.1X_01_H02

value: olig2:eGFP+ OPCs


title: L75P1

value: Adenocarcinoma


title: BS_Seq_uvr8_rep2

first: Xuehua

last: Zhong

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: uvr8-6 mutant without UVB treatment.  Duplicate biological replicate 2.

data_processing:
Bisulfite-seq reads were filtered using Trimmomatic and then aligned to the TAIR10 genome using BSMAP. For RNA-seq analysis, reads were filtered with Trimmomatic and then aligned to the TAIR10 genome using HISAT2. The alignments were then filtered with a bash code to keep the uniquely mapped reads. The quantification of gene expression was performed with Cufflinks.
Genome_build: TAIR10
Supplementary_files_format_and_content: methratio output files  were converted to bedGraph via custom awk scripts and bedGraph files were converted to BigWig files via the UCSC "bedGraphToBigWig" executable script

organism: Arabidopsis thaliana

source_name: DNA was isolated from 10 day old seedlings without UV treatment (see above), bisulfite converted, library prepped and sequenced

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) + 1% sucrose throughout treatment.  Treatment began on Day 1 after sowing with 1.5  mE of UV-B (315 nm) and 60 mE white light  and terminated on Day 10 of treatment when the plants were frozen in liquid nitrogen before mRNA or DNA extraction for sequencing.

extract_protocol:
RNA was extracted by PureLink RNA Mini Kit (Cat no. 12183018A. Invitrogen). DNA was extracted via the Qiagen Dneasy DNA extraction kit (catalog # 69104).
RNA-seq libraries were constructed using the illumina TruSeq Stranded mRNA LT kit (ref no15032612) following manufacterers' instructions. For bisulfite-sequencing libraries, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator (Covaris), followed by end-repair, 3’-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit (Illumina). Then bisulﬁte conversion was performed using a Zymo EZ DNA Methyl-ation-Lightning kit (Zymo Research). The bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12-15 cycles using KAPA HiFi HotStart Uracil+ Kit  (KAPA Biosystems), purified with Agencourt beads (NuGen).

tag: ecotype

value: uvr8-6 T-DNA knock-out mutant

value: whole seedling

value: uvr8-6 mutant without UVB treatment.


title: MCD_EmKCs 2

value: Liver


title: MCD_EmKCs 1

value: Kupffer Cells


title: SHAM.1X_01_D03


title: BS_Seq_uvr8_rep1

description: uvr8-6 mutant without UVB treatment. Duplicate biological replicate 1


title: HNES1FR_p4


title: E49P2

value: Esophagus

value: Wildtype


title: Chow_EmKCs 6

value: EmKCs

value: Female

value: Chow


title: BS_Seq_uvr8_pUV

description: uvr8-6 mutant with UVB treatment

source_name: DNA was isolated from 10 day old seedlings with UV treatment (see above), bisulfite converted, library prepped and sequenced

value: uvr8-6 mutant with UVB treatment


title: E54P1

value: Head and Neck


title: SHAM.1X_01_B02

value: adult

value: spinal cord

value: sham control


title: E48P1

value: Squamous cell carcinoma


title: SHAM.1X_01_F02

value: olig2:eGFP+ OPCs


title: BS_Seq_Col_for_uvr8

description: Col-0 without UVB treatment. Control for uvr8-6 mutant.

value: wildtype

value: Col-0 without UVB treatment.


title: FAT1KO_A2

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (hg38/GRCh87) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations GRCh38.87 and normalized to 20 millions of aligned reads.
Genome_build: hg38/GRCh87
Supplementary_files_format_and_content: .tsv / normalized gene expression

extract_protocol:
RNA extraction from cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.
Bulk RNA-seq

tag: sample

value: Cancer cell line

value: FAT1 KO


title: Chow_EmKCs 4

tag: tissue

value: Liver

value: Kupffer Cells


title: BS_Seq_UVR8-FLAG_pUV

description:
UVR8-FLAG transgenic plant with UVB treatment.
UVR8 protein is tagged with 3x FLAG at C-terminus

value: UVR8-OX transgenic line

value: whole seedling


title: SHAM.1X_01_E01


title: Chow_EmKCs 5

value: EmKCs

value: Female


title: HNES1F_p1

value: hNaive PSC derived hFS cells


title: FAT1KO_A21


title: Chow_EmKCs 3

value: Chow


title: A6CTL

value: FAT1 WT


title: BS_Seq_Col_pUV

description: Col-0 with UVB treatment.

