title: RA

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: 10X single-nuclei

data_processing:
The Cell Ranger pipeline from 10X Genomics was used.
"cellranger mkfastq" was used to demultiplex the raw base call files and create FASTQ files.
"celllranger count" was used to align, filter, and generate count matrices from the FASTQ files.
Genome_build: bTaeGut1_v1.p
Supplementary_files_format_and_content: gzipped tab-delimited text file with columns as genes, rows as cells.

organism: Taeniopygia guttata

source_name: RA

extract_protocol:
Birds were rapidly decapitated and brains were dissected out and placed in ice-cold ACSF (126 mM NaCl; 3 mM KCl; 1.25 mM NaH2PO4; NaHCO3; 10 mM D-(+)- glucose, 2 mM MgSO4; 2 mM CaCl2) bubbled with carbogen gas (95% O2, 5% CO2). Each hemisphere was glued to a specimen tube and sectioned with a VF-200 Compresstome (Precisionary Instruments). Sagittal 200 µM slices were made in ice-cold ACSF. Brain regions were dissected by hand with scissors under a dissecting microscope and then placed in a tube with ACSF over ice. Each tube contained 1-3 samples of a brain region from the same hemisphere of a single individual. When all tissue was collected, excess ACSF was removed from each tube, samples were flash-frozen in liquid nitrogen, and stored at -80 °C. For nuclei extraction, samples were thawed over ice, brain regions were then pooled and dounce-homogenized in 500 µL of ice-cold Lysis Buffer (10 mM Tris-HCL; 10 mM NaCL; 3 mM MgCl2; 0.1% IGEPAL CA-630), samples were transferred to clean 1.5 mL tubes. 900 µL of 1.8 Sucrose Cushion Solution (NUC201-1KT, Sigma, MO, USA) was added to each tube and pipette mixed ten times. In a clean 2 mL tube, 1400 µL of nuclei sample was layered on top of 500 µL Sucrose Cushion Solution without mixing. Samples were centrifuged at 13,000 x g for 45 min at 4 °C. 300 µL Nuclei Suspension Buffer (1% UltraPure BSA (AM2618, Thermo Fisher Scientific, MA, USA) and 0.2 RNase inhibitors (Clontech, #2313A) in PBS) was added to 100 µL supernatant and re-suspended. Samples were then centrifuged at 550 x g for 5 min at 4 °C. All but 50 µL supernatant was discarded and the nuclear pellet was resuspended and filtered through a FLOWMI tip strainer (Bel-Art Products, #H13680-0040, NJ, USA) into a new tube. Nuclei were counted in a 1:20 dilution of nuclei solution in Trypan Blue loaded onto a hemocytometer. Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 according to the manufacturer’s instructions and sequenced using an Illumina NovaSeq 6000 at the North Texas Genome Center at UT Arlington with 28 cycles R1 and 124 cycles R2.
Followed 10X Genomics kit manufacturer guidelines.

treatment_protocol: Birds were housed in normal colony conditions. Tissue was collected midday between 12:00-14:00 when birds were behaving regularly.

value: M


title: Bulk RNA-sequencing of the AP_1974

status: Public on Feb 12 2021

type: SRA

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic

data_processing:
Read alignment: Base calling and demultiplexing was performed with Illumina bcl2fastq version 2.17.1.14. The sequencing data was aligned using STAR version 2.5.2a with default parameters.
Normalization: Counts were subject to variance stabilizing transformation normalization using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bulkRNA_normdata.csv.gz: comma-separated, gzip archived. Content: gene*sample matrix containing the normalized gene expression counts.
Supplementary_files_format_and_content: bulkRNA_metadata.csv.gz: comma-separated, gzip archived. Content: bulkRNA-seq metadata. Columns: tissue, treatment, animal, file.

molecule: total RNA

organism: Mus musculus

source_name: AP

growth_protocol: Animals were single-housed with ad libitum access to 60% HFD (#12492 Research Diets) and tap water in controlled environment (temperature 22 ± 2°C; relative humidity 50 ± 10%; 12-hour light/dark cycle).

extract_protocol:
RNA extraction was performed using the PicoPure RNA Isolation Kit (Applied Biosystems, Foster City, USA) as recommended by manufacturer, including an Ambion DNase treatment (Invitrogen, Carlsbad, USA).
Stranded mRNA libraries were produced using the TruSeq Stranded mRNA Kit (Illumina, San Diego, USA), followed by sequencing of single-end, 75 base pair reads on an Illumina NextSeq 500 platform.

treatment_protocol: Amimals were dosed with liraglutide once daily, subcutaneous, for seven days. Dosing of the animals was gradually up-titrated (0.2, 0.4, 1.0 mg/kg). Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.

tag: strain

tag: Sex

value: male

tag: age

value: 31 weeks

tag: number of mice

tag: tissue

value: AP


title: Myotube_NGT_23a

type: genomic

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturer’s recommendations. Myoblasts and myotubes from one subject were always analyzed on the same chip and the samples from controls and individuals with type 2 diabetes were evenly distributed on the chips to reduce batch effects.

data_processing: The raw methylation score for each probe represented as methylation β-values was calculated using GenomeStudio Methylation module software. All included samples showed a high quality bisulfite conversion efficiency (signal intensity > 4000) and also passed all GenomeStudio quality control steps based on built in control probes for staining, hybridization, extension and specificity. Before further analysis, the DNA methylation data was exported from GenomeStudio and subsequently analyzed using Bioconductor and the lumi package. β-values were converted to M-values. Next, data were background corrected by subtracting the median M-value of the 600 built in negative controls and was further normalized using quantile normalization. Data were further processed using BMIQ to correct for probe type and COMBAT for batch correction. As a result, 5,365 probes with a mean detection p-value >0.01, 65 rs-probes, 86 Y-chromosome probes, 2,835 ch-probes targeting non-CpG sites, 13,731 probes based on at least 49 cross reactivity 5 and 5,020 probes with a MAF >0.1 were excluded.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Myotube, NGT

growth_protocol: Muscle stem cells were isolated from human vastus lateralis muscle biopsies (n=14 individuals with type 2 diabetes [T2D], and n=14 control individuals with normal glucose tolerance [NGT]). Isolated myoblasts were cultured in growth medium (HAM’s/F10 supplemented with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% Amphotericin B) until 70% confluent. To induce differentiation, cells were incubated in differentiation medium 1 (DMEM with 1.0 g/l L glucose supplemented with 10% FBS and 1% penicillin/streptomycin) for 2 days, followed by differentiation medium 2 (DMEM with 4.5 g/l L glucose supplemented with 2% horse serum and 1% penicillin/streptomycin) until cells were fully differentiated, as determined by visual confirmation of myotube formation (>3 nuclei per myotube in approximately 70% of cells) on day 7. Cells were harvested both as proliferating myoblasts (<50% confluent) and as differentiated myotubes.

extract_protocol: DNA was extracted by using DNeasy Blood and Tissue kit (Qiagen #69504, Hilden, Germany). Quantity and purity of DNA were determined using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: diabetes status

value: Normal glucose tolerance (NGT)


title: HVC_2

country: USA

description: 10X single-nuclei

source_name: HVC


title: Myotube_NGT_24a

scan_protocol: According to the manufacturer’s recommendations.


title: Bulk RNA-sequencing of the AP_1966


title: Bulk RNA-sequencing of the AP_1970


title: Myoblast_NGT_18a

source_name: Myoblast, NGT

label_protocol: According to the manufacturer’s recommendations.


title: HVC_1

description: 10X single-nuclei


title: Myotube_NGT_18a


title: Myotube_NGT_21a


title: Myoblast_NGT_13a


title: Myoblast_NGT_21a


title: Myotube_NGT_13a


title: Myoblast_NGT_14a


title: Bulk RNA-sequencing of the AP_1962


title: Myoblast_NGT_24a


title: Myoblast_NGT_23a


title: Myotube_NGT_115a


title: Bulk RNA-sequencing of the AP_1934

treatment_protocol: Amimals were dosed with saline once daily, subcutaneous, for seven days and weight-matched to the semaglutide-administered group. Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.


title: Bulk RNA-sequencing of the NTS_1991

source_name: NTS

treatment_protocol: Amimals were dosed with saline once daily, subcutaneous, for seven days. Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.

value: NTS


title: Myoblast_T2D_119a

source_name: Myoblast, T2D

value: Type 2 diabetes (T2D)


title: ER-RAS Induced + shXPO7_5 D5shX5A

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava version 1.8.4 was used for basecalling.
RNA-seq reads were aligned to human genome hg19 (GRCh37) using TopHat2 version 2.0.11
Gene annotation information from Ensembl GRCh37 were employed
Rsubread featureCounts version 1.18.0 was used to generate gene-based read counts matrix
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing gene-based read counts matrix

source_name: ER-RAS Induced + shXPO7_5 D5shX5

growth_protocol: IRM90 ER:RAS were grown in DMEM 10% FBS for 7 days. Media was changed at Day 4

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit, following the instructions.
Libraries were prepared according to Illumina's kit instructions (mRNA stranded library prep kit)

treatment_protocol: To induce RAS expression, cells were treated with 4OHT [100nM]

tag: cell line

value: IMR90 ER:RAS

tag: passage

tag: days after 4oht induction


title: Bulk RNA-sequencing of the AP_1954


title: ER-RAS Induced + shXPO7_5 D5shX5T


title: Bulk RNA-sequencing of the AP_1950


title: ER-RAS Induced + shXPO7_3 D5shX3B

source_name: ER-RAS Induced + shXPO7_3 D5shX3


title: ER-RAS Induced + shXPO7_5 D5shX5B


title: Myoblast_NGT_112a


title: Myotube_NGT_112a


title: Bulk RNA-sequencing of the AP_1944


title: ER-RAS Induced + shXPO7_3 D5shX3A


title: peripheral blood C019

city: Ribeirão Preto

first: Carla

middle: Barbosa

last: Nonino

state: São Paulo

address: Bandeirantes Avenue, 3900

department: Health Sciences Department

country: Brazil

institute: University of São Paulo

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation Beadchip 450 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Champ package for Rstudio was used to process data.