value: Col-0 with UVB treatment.


title: SHAM.1X_01_F01

value: adult

value: spinal cord

value: sham control


title: Chow_EmKCs 2


title: SHAM.1X_01_D02

value: olig2:eGFP+ OPCs


title: B38


title: BS_Seq_Col_mUV

description: Col-0 without UVB treatment.

value: wildtype

value: Col-0 without UVB treatment.


title: SARS-CoV-2 GFP P1

status: Public on Dec 03 2020

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

description: Caco-2-N cells infected with P1 virus

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to GRCh38 and SARS2 genome (MN908947) by using Hisat2.1.0 . Then, RPKM values of each virus genes and GFP gene were calculated. To quantify the junction-reads from virus subgenomic RNAs, STAR2.7.5c was used for reads mapping. The junction-reads was defined and quantified as described in Kim, Cell, 2020.
Genome_build: SARS2 (MN908947)
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each RNA-seq samples.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Caco-2-N cells

extract_protocol:
Total RNA was extraced by Trizol reagent.
For strand specific RNA-seq, depletion of ribosomal RNA (rRNA) and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit.

treatment_protocol: Caco-2 cells are infected with P1 or P10 SARS-CoV-2-GFP/delN trVLP.

value: Caco-2 cells stably expressing viral N gene

tag: infection

value: P1 virus

tag: days post infection

value: 3 dpi


title: SARS-CoV-2 GFP P10

description: Caco-2-N cells infected with P10 virus

value: P10 virus


title: Chow_EmKCs 1

value: Liver

value: Kupffer Cells


title: SHAM.1X_01_C01


title: BS_Seq_UVR8-FLAG_mUV

description:
UVR8-FLAG transgenic plant without UVB treatment.
UVR8 protein is tagged with 3x FLAG at C-terminus

value: UVR8-OX transgenic line

value: whole seedling


title: DMSO-1

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: FPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida auris CDC_B8441 genome (GCA_002759435.2)
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candidozyma auris

source_name: candida auris

growth_protocol: C. auris cells of strain BJCA001 were inoculated into YPD and cultured at 35 oC for 24h.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C. auris cells of strain BJCA001 were inoculated into RPMI1640 medium and treated with DMSO and myriocin at 35 oC for 2h.

value: wild type

tag: agent

value: DMSO


title: DMSO-2

tag: genotype


title: DMSO-3


title: Myriocin-2

value: Myriocin


title: shortRNA_chr_rescue_rep1

first: Eric

last: Miska

address: tennis court road

institute: University of Cambridge

description: nuclear fractionation chromatin

data_processing:
ChIP-seq data mapping was done with BWA. RNA-seq data setes were mapped via STAR.
ChIP peak calling was done with MACS2 and linear enrichment was obtained with MACS2 bdgcmp function.
RNA-seq counting over genes and transposons was done with featureCounts.
Differential analysis of genes was performed via DEseq2 in Rstudio.
Log2 and Z-score transformation of ChIP-seq data was performed via custom scripts in Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: bw: big wigle format contains log2 or Z-score for ChIP-seq libraries per replicate.

source_name: whole animal

extract_protocol:
All RNA samples were collected with Trizol and treated with Dnase I.
for polyA selected total RNA and ChIP-seq libraries, NEB-NEXT Ultra for Illumina was used. For, ribo-zero depleted total RNA libraries, NEB-NEXT Ultra II Directional for Illumina was used. For small-RNA-seq, Illumina TRU-SEQ was ued.