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from the collected whole blood, the technique adopted was automated by magnetic spheres, using the Maxwell MDx equipment.

tag: gender

value: Female

tag: bmi

tag: ac

tag: fm

tag: fm%

tag: cell type

value: leucocytes peripheral blood


title: ER-RAS Induced + shXPO7_3 D5shX3T


title: Bulk RNA-sequencing of the AP_1936


title: Myotube_NGT_14a


title: Bulk RNA-sequencing of the AP_1940


title: peripheral blood C021


title: ER-RAS Induced D5plusB

source_name: ER-RAS Induced D5plus


title: peripheral blood C022


title: Bulk RNA-sequencing of the AP_1958


title: peripheral blood C020


title: Myotube_NGT_105


title: Bulk RNA-sequencing of the AP_1928


title: Bulk RNA-sequencing of the AP_1932


title: peripheral blood C018


title: Bulk RNA-sequencing of the AP_1920


title: ER-RAS Induced D5plusT


title: peripheral blood C017


title: Myoblast_NGT_115a


title: peripheral blood C013


title: HVC_3

description: 10X single-nuclei


title: ER-RAS Non-induced D5minusC

source_name: ER-RAS Non-induced D5minus


title: peripheral blood C010


title: peripheral blood C014


title: Bulk RNA-sequencing of the AP_1975

treatment_protocol: Amimals were dosed with semaglutide once daily, subcutaneous, for seven days. Dosing of the animals was gradually up-titrated (0.02, 0.04, 0.1 mg/kg). Animals were terminated by decapitation under CO2/O2 anaesthesia the day after the last dose.


title: peripheral blood C009


title: peripheral blood C012


title: peripheral blood C006


title: peripheral blood C005


title: ER-RAS Non-induced D5minusA


title: peripheral blood C008


title: peripheral blood C016


title: ER-RAS Non-induced D5minusT


title: Bulk RNA-sequencing of the AP_1967


title: ER-RAS Induced D5plusA


title: peripheral blood C003


title: peripheral blood P030


title: KG1a CD34+CD38- ESAM-Hi cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: KG1a CD34+CD38- ESAM-Hi cells

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

source_name: KG1a CD34+CD38- ESAM-Hi cells

extract_protocol:
RNA was extracted using RNeasy Mini Kit according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: KG1a CD34+CD38- ESAM-Neg or CD34+CD38- ESAM-Hi cells were sorted by flow cytometry.

value: KG1a cells

tag: sorted cell

value: KG1a CD34+CD38- ESAM-Hi cells


title: IMR-5

city: Solna

first: Johan

last: Holmberg

state: Stockholm

address: Solnavägen 9

department: CMB

institute: Karolinska Institute

data_processing:
Basecalling was performed using Illumina Casava1.8 software.
Fusion detection was analyzed by FusionCatcher version 0.99 with default settings using raw fastq files.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files include fusion transcripts detected by FusionCatcher in each cell line.

source_name: neuroblastoma cell line

growth_protocol: Growth media: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine; and cells were grown in 10 cm dishes up to 70-80% confluence before harvesting and extraction for total RNA

extract_protocol:
Total RNA was extracted by PerfectPure RNA Cultured Cell Kit from 5 PRIME according to manufacture's instructions
RNA-seq libraries were prepared according to TruSeq RNA Library Preparation Kit v2 (Illumina)


title: Bulk RNA-sequencing of the AP_1963


title: Bulk RNA-sequencing of the AP_1951


title: Bulk RNA-sequencing of the AP_1971


title: SK-N-AS

value: SK-N-AS


title: LAN1


title: Myoblast_NGT_105


title: peripheral blood C004


title: Bulk RNA-sequencing of the AP_1959


title: peripheral blood P029


title: peripheral blood P019


title: Bulk RNA-sequencing of the AP_1948


title: peripheral blood P041


title: peripheral blood P042


title: peripheral blood P025


title: SK-N-BE(1)


title: Bulk RNA-sequencing of the AP_1945


title: Bulk RNA-sequencing of the AP_1941


title: Bulk RNA-sequencing of the AP_1937


title: Ski7_E4_R3_RiboMinus

city: Vienna

first: Luis Enrique

last: Cabrera Quio

address: Campus Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode
BAM files containing sequencing reads were converted to fastq files using samtools (v1.9)
Barcoded libraries were demultiplexed using fastx-toolkit (v0.0.14)
Sequencing adapters were trimmed with cutadapt (v1.18) and only reads longer than 25 bases were kept
Reads were aligned to GRCz11 with Hisat2 v2.1.0, using the Ensembl transcriptome release 92. The following parameters were used: hisat2 -q --dta --rna-strandness R -k 12 --no-unal
Quantification of uniquely mapped reads (raw reads) was done with HTSeq (v0.9.1)
Quantification at the gene level (to obtain transcript per million (TPM)) was perfomed using Kallisto (v0.43.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab delimited files containing raw reads or TPM

organism: Danio rerio

source_name: zebrafish embryo

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle)

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol. To obtain polyA+ RNA, the poly(A) selection kit from LEXOGEN was used. For rRNA depleted samples, RiboCop rRNA depletion kit from LEXOGEN was used.
Strand-specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina

tag: genotype

tag: developmental stage

value: sphere

value: TLAB


title: Bulk RNA-sequencing of the AP_1955

tag: strain

tag: Sex


title: Bulk RNA-sequencing of the AP_1933

tag: age

tag: number of mice


title: peripheral blood P028


title: peripheral blood P014


title: peripheral blood P017


title: SK-N-FI

value: SK-N-FI


title: Bulk RNA-sequencing of the AP_1929

tag: tissue


title: Ski7_E4_R1_RiboMinus


title: SK-N-SH

tag: cell line

value: SK-N-SH


title: Ski7_E3_R2_RiboMinus

value: 1000 cell


title: Ski7_E3_R3_RiboMinus


title: Ski7_E3_R1_RiboMinus


title: peripheral blood P009


title: SH-SY5Y


title: Ski7_E2_R3_RiboMinus

value: 64 cell


title: HA_CTRL_2

city: Oxford

first: Colin

last: Goding

address: ORCRB

institute: LICR, University of Oxford

library_source: genomic

data_processing:
Base calling was performed with RTA 1.17.
Sequenced reads were mapped to the human reference genome hg19 using bowtie 1.0.0 with arguments -m 1 --strata --best -y -S -l 40
MACS2 was used to call peaks and create bedgraphs for every bp with equalized library sizes.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig representing read counts per bp for equal-sized libraries.

source_name: 501mel_3HA-empty vector

growth_protocol: 501mel cells were grown to 80% confluence in RPMI-1640 (Gibco) supplemented with 10% FBS (BioSera).

extract_protocol:
3HA-MITF ChIP was performed on 0.4% PFA-fixed chromatin that was sheared with a Covaris S220 as previously described (Strub et al., 2011). 70 ug chromatin was used for anti-HA immunoprecipitation.
Libraries were prepared using recommended Illumina protocols

value: melanoma cell line

tag: genotype/variation

value: expressing 3HA-empty vector

tag: chip antibody

value: HA (12CA5, Roche)


title: Ski7_E4_R2_RiboMinus


title: peripheral blood P003

tag: gender


title: peripheral blood P013

tag: bmi


title: Ski7_E2_R2_RiboMinus


title: Bulk RNA-sequencing of the AP_1921

value: male

value: 31 weeks

value: AP


title: MITF_K243Q

value: expressing 3HA-MITF-K243Q


title: Ski7_E2_R1_RiboMinus


title: MITF_3

value: expressing 3HA-MITF-WT


title: Bulk RNA-sequencing of the AP_1969


title: peripheral blood P002

value: Female

tag: ac

value: leucocytes peripheral blood


title: Ski7_O4_R1_RiboMinus

source_name: zebrafish oocyte

value: oocyte stage IV-V


title: Ski7_E1_R3_RiboMinus

value: 2 cell


title: Input


title: Ski7_E1_R2_RiboMinus

value: TLAB


title: Bulk RNA-sequencing of the AP_1973


title: Ski7_O4_R3_RiboMinus


title: HA_CTRL_1


title: peripheral blood P004

tag: fm


title: Ski7_E1_R1_RiboMinus


title: Ski7_O4_R2_RiboMinus


title: Bulk RNA-sequencing of the AP_1961


title: MITF_K243R

value: expressing 3HA-MITF-K243R


title: Ski7_O3_R3_RiboMinus

value: oocyte stage III


title: Bulk RNA-sequencing of the AP_1957


title: Bulk RNA-sequencing of the AP_1953


title: MITF_2


title: Ski7_O2_R3_RiboMinus

value: oocyte stage II


title: Ski7_O2_R2_RiboMinus


title: Ski7_O3_R1_RiboMinus


title: Ski7_O3_R2_RiboMinus


title: Bulk RNA-sequencing of the AP_1949


title: MITF_1


title: Ski7_O2_R1_RiboMinus


title: Ski7_O1_R3_RiboMinus

value: oocyte stage I


title: Scer_WT_SuperScript_rep1

city: Planegg

first: Danny

last: Nedialkova

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute for Biochemistry

description:
Scer_anticodon_counts.csv
Scer_isodecoder_counts.csv

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v2.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline using the common parameters --snp-tolerance --cluster --min-cov 2000 --max-mismatches 0.1 --cca-analysis --remap --remap-mismatches 0.075 and unique options for --control-condition and --cluster-id (0.90 for budding yeast, 0.95 for fission yeast and Drosophila, and 0.97 for human samples). HEK293T samples were addiitonally aligned to a collapsed non-redundant reference with Bowtie (parameters -m 1 -v3 --best --strata) or Bowtie 2 in local mode (--local -k 100 --very-sensitive --ignore-quals --np 5 --reorder).
Genome_build: S288c, 972h, dm6, hg19

organism: Saccharomyces cerevisiae

source_name: WT exponential phase

growth_protocol: S. cerevisiae cells (BY4741 wild-type, trm7∆, trm1∆, and trm10∆ Euroscarf) were grown in yeast extract-peptone-dextrose (YPD) medium. D. melanogaster BG3-c2 cells were cultured at 26℃ in Schneider’s Drosophila Medium (Gibco) supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, and 10 µg/ml human insulin. HEK293T cells were grown at 37℃ in DMEM supplemented with 10% fetal bovine serum (Sigma Aldrich). The kucg2 human induced pluripotent stem cell line (obtained from HipSci24) was cultured at 37oC in mTeSR1 (STEMCELL Technologies).

extract_protocol:
RNA from Drosophila BG3-c2, HEK293T, and human iPS cells was isolated with Trizol (Sigma Aldrich) according to the manufacturer’s instructions. For total RNA isolation from yeast, frozen cells were resuspended in 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0, 1% SDS (1 ml per 50 OD600 units). An equal volume of hot acid phenol (pH=4.3) was added, and the cell suspension was vortexed vigorously followed by incubation at 65℃ for 5 min with intermittent mixing. After addition of 1/10 volume 1-Bromo-3-chloropropane (BCP, Sigma Aldrich), samples were centrifuged at 10,000 x g for 5 min and the aqueous phase was transferred to a new tube. Following an additional round of hot acid phenol/BCP and a round of BCP only extraction, RNA was precipitated from the aqueous phase by the addition of 3 volumes of ethanol. For RNA isolation from yeast under conditions that preserve tRNA charging, frozen cells were resuspended in ice-cold 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0. One volume of cold acid phenol (pH=4.3) was added and cells were lysed with glass beads. One-tenth volume of BCP was then added and the samples were centrifuged at 10,000 x g/4℃ for 5 min, followed by a second round of cold phenol-BCP and one round of BCP-only extraction. RNA was ethanol-precipitated from the aqueous phase and pellets were washed in 80% ethanol containing 50 mM sodium acetate, pH=4.5, briefly air-dried, and resuspended in 50 mM sodium acetate pH=4.5, 1 mM EDTA pH=8.0. Two synthetic standards corresponding to E.coli tRNALys(UUU) with intact 3’-CCA (5’-GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA-3’) or a 3’-CC (5’- GGGTCGTTAGCTCAGTTGGTAG AGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACC-3’) were added to 5 - 10 µg of total RNA in a 3:1 molar ratio at 0.06 pmol/µg, followed by incubation at 37oC in 50 mM Tris-HCl pH=9.0 to deacylate tRNAs. Deacylation was omitted for samples subjected to oxidation and β-elimination. Total RNA was subsequently dephosphorylated and purified by ethanol precipitation in 0.3M sodium acetate pH=4.5 with 25 µg glycogen (Ambion) as a carrier. RNA was resolved on a denaturing 10% polyacrylamide/7M urea/1xTBE gel and species migrating at the size range of mature tRNAs (60 – 90 nt) were excised and gel slices were crushed with disposable pestles. Following addition of 400 µl gel elution buffer (0.3M sodium acetate pH=4.5, 0.25% SDS, 1mM EDTA pH=8.0), the gel slurry was incubated at 65℃ for 10 min, snap-frozen on dry ice, and thawed at 65℃ for 5 min. RNA was eluted overnight at room temperature with continuous mixing. Gel pieces were removed with Costar Spin-X centrifuge tube filters and RNA was recovered from the flow-through by ethanol precipitation in the presence of 25 µg of glycogen.
50 to 200 ng of gel-purified tRNA was ligated to one of four adapters with distinct barcodes.Ligation was performed for 3 hours at 25°C in a 20-µl reaction volume containing pre-adenylated adapter and RNA substrate in a 4:1 molar ratio, 1x T4 RNA Ligase Reaction Buffer, 200 U of T4 RNA ligase 2 (truncated KQ; NEB), 25% PEG 8000, and 10 U SUPERase In (Ambion). Ligation products were separated from excess adapter on denaturing 10% polyacrylamide/7M urea/1xTBE gels. Bands migrating at 95-125 nt were excised and ligation products were recovered from crushed gel slices. Reverse transcription reactions contained 125 nM adapter-ligated tRNA pool, 125 nM primer(5’pRNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’) and 500 nM TGIRT (InGex) in a final volume of 20 µl. Reactions were performed in 50 mM Tris-HCl pH=8.3, 75 mM KCl, 3 mM MgCl2, 5 mM DTT (from a freshly made 100 mM stock), and 10 U SUPERase In. After TGIRT addition, reactions were pre-incubated at 42℃ for 10 min, initiated by addition of dNTPs to a final concentration of 1.25 mM, and incubated at 42℃ for 16 hours in a Themrocycler. For Superscript III RT, template and primer were denatured at 75℃ for 5 min and chilled on ice, and reverse transcription was performed in the presence of 1X First-Strand Buffer, 5 mM DTT, 0.5 mM dNTPs, 10 U SUPERase In, and 200 U Superscript III (Invitrogen) at 57℃ for 60 min. Template RNA was hydrolyzed by the addition of 1 µl 5M NaOH and incubation at 95℃ for 3 min. cDNA between 60 and 150 nt was excised and cDNA was eluted from crushed gel slices in 400 µl 10 mM Tris-HCl pH=8.0, 1 mM EDTA at 70℃/2000 rpm for 1 hour in a Thermoblock, followed by ethanol precipitation. Purified cDNA was circularized with CircLigase ssDNA ligase (Lucigen) in 1x reaction buffer supplemented with 1 mM ATP, 50 mM MgCl2, and 1M betaine for 3 hours at 60℃, followed by enzyme inactivation for 10 min at 80℃. One-fifth of circularized cDNA was directly used for library construction PCR. Amplification was performed with KAPA HiFi Polymerase in 1x GC buffer with initial denaturation at 95℃ for 3 min, followed by five to six cycles of 98℃ for 20 sec, 62℃ for 30 sec, 72℃ for 30 sec. PCR products were purified with DNA Clean&Concentrator (Zymo Research) and resolved on 8% polyacrylamide/1xTBE gels alongside pBR322 DNA-MspI Digest (NEB). The 130-220 bp region of each lane was excised and DNA was eluted from crushed gel slices in 400 µl water with continuous mixing at room temperature overnight. After ethanol precipitation in 0.3M sodium acetate pH=5.5 and 25 µg glycogen, libraries were dissolved in 10 µl 10 mM Tris-HCl pH=8.0, quantified with Qubit, and sequenced for 150 cycles on an Illumina NextSeq platform.

treatment_protocol: To measure tRNA charging levels, RNA oxidation and β-elimination were performed as described (Clark et al., 2016) with minor modifications. 25 µg of total RNA were resuspended in 10 mM sodium acetate pH 4.5 and oxidized by the addition of freshly prepared NaIO4 to a final concentration of 50 mM in a 58-µL volume for 30 min at 22°C. The reaction was quenched by addition of 6 µL 1 M glucose for 5 min at 22°C. RNA was purified with Micro Bio Spin P30 columns (BioRad) followed by two rounds of ethanol precipitation. Pellets were resuspended in 20 µL RNAse-free water and β-elimination was performed by addition of 30 µl 100 mM sodium borate pH=9.5 (freshly prepared) for 90 min at 45°C. RNA was recovered with Micro Bio Spin 30 columns followed by ethanol precipitation.