value: whole animal

tag: selection/treatment

value: nuclear fractionation capped RNA-seq


title: Myriocin-3


title: Myriocin-1


title: ATAC_MIN6

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

data_processing:
Basecalls performed using CASAVA
All libraries were sequenced on the Illumina NextSeq 500 with 100bp paired-end reads.
After trimmed, reads were mapped by Bowtie2 (v2.2.2) with default parameters (m=1). Then duplicate reads were removed using a Picard MarkDuplicates function. Unique reads were performed peak annotations using a MACS2 (v2.1.120160309) with parameters -g mm --B -extsize 200 -nomodel -q 0.05.
To identify differentially enriched peak regions between WT and Prmt1 null cells, we used a getdifferentialPeaks.pl command from HOMER (v.4.8.2) (Heinz et al., 2010) software.
Genome_build: mm10

source_name: MIN6 cell line

growth_protocol: MIN6 cells were incubated in DMEM containing 25mM glucose, supplemented with 15% FBS.

extract_protocol:
Pancreatic islets were isolated from mice. Islets were then dissociated into single cells by trypsinization. FACS purified eYFP+ cells were used for ATAC-seq
ATAC experiments were performed as previously described (Buenrostro et al., 2015) on MIN6 cells and FACS sorted WT and Prmt1 null  cells. Libraries were purified with AMPure XP beads (Beckman Coulter) to remove contaminating primer dimers. Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit (Agilent technologies).


title: ATAC-YFP-biKO rep2

source_name: Pancreatic islet

value: Pancreatic islet


title: ATAC-YFP-WT rep2

value: wile type


title: ATAC-YFP-WT rep1


title: ATAC-YFP-biKO rep1


title: WT_IFNg_rep2

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Biotin-labeled cDNA (5 - 6 ug) was hybridized to an Affymetrix Clariom S Mouse Genechip Array (ThermoFisher Scientific, P/N 902930).

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Array signals were quantile normalized and transformed into log2 transcript expression values by using the robust multi-array average (RMA) algorithm (Affymetrix Expression Console v1.1).

source_name: BMDM from WT mouse, stimulated with IFN-g

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cDNA by using an Affymetrix Whole Transcript Plus Expression kit (ThermoFisher Scientific, P/N 902281).

growth_protocol: Primary mouse bone marrow-derived macrophages (BMDMs) were generated from the bone marrow of wild type and Irf1-/- mutant mice. Cells were grown for 5–6 days in IMDM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% L929 conditioned media, and 1% penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using TRIzol reagent (P/N 15596026, Thermo Fisher Scientific)

treatment_protocol: BMDMs were seeded in antibiotic-free media at a concentration of 1 x 10E6 cells per 12-well plate and incubated overnight. BMDMs were stimulated with the following cytokines where indicated for 48 h: 25 ng/mL of TNF-α (315-01A, Peprotech), 50 ng/mL of IFN-γ (315-05, Peprotech).


title: H4R3me2a_input DNA rep1

data_processing:
Basecalls performed using CASAVA
Sequenced using Illumina NextSeq500 to generate 100bp paired-end reads. Sequenced reads were performed quality control using cut-adapt (v1.1) (Martin, 2011). Quality control parameters were read quality > 30 (Phred score), read length > 20bp and replicated level < 40%.
After trimmed, reads were mapped by Bowtie2 (v2.2.2) with default parameters (m=1). Then duplicate reads were removed using a Picard MarkDuplicates function. Unique reads were performed peak annotations using a MACS2 (v2.1.120160309) with parameters -g mm --B -extsize 200 -nomodel -q 0.05.
Genome_build: mm10

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
MIN6 cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode). Immunoprecipitation was performed with anti-H4R3me2a (39705, Active Motif) or anti-CTCF (07-729, Merck Millipore) antibody. The 250 to 400bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina NextSeq500 to generate 100bp paired-end reads.

value: pancreatic

tag: chip antibody


title: H4R3me2a_input DNA rep2


title: CTCF_ChIPSeq

value: anti-CTCF (07-729, Merck Millipore)


title: IRF-ko_TNF_IFNg_rep2

source_name: BMDM from Irf-/- mouse, stimulated with TNF-a plus IFN-g

value: Primary mouse bone marrow-derived macrophages


title: WT_TNF_IFNg_rep1

source_name: BMDM from WT mouse, stimulated with TNF-a plus IFN-g


title: IRF-ko_unstimulated_rep1

source_name: BMDM from Irf-/- mouse, unstimulated


title: WT_IFNg_rep1


title: H4R3me2a_ChIPSeq rep1

value: anti-H4R3me2a (39705, Active Motif)


title: WT_unstimulated_rep1

source_name: BMDM from WT mouse, unstimulated


title: Prmt1_biKO_8w_WT rep2

data_processing:
Illumina Casava software used for basecalling.
The FastQC (FastQC v0.11.3) and cut-adapt (v1.1) were used to filter sequencing reads of low quality.
Then reads were mapped to mouse genome build mm10 using TopHat (TopHat v2.0.11) with default parameters. The HTseq (v0.9.1) was used for raw read counts. The DESeq2 (DESeq2 v3.1) was used for selecting differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

extract_protocol:
Pancreatic islets were isolated from mice and used for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: biKO 8 weeks


title: Prmt1_biKO_8w_biKO rep2


title: WT_TNF_rep1

source_name: BMDM from WT mouse, stimulated with TNF-a


title: Prmt1_biKO_8w_biKO rep1


title: Prmt1_biKO_12w_WT rep2

value: biKO 12 weeks


title: Prmt1_biKO_8w_WT rep1


title: H4R3me2a_ChIPSeq rep2


title: WT_TNF_rep2


title: WT_TNF_IFNg_rep2


title: Prmt1_biKO_12w_WT rep1


title: Prmt1_biKO_12w_biKO rep2


title: CTCF_input DNA


title: IRF-ko_TNF_IFNg_rep1


title: IRF-ko_unstimulated_rep2


title: Prmt1_biKO_12w_biKO rep1


title: Prmt1_bKO_12w_WT rep2

value: bKO 12 weeks


title: Prmt1_bKO_12w_bKO rep2


title: Prmt1_bKO_12w_WT rep1


title: Prmt1_bKO_12w_bKO rep1


title: LPO 3

city: Edinburgh

first: Amanda

middle: J.

last: Drake

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

data_processing:
Bam files generated by IonTorrent Suite v5.2.0
Peaks were called using MACS2 v2.1
Differential peaks were identified using DiffBind
Peaks were annotated using Homer v4.8
Genome_build: hg19

source_name: Hepatocyte-like cells

growth_protocol: Human ES cells were differentiated to hepatocyte-like cells, over the course of 17 days, as per the protocol from Wang, et al (2017), Defined and Scalable Generation of Hepatocyte-like Cells from Human Pluripotent Stem Cells

extract_protocol:
DNA was isolated from cells using the Monarch Genomic DNA Purification Kit from New England BioLabs
DNA libraries were prepared for sequencing using standard Illumina protocols
DNA immunoprecipitation sequencing

treatment_protocol: At day 17 of differentiation, when cells had differentiated to mature hepatocyte-like cells, they were treated with a cocktail of lactate (10 mM), pyruvate (1 mM), and octanoate (2 mM) to stimulate intracellular lipid accumulation

value: ES-derived hepatocyte-like cells


title: Control 2


title: Control 3


title: Control 1


title: LPO 1


title: LPO 2


title: IgG


title: Seedlings, rps2a2b-1

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

description: high-throughput profiling of transcriptome in rps2a2b (mutant)

data_processing:
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: read count files were generated using htseq-count program

source_name: 12-day-old seedlings

growth_protocol: All seeds were grown on MS plate (with 1% sucrose) at 22°C under long day condition (LD, 16 hours light, 8 hours dark). 12 day after germination (12DAG), whole seedling were harvested for RNA-seq.

extract_protocol:
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
Strand-specific RNA-Seq libraries generated from Col, atprmt3 and rps2a2b were constructed mRNA-Seq library by dUTP method.