tag: treatment

value: 57C SuperScript III RT reaction


title: Bulk RNA-sequencing of the AP_1939


title: Ski7_O1_R1_RiboMinus


title: Scer_ox_trm7_rep3

source_name: trm7Δ oxidized tRNA

value: 50mM NaIO oxidation and sodium borate β-elimination. 42C, 75mM KCl, 16 hour primer-dependant RT reaction


title: Scer_WT_42C_ts_rep1

value: 42C, 75mM KCl, 16 hour  template-switching RT reaction


title: Bulk RNA-sequencing of the AP_1935

source_name: AP

value: male


title: Bulk RNA-sequencing of the AP_1965

value: 31 weeks


title: WT_E4_R3_RiboMinus

value: wild-type

value: sphere


title: Scer_ox_trm7_rep2


title: WT_E4_R2_RiboMinus


title: WT_E3_R3_RiboMinus

value: 1000 cell


title: Bulk RNA-sequencing of the AP_1931

value: AP


title: WT_E4_R1_RiboMinus


title: WT_E3_R2_RiboMinus


title: WT_E3_R1_RiboMinus


title: WT_E2_R3_RiboMinus

value: 64 cell


title: Scer_ox_trm7_rep1


title: Bulk RNA-sequencing of the AP_1927


title: WT_E2_R2_RiboMinus


title: PC3 Electroporated with pEF-GFP in SCM 3

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

department: Chemical & Biological Engineering

institute: Villanova University

data_processing: Data processed using Excel, raw data normalized for TPM and synthesized using vLookup function.

molecule: polyA RNA

source_name: Prostate Cancer Cells

growth_protocol:
Jurkat, HEK-293T, and PC-3 cells, grown using RPMI 1640 media supplemented with 10% FBS and 1% P/S and passaged every 2 days (Jurkats) or 2-5 days (PC-3).
Primary T cells from healthy donors were purchased from Astarte Biologics and grown in X-VIVO™ 15 media following the manufacturer’s protocol for Human T Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific #11131D) of a 1:1 ratio of beads to cells. The culture media was also supplemented with IL-2 at 1 ng/µL to stimulate T cell growth.  Beads were replaced every 7-10 days during passaging, while IL-2 was added every 2-3 days.  Transfections of primary T cells followed the protocol that was optimized for the Jurkat T cells, with 2.75 uL Lipofectamine per 1 ug of pDNA in a 24-well plate.

extract_protocol:
Small sample of cells evaluated using flow cytometry for transfection efficiency at 24 hours post-transfection, and then the remaining sample was lysed and extracted according to the Qiagen RNeasy kit instructions.
Samples sent off for sequencing with BGI for mRNA sequencing.

treatment_protocol: Human T lymphocyte leukemia cells (Jurkat, clone E6-1, ATCC® TIB-152TM) were seeded in 24 well plates at a density of 2x105 cells/well in fetal bovine serum-containing Opti-MEMTM Reduced Serum Medium without phenol red(ThermoFisher Scientific Inc., Waltham, MA) immediately prior to transfection. Transfections with Lipofectamine® LTX were performed according to the manufacturer’s protocol using Lipofectamine LTX, Plus Reagent, and pEF-GFP. 2.75 µl Lipofectamine LTX, 1 µl Plus, and 1 µg pEF-GFP per 200,000 cell well for Jurkats and primary T cells, 1 µl Lipofectamine LTX, 0.5 µl Plus, and 500 ng pEF-GFP per 50,000 cell well for PC-3 cells.

value: Electroporated with pEF-GFP in SCM


title: PC3 Electroporated with pEF-GFP in SCM 2


title: Scer_ox_WT_rep3

source_name: WT oxidized tRNA


title: Bulk RNA-sequencing of the AP_1923


title: Scer_ox_WT_rep2


title: peripheral blood P006

value: Female

tag: fm%

tag: cell type

value: leucocytes peripheral blood


title: WT_E2_R1_RiboMinus

tag: genotype

value: TLAB


title: BMDM_HK18_Rep3

city: Boulder

first: Lara

last: Janiszewski

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
Data quality assessed with fastqc (0.11.2) and the first 10 bases were trimmed with Trimmomatic (0.36)
Reads were mapped with TopHat(2.0.6)/Samtools (0.1.18)/bowtie2 (2.0.2) using --b2-very-sensitive, fr-firststrand settings.
Read counting was completed with EdgeR Subread featureCounts (1.6.0) MetaFeature mapping was paired end, with both ends mapped, and no MultiOverlap allowed.
Analysis of differential expression was done with DESeq2 (1.18.1) but the nature of this dataset violates the DESeq2 assumption that most genes do not change expression between conditions. Therefore, all genes with differential expression padj < 0.05 in binary comparisons were compiled and excluded from the final dds normalization.
A log ratio test (reduced = ~ 1) was performed to find globally differentially expressed genes. This dataset (p < 0.01) was further filtered with two Transcripts Per Million (TPM) requirements. Inclusion in the final analysis indicates that a gene has an overall mean TPM > 5, and at least one condition with a mean TPM > 10.
DEGReport R package(1.24.1) for rlog calculation and expression clustering. Heatmap gene dendrograms were constructed using hierarchical clustering package hclust and ggdendro (0.1.22), and this gene order was used to construct global and cluster heatmaps with ggplot (Tidyverse R package 1.3.0).
Genome_build: mm10 gtf file from UCSC (July 2015 version).
Supplementary_files_format_and_content: .txt files containing featureCounts raw counts and DESeq2 normalized counts

growth_protocol: Monocytes were plated at 200,000 cells/well in uncoated plastic 12 well plates in DMEM based media + 20% FBS, 10 pg/uL recombinant murine macrophage colony stimulating factor (PeproTech, Inc.), 2 mM L-glutamine, 1 mM sodium pyruvate, penicillin/streptomycin (50 IU/mL penicillin and 50 ug/mL streptomycin). Media was refreshed on day 3, infection was carried out on day 6

extract_protocol:
Qiagen RNEasy kit was used on all samples after 1 freeze/thaw cycle. DNAse I treatment was done on the column per the protocol.
Illumina TruSeq LT kit with polyA selection

treatment_protocol: Salmonella Typhimurium SL1344 was cultured to stationary phase in LB with [antibiotics] at 37 °C with aeration. Bacteria were washed with PBS and opsonized for 30 minutes at room temperature in a 1:1 solution of mouse serum (Sigma) and cell culture media (Gibco). Half of the bacteria was heat killed at 60° C for 3 minutes, then placed on ice. One well of macrophages was scraped and counted, and bacteria were diluted in macrophage media without antibiotics to an MOI of 30. Plated macrophages were washed 3 times with PBS, then treated with antibiotic free macrophage media containing live, heat killed, or no bacteria. 30 minutes later bacterial media was removed, cells were washed 3x with PBS, and macrophage media containing 100 g/mL gentamycin was added. 90 minutes later media was again removed. RNEasy lysis buffer was added directly to wells designated as 2 Hr samples. Macrophage media with 10 g/mL gentamycin was added to wells designated as 18 Hr samples.

value: Bone marrow derived macrophages (BMDMs)

value: Heat killed Salmonella

tag: collection time point

value: 18 Hrs


title: PC3 Electroporated with pEF-GFP in SCM 1


title: CHP-212


title: WT_E1_R2_RiboMinus

tag: developmental stage

value: 2 cell

tag: strain


title: BMDM_HK18_Rep2


title: Scer_ox_WT_rep1

value: 50mM NaIO oxidation and sodium borate β-elimination. 42C, 75mM KCl, 16 hour primer-dependant RT reaction


title: Scer_trm10

value: 42C, 75mM KCl, 16 hour primer-dependant RT reaction


title: BMDM_Alive18_Rep3

value: Live Salmonella


title: WT_E1_R3_RiboMinus


title: PC3 Electroporated no DNA SCM 3

value: Electroporated w/o plasmid


title: WT_E1_R1_RiboMinus

value: wild-type


title: PC3 Electroporated no DNA SCM 2


title: PC3 Electroporated no DNA SCM 1


title: PC3 Transfected SCM rep 3

value: pEF-GFP with Lipofectamine in SCM


title: Scer_WT25_trm10_75

source_name: WT + trm10Δ


title: WT_O4_R3_RiboMinus

value: oocyte stage IV-V


title: WT_O4_R2_RiboMinus


title: PC3 Transfected SCM rep 2


title: WT_O4_R1_RiboMinus


title: BMDM_Alive18_Rep1


title: Scer_WT75_trm10_25


title: Scer_trm1


title: Scer_WT_rep3

source_name: WT


title: PC3 Transfected SCM rep 1


title: BMDM_HK18_Rep1


title: BMDM_HK2_Rep2

value: 2 Hrs


title: Scer_WT25_trm1_25

source_name: WT + trm1Δ


title: PC3 Untransfected SCM rep 3

value: No plasmid


title: WT_O3_R2_RiboMinus

value: oocyte stage III


title: Scer_WT75_trm1_75


title: PC3 Untransfected SCM rep 2


title: BMDM_HK2_Rep1


title: BMDM_Alive18_Rep2


title: Scer_WT_rep2


title: BMDM_Alive2_Rep3


title: WT_O3_R1_RiboMinus


title: Scer_WT_rep1


title: BMDM_Alive2_Rep2


title: HEK-293T Transfected rep 3

source_name: Human embryonic kidney cell

value: pEF-GFP with Lipofectamine in SFM


title: KG1a CD34+CD38- ESAM-Neg cells

description: KG1a CD34+CD38- ESAM-Neg cells

source_name: KG1a CD34+CD38- ESAM-Neg cells

value: KG1a cells

tag: sorted cell

value: KG1a CD34+CD38- ESAM-Neg cells


title: BMDM_HK2_Rep3

value: Bone marrow derived macrophages (BMDMs)


title: Hu60 RUL 280pos

city: Boston

first: avinash

last: waghray

state: MA

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

data_processing:
For mRNA-Seq analysis, the raw fastq files were mapped to the human genome using STAR (Version 20201). The output files were processed through Cufflinks (Version 2.2.1.3)) and Cuffdiff (Version 2.2.1.6) to conduct differential gene expression analysis.
Genome_build: hg38

source_name: human adult lung Hu60

extract_protocol:
trizol extraction; poly A pulldown. For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent (Thermofischer Scientific, 15596026) following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer.
trueseq

value: lung

tag: cel population

value: HT2-280+ population

tag: Sex

value: Male

tag: subject id


title: BMDM_Alive2_Rep1


title: WT_O2_R2_RiboMinus

value: oocyte stage II

value: TLAB


title: HEK-293T Transfected rep 2

tag: cell line


title: Hu60 RUL NGFRpos

tag: tissue

value: NGFR/CD271+ population


title: BMDM_Control_Rep3


title: WT_O3_R3_RiboMinus


title: WT_O2_R1_RiboMinus


title: Hu60 1B NGFRpos


title: BMDM_Control_Rep2


title: BMDM_Control_Rep1


title: WT_O1_R2_RiboMinus

value: oocyte stage I


title: PC3 Untransfected SCM rep 1


title: Hu56 RUL 280pos

source_name: human adult lung Hu56


title: Primary T Transfected rep3

source_name: Primary T Lymphocyte

value: Primary T Lymphocyte


title: HEK-293T Untransfected rep 1


title: WT_O1_R1_RiboMinus

value: wild-type


title: WT_O2_R3_RiboMinus


title: Hu56 RUL NGFRpos


title: Alkbh5 EV_rep3

city: Nashville

first: James

middle: G.

last: Patton

state: TN

address: 2325 Stevenson Center

department: Department of Biological Sciences

institute: Vanderbilt University

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
TIGER (https://github.com/shengqh/TIGER), was used to perform small RNA-seq analysis, including reads mapping, miRNA quantification and differential analysis.
Specifically, Bowtie was used to map reads to the human miRNAs from miRBase v22, tRNA, rRNA,  snRNA, snoRNA, lincRNA, yRNA, other miscellaneous sRNAs, and the human reference genome hg19.
DESeq2 was used to detect differential expression between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: A count table that provides complete data with values for all features and all samples
Supplementary_files_format_and_content: raw counts

source_name: Colorectal cancer cell line

growth_protocol: Cell lines were grown in DMEM in the presence of 10% fetal bovine serum, 1% L-glutamine, 1% non-essential amino acids and antibiotics

extract_protocol:
RNA was harvested using Trizol reagent. Libraries were generated using NextFlex small RNA library preparation kit v3 with modified step F.
Libraries were size-selected using Pippin Prep and quality was assessed by 2100 Bioanalyzer. Libraries were sequenced using the Illumina NextSeq500 system.

treatment_protocol: Stable cell lines were generated expressing shRNAs against Mettl3 and Alkbh5.   EVs were purified from cell media after 48 hours

tag: shRNA

value: KRAS mutant colorectal cancer cell line

value: extracellular vesicles (EVs)


title: Primary T Transfected rep2


title: Hu56 1B NGFRpos


title: Alkbh5 EV_rep2


title: Primary T Transfected rep1


title: Ski7_E4_R2_polyA

source_name: zebrafish embryo

value: sphere


title: Ski7_E4_R3_polyA


title: HEK-293T Untransfected rep 2

value: No plasmid


title: Hu50 RUL 280pos

source_name: human adult lung Hu50


title: Ski7_E4_R1_polyA


title: Mettl3 EV_rep3


title: Ski7_E3_R3_polyA

value: 1000 cell


title: WT_O1_R3_RiboMinus

source_name: zebrafish oocyte


title: Hu50 1B NGFRpos


title: Primary T Untransfected rep2


title: Mettl3 EV_rep2


title: Primary T Untransfected rep1


title: Jurkat Transfected rep3

source_name: Acute T Cell Leukemia

value: Jurkat E6-1

value: pEF-GFP with Lipofectamine in SFM


title: Mettl3 EV_rep1


title: EC-MW-5984_HT29_WT2

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

data_processing:
Fastq read adaptor trimming by cutadapt 1.9.1
Read alignment by Bowtie2 2.2.6,
Fraction of mitochondrial reads by SAMstats and postalignment filtering by SAMtools
Duplicates friltering by mark-duplicate
Peak calling by MACS2 macs2 callpeak --nomodel --shift -100 --extsize 200 --broad -t
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: HT29_CHD2 WildType

growth_protocol: cells were incubated in a 95% air and 5% CO2 humidified atmosphere at 37°C, and the medium was replaced every 48hrs. In logarithmic phase HT-29 cells were obtained and resuspended in DMEM medium (Gibco) supplemented with 10% FBS (Hyclone, Logan, UT, USA)

extract_protocol:
50,000 (viability >90%) cells were pelleted at 500 RCF at 4°C for 5 min. Cell pellet was resuspended in cold ATAC-Resuspension Buffer (RSB) (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and incubated on ice. RSB was washed out with cold ATAC-RSB (containing 0.1% Tween-20 but NO NP40 or digitonin). Nuclei were pelleted at 500 RCF for 10 min at 4°C. Cell pellet was resuspended in 50 ul of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O). Reaction was incubated 37°C for 30 minutes in a thermomixer with 1000 RPM mixing.
The tagmented nuclei was sequenced using an Illumina (PE, 2x50 bp).

value: human colorectal adenocarcinoma cell line with epithelial morphology

tag: genotype/variation

value: CHD2 WildType


title: EC-MW-5984_HT29_WT3


title: Ski7_E3_R2_polyA


title: Jurkat Transfected rep2


title: DKO-1 EV_rep3

value: control


title: Primary T Untransfected rep3


title: DKO-1 EV_rep2


title: Hu50 RUL NGFRpos

value: lung

value: Male


title: Alkbh5 EV_rep1


title: Ski7_E2_R3_polyA

value: 64 cell

value: TLAB


title: Ski7_E3_R1_polyA


title: Ski7_E2_R2_polyA


title: EC-MW-5984_HT29_OE3

source_name: HT29_CHD2 Overexpressed

value: CHD2 Overexpressed


title: Ski7_E2_R1_polyA


title: EC-MW-5984_HT29_OE2


title: Alkbh5 cell_rep3

value: cellular


title: Jurkat Transfected rep1


title: Jurkat Untransfected rep3


title: Jurkat Untransfected rep2


title: EC-MW-5984_HT29_OE1


title: Alkbh5 cell_rep2


title: Ski7_E1_R3_polyA

value: 2 cell


title: Jurkat Untransfected rep1


title: Alkbh5 cell_rep1

value: KRAS mutant colorectal cancer cell line


title: DKO+3a2 ESC BrdUIP_LateS replicate 2

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

institute: Mie University

data_processing:
Reads were mapped to the mm10 mouse reference genome using Bowtie2 and reads with MAPQ<20 were omitted from downstream analysis. Data analyses were performed using SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and R/Bioconductor (http://www.r-project.org; http://www.bioconductor.org). Numbers of total reads in each sample were normalized per million reads in SeqMonk. The ratio of sequence reads between early and late S phase samples was determined in 5-Kb windows and loess-smoothed over a 300-Kb window size in R/Bioconductor. The smoothed dataset was used to generate a replication domain map.
Genome_build: mm10
Supplementary_files_format_and_content: The ratio of sequence reads between early and late S phase samples

source_name: DKO+3a2 ESC BrdUIP_LateS

growth_protocol: ES cells were maintained on gelatin-coated culture dishes in knockout Dulbecco’s modified eagle medium (Thermo Fisher Scientific, Cat#10829) supplemented with 7.5% ES-qualified FBS (GE Healthcare, Cat#SH30070.03E), 7.5% Knockout serum replacement (Thermo Fisher Scientific, Cat#10828-028), 2 mM L-glutamine (Thermo Fisher Scientific, Cat#25030–081), 10 mM Hepes (Thermo Fisher Scientific, Cat#15630–080), 100U/ml penicillin/streptomycin (Thermo Fisher Scientific, Cat#15070–063), 0.1 mM non-essential amino acids (Thermo Fisher Scientific, Cat#11140–050), 0.1 mM beta-mercaptoethanol (Thermo Fisher Scientific, Cat#21985–023), in the presence of leukemia inhibitory factor (LIF) at 37°C with 5% CO2.