treatment_protocol: The seedlings grown at 22°C under 16 h of light followed by 8 h of darkness

value: rps2a2b (mutant)

value: seedlings


title: Input Control


title: Input LPO


title: Seedlings, col-2

description: high-throughput profiling of transcriptome in Col (wild type)

value: Col (wild type)


title: Seedlings, atprmt3-2

description: high-throughput profiling of transcriptome in atprmt3 (mutant)

value: atprmt3 (mutant)


title: Seedlings, col


title: WT_unstimulated_rep2

value: wild type


title: late S

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

institute: Institut Jean-Pierre Bourgin - INRAE

data_processing:
Preprocessed high quality reads were mapped to C/T-converted TAIR10 genome using bismark default settings (Krueger and Andrews, 2011).
Differentially methylated regions (DMRs) were defined as 100bp bins containing at least 4, 6 or 8 differentially methylated mCGs, mCHGs or mCHHs, respectively, and absolute methylation difference of 0.35. DMRs localizing 200bp of each other were merged.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation values (CG,CHG,CHH)

source_name: cell culture nuclei

growth_protocol: Arabidopsis cultured cells (ecotype Col-0) were grown in 50 mL medium and propagated every 7 days by transferring a 6 mL aliquot to a fresh 50 mL fresh and pre-warmed medium. EdU incorporation was performed in the logarithmic phase of the growth curve, by diluting 25 mL of 7-day cells in an equal volume of fresh, prewarmed medium and grown for 16 h before labeling for 1 h with  a final concentration of 10 μM EdU. Similarly, G1 and G2 nuclei were also sorted from 8-day cultures (Figure S1B) without addition of fresh medium, when cell cycle arrest occurs and the cells enter quiescence.

extract_protocol: Genomic DNA was isolated from sorted nuclei using phenol/chlorophorm and fragmented by Covaris. Library preparation of genomic DNA fragments was performed using the NEXTflex Bisulfite Sequencing kit (Bioo Scientific) and the EZ DNA Methylation-Gold Kit (Zymo) following manufacturer instructions.

tag: sample type

value: cell culture nuclei

tag: cell cycle stage

value: late S


title: mid S

value: mid S


title: G2


title: early S

value: early S


title: G2 - 8days

value: G2 - 8days


title: G1 - 8days

value: G1 - 8days


title: Control-2

city: Quebec City

first: Deepthi

last: Sudarshan

state: Quebec

address: 9 Rue Mc Mahon

country: Canada

institute: Université Laval

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We first log2 transformed and quantile normalized the data before using them for the analyses presented in the paper. All the data were pre-processed using the lumi Bioconductor package

source_name: K562 from ATCC

label_protocol: Standard Illumina label protocol

growth_protocol: RPMI, 10% FBS, 1ug/ml Puromycin

extract_protocol: Total RNA were extracted using Nucleospin RNA II Kit (Takara) , following manufacturer’s instructions

treatment_protocol: No Treatment

value: Insertion of Tag only at the AAVS1 locus by Zinc finger Nuclease, puromycin selection

tag: cell line


title: PHF1-1

description: Replicate 1

value: Insertion of PHF1- 3FLAG, 2HA Tag at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: Control-1

description: Replicate 1


title: EPC-PHF-1

description: Replicate 1

value: Insertion of EPC1-PHF1- 3FLAG, 2HA Tag at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: EPCtrunc-1

description: Replicate 1

value: Insertion of EPC1(1-581) 3FLAG, 2HA Tag at the AAVS1 locus by Zinc finger Nuclease, puromycin selection


title: EPCtrunc-2

description: Replicate 2


title: EPC-PHF-2

description: Replicate 2


title: PHF1-2

description: Replicate 2


title: OAW42-R cells

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: human ovarian carcinoma cell line

hyb_protocol: Labeled and fragmented ss-cDNA (5.5 ug) was hybridized to Affymetrix arrays (Genechip HTA human array)

scan_protocol: GC30007G scanner

data_processing: The data obtained for the whole set of samples were normalized by RMA process (Affymetrix Expression Consol). Probe-set annotation, quantitative expressions of all the transcripts and comparisons between the different groups of samples were analyzed using the Affymetrix software TAC.v3

source_name: OAW42-R cells

label_protocol: Sample RNAs (100 ng) were converted to biotin-labeled single-strand cDNAs using the Affymetrix Genechip WT Plus

growth_protocol: OAW42 and OAW42 R cells were grown in DMEM medium supplemented with 4500 mg/l glucose, 2 mM Glutamax™, 1 mM sodium pyruvate, 10% fetal calf serum, 33 mM sodium bicarbonate (Gibco BRL, Lyon, France) and 20 UI/l recombinant human insulin (NovoRapid (insuline asparte); Novo Norsdisk).