extract_protocol:
Cells were washed twice with ice-cold PBS, trypsinized, and then fixed in 75% ethanol. These cells were resuspended in PBS containing 1% FBS, stained with propidium iodide (20 μg/ml) for 30 min in the presence of RNase A (250 μg/ml), and then were sorted into early and late S phase fractions by FACSCalibur flow cytometer (BD Biosciences). After phenol-chloroform extraction of DNA from 10,000 cells, sonication was performed to cut the DNA into an average size of about 100-600 bp. Then, immunoprecipitation with anti-BrdU mouse monoclonal antibody (BD Biosciences, #555627) was performed in each fraction to enrich BrdU-substituted replicating DNA. Isolated early and late replicating DNA was amplified individually by WGA (Sigma. SEQXE).
Libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683) according to the standard instruction.

treatment_protocol: Cells were labeled with 50 µM BrdU for 2 h before harvest.

tag: strain background

value: Embryonic stem cells

tag: sample state

value: BrdU-IP

tag: ip antibody

value: BrdU (BD Biosciences, 555627)


title: EC-MW-5984_HT29_KD2

source_name: HT29_CHD2 knockdown

value: CHD2 knockdown


title: EC-MW-5984_HT29_WT1


title: Ski7_E1_R2_polyA


title: Mettl3 cell_rep3


title: Ski7_E1_R1_polyA


title: DKO+3a2 ESC BrdUIP_EarlyS replicate 2

source_name: DKO+3a2 ESC BrdUIP_EarlyS


title: DKO-1 EV_rep1

value: extracellular vesicles (EVs)


title: Mettl3 cell_rep2


title: EC-MW-5984_HT29_KD1


title: DKO+3a2 ESC BrdUIP_LateS replicate 1


title: Mettl3 cell_rep1


title: Ski7_FER_R2_polyA

source_name: zebrafish egg

value: fertilized egg


title: DKO+3a2 ESC BrdUIP_EarlyS replicate 1


title: Ski7_FER_R1_polyA


title: DKO ESC BrdUIP_LateS replicate 2

source_name: DKO ESC BrdUIP_LateS

value: DKO


title: DKO-1 cell_rep2


title: DKO-1 cell_rep3


title: Ski7_ACT_R3_polyA

value: activated egg


title: DKO ESC BrdUIP_EarlyS replicate 2

source_name: DKO ESC BrdUIP_EarlyS


title: Ski7_ACT_R2_polyA


title: EC-MW-5984_HT29_KD3

value: human colorectal adenocarcinoma cell line with epithelial morphology


title: DKO-1 cell_rep1

value: control


title: DKO ESC BrdUIP_LateS replicate 1


title: DKO ESC BrdUIP_EarlyS replicate 1


title: TKO ESC BrdUIP_LateS replicate 2

source_name: TKO ESC BrdUIP_LateS

value: TKO


title: Ski7_FER_R3_polyA


title: TKO ESC BrdUIP_EarlyS replicate 2

source_name: TKO ESC BrdUIP_EarlyS


title: Ski7_INA_R2_polyA

value: inactive egg


title: Ski7_O4_R3_polyA

value: oocyte stage IV-V

value: TLAB


title: TKO ESC BrdUIP_LateS replicate 1


title: human_DE_Day4_Rep2_ATAC

city: Irvine

first: Seyed

middle: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3 519 Ring Rd

department: Developmental and Cellular Biology

institute: University of California, Irvine

data_processing:
RNA-seq
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 or rn6 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) by defaults with gene annotations from GENCODE v28, and results were output in transcripts per million (TPM).
Protein coding and long non-coding RNA genes with greater than 1 TPM in both replicates in at least two timepoints were kept. Gene counts were TMM normalized using edgeR (version 3.18.1) and log2-transformed for Differential Gene Expression Analysis maSigPro, and TPMs were quantile normalized for all heatmaps and figures
Genome_build: hg38 or rn6
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM; Supplementary file contains tab-separated file with expression values
ATAC-seq
Adapters were trimmed from reads using trimmomatic (version 0.35) then were mapped to the mitocondrial genomes from hg38 or rn6 by bowtie2 (version 2.2.7) using --very-sensitive and no discourdant alignments with a maximum fragment length of 2000, reads that did not align to the mitocondria were then mapped to the respective genomes listed previously with the same settings that were used to map to the mitochondria.
Peak calling was done using homer (version 4.7) using default settings with -style factor and size as both 150 and 500bp
Irreproducible Discovery Rate (IDR) was used using ENCODE methods to determine the highly reproducible peaks in both replicates for each time-point. Only peaks passing IDR filters were used to combine ATAC samples into a matrix using homer annotatePeaks.pl from the peaks passing IDR filter and all the peak files and tag directories from homer findPeaks.pl
Supplementary_files_format_and_content: Only peaks annotated within 20kb of a TSS were used

source_name: Differentiation of H1 - Human Embryonic Stem cells into Definitive Endoderm Cells

extract_protocol:
Approximately 50,000 embryonic stem cells and differentiated cells were collected for ATAC-seq. ATAC-seq was performed as previously described (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396) with one amendment. DNA size exclusion was utilized
Cells were lifted using Accutase. Total RNA was extracted by using the RNeasy kit (QIAGEN). DNA was extracted by using omni ATAC protocol previously described

tag: differentiation

value: Definitive Endoderm

tag: day of differentiation

value: Day 4


title: WT ESC BrdUIP_LateS replicate 2

source_name: WT ESC BrdUIP_LateS

value: WT

tag: cell type


title: human_DE_Day4_Rep1_ATAC


title: human_DE_Day3_Rep2_ATAC

value: Day 3


title: Ski7_INA_R1_polyA

tag: genotype


title: Ski7_INA_R3_polyA

tag: developmental stage


title: Ski7_O4_R2_polyA

tag: strain


title: Ski7_O4_R1_polyA


title: WT ESC BrdUIP_EarlyS replicate 2

source_name: WT ESC BrdUIP_EarlyS

value: Embryonic stem cells

value: BrdU-IP


title: WT ESC BrdUIP_LateS replicate 1

value: BrdU (BD Biosciences, 555627)


title: human_DE_Day2_Rep1_ATAC

value: Day 2


title: Ski7_ACT_R1_polyA


title: human_DE_Day5_Rep2_ATAC

value: Day 5


title: Ski7_O3_R3_polyA

value: oocyte stage III


title: Bulk RNA-sequencing of the AP_1943

source_name: AP

value: male

tag: age

value: 31 weeks

tag: number of mice

value: AP


title: human_DE_Day1_Rep2_ATAC

value: Day 1


title: Ski7_O3_R2_polyA


title: WT ESC BrdUIP_EarlyS replicate 1


title: Ski7_O1_R2_RiboMinus

value: oocyte stage I


title: human_DE_Day5_Rep1_ATAC


title: Wilms' tumor sample control group2

type: RNA

city: Chongqing

first: He

middle: xing

last: yue

address: 136, Zhongshan 2nd RD, Yuzhong District

country: China

institute: Children’s Hospital of Chongqing Medical University

hyb_protocol: DNA in hybridization solution was denatured at 95C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: blood

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: disease state

value: control

tag: tumor stage

value: blood


title: human_DE_Day3_Rep1_ATAC

value: Definitive Endoderm


title: Wilms' tumor sample control group1


title: human_DE_Day2_Rep2_ATAC


title: Wilms' tumor  samples 2

value: Wilms tumor


title: Spom_WT_rep2

description:
Spom_anticodon_counts.csv
Spom_isodecoder_counts.csv

organism: Schizosaccharomyces pombe

source_name: WT exponential phase

tag: treatment

value: 42C, 75mM KCl, 16 hour primer-dependant RT reaction


title: Spom_WT_rep1


title: human_DE_Day1_Rep1_ATAC


title: Ski7_O3_R1_polyA

source_name: zebrafish oocyte

value: TLAB


title: Ski7_O2_R3_polyA

value: oocyte stage II


title: Ski7_O2_R2_polyA


title: human_NPC_Day8_Rep1_ATAC

source_name: Differentiation of H1 - Human Embryonic Stem cells into Neural Progenitor Cells

value: Neural Progenitor Cells

value: Day 8


title: human_NPC_Day7_Rep2_ATAC

value: Day 7


title: human_NPC_Day8_Rep2_ATAC


title: rat_DE_Day7_Rep2_ATAC

organism: Rattus norvegicus

source_name: Differentiation of RRRC - Rat Embryonic Stem cells into Definitive Endoderm Cells


title: rat_DE_Day7_Rep1_ATAC


title: Wilms' tumor  samples 1

tag: tissue


title: Ski7_O1_R3_polyA


title: Ski7_O2_R1_polyA


title: human_NPC_Day7_Rep1_ATAC


title: mPFC_FUS_NLS3_22months_old

city: Strasbourg

first: Salim

last: Megat

state: Alsace

address: 1 rue Eugène Boeckel

country: France

institute: Center for Research in Biomedicine of Strasbourg (CRBS)

data_processing:
Raw reads were mapped to the mouse reference genome GRCm38 with STAR version 2.7.0 111 and default parameters using Ensembl gene annotations (version 87). Gene-level abundance estimates were estimated using the option --quantMode geneCount in STAR. We filtered the lowly expressed genes wherein each gene was required to have at least 15 counts across all samples. The filtered set of genes was used for the PCA plot and differential expression analysis. Differential gene expression analysis was performed with the ARMOR workflow112 and a cut off FDR value of 0.05 was set in both datasets.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: frontal_cortex_raw_counts.xlsx

source_name: RNA from frontal cortex (mutant)

growth_protocol: Frontal cortex from 6- and 22-months-old mice were dissected and snap frozen in liquid nitrogen. The samples were conserved at -80 until further processing.