extract_protocol: Total RNA extracted with Trizol following provider protocol

treatment_protocol: Normal growth condition

tag: phenotype

value: resistant to cisplatin


title: NIM_TCDD_RNA-seq_rep3

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

data_processing:
Basecalling was done using Illumina Casava software
Sequencing reads were aligned to GRCh38 genome version using hisat2 version 2.0.4
Samtools (version 1.16) was used for converting, sorting and indexing of BAM-files
FeatureCounts of the subread-2.0.1 package was used for gene level counting of the aligned reads using Homo_sapiens.GRCh38.92.gtf as a reference
R-package edgeR v3.30.3 was used in pairwise comparison to identify differentially expressed genes
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: neural progenitors

growth_protocol: hESCs were cultured on Matrigel-coated (BD Biosciences) 6-well plates (Corning) in mTESRTM1 medium (STEMCELL Technologies), which was changed daily. Cells were maintained at 37oC in 5% CO2 and passaged routinely after 3-4 days. Passaging was carried out manually by detaching the colony pieces and plating onto fresh Matrigel-coated plates. Number of passages were held between 30-55.

extract_protocol:
Total RNA was extracted using Blood/Cultured Cell Total RNA Purification Kit (Favorgen) followed by DNase I (Thermo Scientific) treatment
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep (Illumina) according to the manufacturer’s instructions

treatment_protocol: H9 cells were pre-treated with DMSO or 10 nM TCDD followed by neural  (7 day protocol), mesodermal  (5 day protocol) and endodermal  (5 day protocol) differentiation in the presence of DMSO or 10 nM TCDD using) using STEMdiff™ Neural Induction Medium, STEMdiff™ Mesodermal Induction Medium and STEMdiff™ Definite Endoderm Kit Medium respectively (all from STEMCELL Technologies)

value: hESC H9 derived neural progenitors

value: TCDD


title: OAW42 cells

description: human ovarian carcinoma cell line

source_name: OAW42 cells

value: sensitive to cisplatin


title: NIM_DMSO_RNA-seq_rep2

value: DMSO


title: 22Rv1-CCS1477-2

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
alignment to hg19 with STAR v2.5.2a
Generate count table using featureCounts Version 1.5.0-p3
Differential expression using DESeq2_1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix

growth_protocol: 22Rv1 cells were seeded at equal density, in hormone-deficient media.

extract_protocol:
RNA Seq was prepared according to manufacturesrs instructions ( RNAeasy Mini kit, Qiagen)
RNA-Seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Gold kit (protocol# 15031048 Rev E)

treatment_protocol: After 72-hours, cells were treated with either vehicle control, 100 nM JQ1, or 96 nM CCS1477. After 24-hours, cells were harvested and lysed, and RNA was extracted

value: prostate cancer cell line 22Rv1

value: CBP/p300 inhibition (CCS1477)


title: 22Rv1-JQ1-3

value: BET inhibition (JQ1)


title: 22Rv1-JQ1-2


title: 22Rv1-CCS1477-1


title: 22Rv1-Control-2

value: control


title: NIM_TCDD_RNA-seq_rep2


title: NIM_DMSO_RNA-seq_rep3


title: NIM_DMSO_RNA-seq_rep1


title: 22Rv1-Control-1


title: 22Rv1-JQ1-1


title: MIM_TCDD_RNA-seq_rep3

source_name: mesoderm

value: hESC H9 derived mesoderm


title: NIM_TCDD_RNA-seq_rep1


title: 22Rv1-CCS1477-3


title: MIM_TCDD_RNA-seq_rep1


title: MIM_TCDD_RNA-seq_rep2


title: MIM_DMSO_RNA-seq_rep3


title: G1

value: cell culture nuclei


title: MIM_DMSO_RNA-seq_rep2


title: 22Rv1-Control-3


title: hESC_TCDD_RNA-seq_rep3

source_name: hESC H9

value: human embryonic stem cells


title: MIM_DMSO_RNA-seq_rep1


title: hESC_TCDD_RNA-seq_rep2


title: hESC_TCDD_RNA-seq_rep1


title: hESC_DMSO_RNA-seq_rep3


title: hESC_DMSO_RNA-seq_rep1


title: hESC_DMSO_RNA-seq_rep2


title: EIM_TCDD_RNA-seq_rep3

source_name: endoderm

value: hESC H9 derived endoderm


title: EIM_DMSO_RNA-seq_rep3


title: EIM_TCDD_RNA-seq_rep2


title: EIM_TCDD_RNA-seq_rep1


title: EIM_DMSO_RNA-seq_rep1


title: EIM_DMSO_RNA-seq_rep2


title: NIM_DMSO_ChIP-seq_AHR_rep2

data_processing:
Basecalling was done using Illumina Casava software
Alignment of sequences in fastq files was done using Bowtie 2 version 2.2.3 with following parameters: -k 2 -N 1 --mm -x
Sam files were converted to bam files followed by sorting and indexing using Samtools version: 1.6
deepTools bamcoverage version 2.5.3 was used to create bigwig files using following parameters --normalizeTo1x --ignoreDuplicates --minMappingQuality 40 -bl
Peaks were called using callpeak command of MACS2 version 2.1.0 with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: read coverage in bigwig format
Supplementary_files_format_and_content: peaks in narrowPeak format

extract_protocol:
Prior ChIP cells were treated with DMSO or 100 nM TCDD at 37oC for 1.5 h.1% formaldehyde was used for cross-linking the cells at RT for 10 min. Cross-linking was stopped with glycin at RT for 5 min. Following steps until eluation were performed at 4oC. Cells were washed twice with cold PBS, ~10M cells per sample were harvested by scraping and centrifuged at 1000g for 5 min. For nuclei isolation, pellet was resuspended in 250 µl Nuclei Lysis Buffer 1 (50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.25% Triton X-100, 10 mM KCl) and incubated for 10 min with gentle agitation. Following centrifugation at 1350g for 5 min, pellet was resuspended in 250 µl Nuclei Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min with gentle agitation. Nuclei were centrifuged at 1350g for 5 min and pellet resuspended in 100 µl SDS Lysis buffer (1% SDS, 20 mM EDTA, 50 mM Tris-HCl pH 8.0, Protease inhibitor cocktail). Lysis was performed on ice for 10 min and chromatin was sheared to appropriate length fragments using BioRuptor Plus sonicator (Diagenode) (10 cycles of 30 sec ON/OFF). Lysates were then diluted with 10X ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, Protease inhibitor cocktail) to total volume 1ml and centrifuged at 10000g for 10 min. Supernatant was collected, 1% was frozen for Input control and 500 µl sample was incubated overnight with 8 ug anti-AHR antibody (SA-210). Lysates were incubated for 2 h with Protein G Dynabeads (Thermo Scientific). Beads were washed for 5 min with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), LiCl buffer (0,25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Tube switch was performed in between last two washes to enhance specificity [71]. Chromatin-antibody complexes were eluted from Dynabeads twice with 250 µl of elution buffer (50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS) at 65oC for 15 minutes on a rotator and eluates were combined. NaCl at final concentration of 300 mM was added and tubes were incubated overnight at 65oC. Proteins were digested using 40 µg/ml Proteinase K (Thermo Scientific) at 50oC for 2 h and RNA digested using 20 µg/ml RNase A (Thermo Scientific) at 37oC for 30 min. DNA was purified using FavorPrep™ PCR Clean-UP Kit (Favorgen).
Immunoprecipitated and input DNA was used for library preparation with Ovation Ultralow Library System Kit V2 (NuGen) according to manufacturer’s instructions.

treatment_protocol: hESC H9 cells pre-treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days prior differentiation into endoderm (5 day protocol) or neural progenitors (7 day protocol) using STEMdiff™ Definite Endoderm Kit Medium or STEMdiff™ Neural Induction Medium  (both STEMCELL Technologies)

value: anti-AHR antibody (SA-210)


title: NIM_TCDD_ChIP-seq_AHR_rep1