extract_protocol: Briefly, RNA from cortex of 22-months-old male Fus∆NLS/+ mice and their control littermates were extracted with TRIzol (Invitrogen). RNA quality was measured using the Agilent Bioanalyzer system or RNA screenTape (Agilent Technologies) according to the manufacturer’s recommendations. Samples were processed using the Illumina TruSeq single Stranded mRNA Sample Preparation Kit according to manufacturer’s protocol. Generated cDNA libraries were sequenced using an Illumina HiSeq 4000 sequencer with 4–5 biological replicates sequenced per condition using single read, 50 cycle runs. RNA from the cortex of 6-months-old male Fus∆NLS/+ and control littermate mice was extracted and libraries were generated using the Illumina TruSeq single Stranded mRNA Sample Preparation Kit. The cDNA libraries were sequenced on a HiSeq 4000 with 3 biological replicates per condition using single-end 50bp read. Total reads sequenced varies from 35 to 45 million reads. Complete QC report will be made publicly available.

value: frontal cortex

tag: gender

value: 22 months


title: mPFC_FUS_NLS4_22months_old

value: male


title: mPFC_FUS_NLS2_22months_old


title: Ski7_O1_R2_polyA


title: human_NPC_Day6_Rep2_ATAC

value: Day 6


title: mPFC_FUS_NLS5_22months_old


title: rat_DE_Day6_Rep2_ATAC


title: rat_DE_Day6_Rep1_ATAC


title: Ski7_O1_R1_polyA


title: mPFC_FUS_NLS6_6months_old

value: 6 months


title: rat_DE_Day5_Rep2_ATAC

value: Day 5


title: rat_DE_Day5_Rep1_ATAC


title: human_NPC_Day5_Rep2_ATAC


title: WT_E4_R3_polyA

source_name: zebrafish embryo

value: wild-type

value: sphere


title: WT_E4_R2_polyA


title: mPFC_FUS_NLS4_6months_old


title: mPFC_FUS_NLS2_6months_old


title: mPFC_FUS_NLS3_6months_old


title: mPFC_FUS_NLS1_22months_old


title: rat_DE_Day4_Rep1_ATAC

value: Day 4


title: human_NPC_Day4_Rep1_ATAC


title: human_NPC_Day6_Rep1_ATAC


title: WT_E4_R1_polyA


title: WT_E3_R3_polyA

value: 1000 cell


title: human_NPC_Day3_Rep2_ATAC

value: Day 3


title: mPFC_FUS_NLS5_6months_old


title: WT_E3_R2_polyA


title: rat_DE_Day3_Rep2_ATAC

value: Definitive Endoderm


title: WT_E3_R1_polyA

value: TLAB


title: rat_DE_Day3_Rep1_ATAC


title: mPFC_WT5_22months_old

source_name: RNA from frontal cortex (control)

value: WT


title: mPFC_WT4_22months_old


title: human_NPC_Day3_Rep1_ATAC

value: Neural Progenitor Cells


title: human_NPC_Day2_Rep2_ATAC

value: Day 2


title: WT_E2_R3_polyA

value: 64 cell


title: human_NPC_Day5_Rep1_ATAC


title: TKO ESC BrdUIP_EarlyS replicate 1

tag: genotype/variation

value: TKO

value: Embryonic stem cells

value: BrdU-IP

value: BrdU (BD Biosciences, 555627)


title: WT_E2_R2_polyA


title: rat_DE_Day4_Rep2_ATAC


title: human_NPC_Day2_Rep1_ATAC


title: mPFC_WT3_22months_old

value: frontal cortex

value: male

value: 22 months


title: human_NPC_Day1_Rep2_ATAC

value: Day 1


title: rat_DE_Day2_Rep1_ATAC


title: rat_DE_Day1_Rep1_ATAC


title: human_NPC_Day1_Rep1_ATAC


title: mPFC_WT2_22months_old


title: human_ESC_Day0_Rep2_ATAC

source_name: H1 Embryonic Stem Cells

value: Embryonic Stem Cells

value: Day 0


title: mPFC_FUS_NLS1_6months_old

value: 6 months


title: rat_DE_Day2_Rep2_ATAC

value: Definitive Endoderm


title: human_ESC_Day0_Rep1_ATAC


title: mPFC_WT6_6months_old


title: WT_E1_R3_polyA

value: wild-type

value: 2 cell

value: TLAB


title: WT_E2_R1_polyA


title: mPFC_WT5_6months_old

value: WT


title: WT_E1_R1_polyA


title: WT_E1_R2_polyA


title: rat_NPC_Day8_Rep1_ATAC

source_name: Differentiation of RRRC - Rat Embryonic Stem cells into Neural Progenitor Cells

value: Neural Progenitor Cells

value: Day 8


title: human_DE_Day5_Rep2_RNA

extract_protocol:
Nextera DNA Library Prep Kit (20018704, Illiumina)
Between 19 and 38 ng of RNA were converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (FC-121-1030, Illumina) for control-3, control-4, and FSHD2-2 libraries, and the Nextera DNA Flex Library Prep Kit (20018704, Illumina) for control-1, control-2 and FSHD2-1 libraries. Libraries were sequenced on the Illumina NextSeq500 platform using paired-end 43 bp mode.
Cells were lifted using Accutase. Total RNA was extracted by using the RNeasy kit (QIAGEN). DNA was extracted by using omni ATAC protocol previously described

value: Day 5


title: rat_NPC_Day8_Rep2_ATAC


title: WT_FER_R3_polyA

source_name: zebrafish egg

value: fertilized egg


title: rat_NPC_Day7_Rep2_ATAC

value: Day 7


title: human_DE_Day5_Rep1_RNA


title: rat_NPC_Day7_Rep1_ATAC


title: human_DE_Day4_Rep2_RNA

value: Day 4


title: rat_DE_Day1_Rep2_ATAC


title: WT_FER_R2_polyA


title: rat_NPC_Day6_Rep2_ATAC

value: Day 6


title: WT_FER_R1_polyA


title: mPFC_WT3_6months_old

value: frontal cortex

value: male


title: mPFC_WT2_6months_old


title: mPFC_WT1_22months_old

value: 22 months


title: mPFC_WT4_6months_old


title: human_DE_Day4_Rep1_RNA


title: rat_NPC_Day6_Rep1_ATAC


title: mPFC_WT1_6months_old


title: human_DE_Day3_Rep2_RNA

value: Day 3


title: WT_ACT_R3_polyA

value: activated egg


title: rat_NPC_Day5_Rep2_ATAC


title: rat_NPC_Day5_Rep1_ATAC


title: WT_ACT_R2_polyA


title: human_DE_Day3_Rep1_RNA

value: Definitive Endoderm


title: WT_ACT_R1_polyA

value: wild-type


title: TIL-BC3

city: Freiburg

first: Michael

last: Schulz

address: Breisacher Straße 64

department: Institute for Neuropathology

institute: University Hospital Freiburg

data_processing:
FastQC Analysis
quality score filtering, poly-A trimming, artifact removal, removal of ‘N’ containing reads and clearing of rRNA contamination using a pipeline provided by the HUSAR platform, DKFZ.
Genomic mapping to Mouse genome GRCm38 was performed using TopHat2 (version 2.0.14)
The number of reads per gene was determined using HTSeq count.
Paired differential analysis was performed using   ‘DESeq2’  (version 1.18.1)
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: .csv format, processed data files contain annotated ENSEMBL IDs and gene names as well as readcounts which were annotated from HTSeq counts

source_name: mouse brain metastasis

extract_protocol:
Myeloid and lymphoid cells from (tumor-bearing) mice brain or peripheral blood were FACS purified, stored in Trizol LS and RNA isolated according to standard protocols (commercial processing)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6J (CRL)

value: brain metastasis

value: tumor-infiltrating lymphocyte B220

value: BRM

tag: name in supplementary file


title: human_DE_Day2_Rep1_RNA

value: Day 2


title: TIL-BC2


title: human_DE_Day2_Rep2_RNA


title: rat_NPC_Day4_Rep2_ATAC

value: Neural Progenitor Cells


title: WT_INA_R3_polyA

value: inactive egg

value: TLAB


title: TIL-CD4-3

value: tumor-infiltrating lymphocyte CD4


title: rat_NPC_Day4_Rep1_ATAC

value: Day 4


title: WT_INA_R2_polyA


title: TIL-CD4-2


title: human_DE_Day1_Rep2_RNA

value: Day 1


title: human_DE_Day1_Rep1_RNA


title: WT_INA_R1_polyA


title: rat_NPC_Day3_Rep2_ATAC


title: WT_O4_R3_polyA

value: oocyte stage IV-V


title: human_NPC_Day8_Rep2_RNA

value: Day 8


title: rat_NPC_Day2_Rep2_ATAC


title: TIL-CD4-1


title: TIL-CD8-3

value: tumor-infiltrating lymphocyte CD8


title: human_NPC_Day8_Rep1_RNA


title: WT_O4_R2_polyA


title: rat_NPC_Day2_Rep1_ATAC


title: WT_O4_R1_polyA


title: TIL-CD8-2


title: TIL-BC1


title: rat_NPC_Day1_Rep2_ATAC


title: human_NPC_Day7_Rep1_RNA

value: Day 7


title: TIL-CD8-1


title: rat_NPC_Day1_Rep1_ATAC


title: WT_O3_R3_polyA

value: oocyte stage III


title: human_NPC_Day7_Rep2_RNA


title: TAM-MDM3

value: monocyte-derived macrophage


title: TAM-MDM2

value: C57BL/6J (CRL)


title: rat_ESC_Day0_Rep2_ATAC

source_name: RRRC - Rat Embryonic Stem Cells

value: Embryonic Stem Cells

value: Day 0


title: WT_O3_R2_polyA

value: wild-type


title: WT_O3_R1_polyA


title: rat_NPC_Day3_Rep1_ATAC

value: Day 3


title: human_NPC_Day6_Rep1_RNA

value: Neural Progenitor Cells

value: Day 6


title: rat_ESC_Day0_Rep1_ATAC


title: TAM-MDM1

value: brain metastasis

value: BRM


title: human_NPC_Day6_Rep2_RNA


title: human_NPC_Day5_Rep2_RNA

value: Day 5


title: rat_DE_Day7_Rep2_RNA

value: Definitive Endoderm


title: TAM-MG3

value: microglia


title: WT_O2_R3_polyA

value: oocyte stage II

value: TLAB


title: rat_DE_Day7_Rep1_RNA

value: Day 7


title: TAM-MG2


title: WT_O2_R2_polyA


title: WT_O2_R1_polyA


title: human_NPC_Day5_Rep1_RNA


title: rat_DE_Day6_Rep2_RNA


title: TAM-MG1


title: human_NPC_Day4_Rep1_RNA

value: Day 4


title: WT_O1_R3_polyA

value: oocyte stage I


title: human_NPC_Day3_Rep2_RNA


title: TA-MONO2

value: C57BL/6J (CRL)

value: inflammatory monocyte


title: rat_DE_Day5_Rep2_RNA


title: rat_DE_Day6_Rep1_RNA


title: TA-MONO3


title: WT_O1_R2_polyA


title: WT_O1_R1_polyA


title: human_NPC_Day2_Rep2_RNA

value: Day 2


title: rat_DE_Day5_Rep1_RNA


title: MhcAmyrelOE_10daysOld_HEAD_C

city: Memphis

first: Yong-Dong

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Mhc>Amyrel (muscle-specific Amyrel overexpression) replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequences derived from mRNA paired-end 100-bp sequences were mapped to the Drosophila melanogaster genome (BDGP5 release 75) with the STAR aligner, and the read counts were reported
Genome_build: BDGP5
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

organism: Drosophila melanogaster

source_name: Heads (enriched from brains and retinas) from 10-day-old male flies

extract_protocol:
Total RNA was extracted from Drosophila thoraces, which consist primarily of skeletal muscle, and from Drosophila heads, which were enriched from brains and retinas, from 10-day-old male flies
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 4000 platform.

value: heads

tag: Sex

value: male

value: 10 days


title: human_NPC_Day2_Rep1_RNA

value: Neural Progenitor Cells


title: rat_DE_Day4_Rep2_RNA


title: TA-MONO1

value: brain metastasis


title: Control_BloodB220-3

source_name: mouse peripheral blood

value: peripheral blood

value: blood B220 + cell


title: rat_DE_Day4_Rep1_RNA

value: Definitive Endoderm


title: Control_BloodB220-2


title: MhcAmyrelOE_10daysOld_HEAD_B

description: Mhc>Amyrel (muscle-specific Amyrel overexpression) replicate 2


title: human_NPC_Day1_Rep2_RNA

value: Day 1


title: MhcAmyrelOE_10daysOld_HEAD_A

description: Mhc>Amyrel (muscle-specific Amyrel overexpression) replicate 1


title: Control_BloodB220-1


title: human_NPC_Day1_Rep1_RNA


title: MhcNCxAmyrel_10daysOld_HEAD_C

description: Mhc>+ (isogenic control) replicate 3

value: Mhc>+ (isogenic control)


title: human_ESC_Day0_Rep2_RNA

value: Embryonic Stem Cells

value: Day 0


title: rat_DE_Day3_Rep1_RNA

value: Day 3


title: Control_BloodCD8-3

value: blood CD8 T cell


title: rat_DE_Day3_Rep2_RNA


title: MhcNCxAmyrel_10daysOld_HEAD_B

description: Mhc>+ (isogenic control) replicate 2


title: rat_DE_Day2_Rep2_RNA


title: Control_BloodCD8-2

value: C57BL/6J (CRL)


title: human_ESC_Day0_Rep1_RNA


title: human_NPC_Day3_Rep1_RNA


title: MhcNCxAmyrel_10daysOld_HEAD_A

description: Mhc>+ (isogenic control) replicate 1


title: Control_BloodCD8-1


title: MhcGal4CG6272_BL33652_n3

description: Mhc>CG6272RNAi (muscle-specific CG6272 RNAi) replicate 3

source_name: Thoraces (muscle) from 10-day-old male flies

value: muscle


title: rat_DE_Day2_Rep1_RNA

value: Day 2


title: Control_BloodCD4-3

value: blood CD4 T cell


title: Exp-13F-Control-A

first: Ricardo

last: de Matos Simoes

address: 450 Brookline AVE

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Multiple Myeloma

growth_protocol: MM.1S cells were seeded in 6-well plates (2x106/well) and cultured overnight prior to treatment.

extract_protocol:
RNA was extracted from the tumor cells using RNA extraction kit (Qiagen) and RNA sequencing was performed using Illumina NextSeq 500 Next Gen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 12h, dBET6 (100nM or 500nM) or JQ1 (500nM) was added to the cultures, then cells were harvested after 4h or 18h and immediately frozen (-80ºC). In order to assess transcriptional modulation by dBET6, RNA was extracted as previously described (Matthews et al., 2015) and analyzed using next-generation sequencing by the Molecular Biology Core Facilities (MBCF, DFCI). All samples and corresponding untreated controls were measured in triplicates and sequenced with technical replication for each sample.


title: rat_DE_Day1_Rep2_RNA


title: Exp-13F-500nM-JQ1-4h-B

value: 500nM JQ1

tag: time point


title: MhcGal4CG6272_BL33652_n2

description: Mhc>CG6272RNAi (muscle-specific CG6272 RNAi) replicate 2

value: male

value: 10 days


title: Control_BloodCD4-2


title: Exp-13F-500nM-JQ1-4h-A


title: rat_NPC_Day8_Rep2_RNA

tag: differentiation

value: Neural Progenitor Cells

value: Day 8


title: MhcGal4CG6272_BL33652_n1

description: Mhc>CG6272RNAi (muscle-specific CG6272 RNAi) replicate 1


title: Exp-13F-500nM-JQ1-18h-B


title: FD_TER94_3TH

description: Mhc>Ter94RNAi (muscle-specific Ter94 RNAi) replicate 3


title: rat_NPC_Day8_Rep1_RNA

tag: day of differentiation


title: Control_Blood_Monocyte3

value: peripheral blood

tag: cell type

value: blood monocyte


title: Exp-13F-500nM-JQ1-18h-A


title: rat_NPC_Day7_Rep2_RNA

value: Day 7


title: Control_BloodCD4-1


title: FD_TER94_1TH

description: Mhc>Ter94RNAi (muscle-specific Ter94 RNAi) replicate 1

tag: genotype


title: Exp-13F-500nM-dBET6-4h-B

value: 500nM dBET6


title: FD_TER94_2TH

description: Mhc>Ter94RNAi (muscle-specific Ter94 RNAi) replicate 2


title: Control_Blood_Monocyte2


title: FD_ProsB5_3TH

description: Mhc>ProsB5RNAi (muscle-specific ProsB5 RNAi) replicate 3


title: Exp-13F-500nM-dBET6-4h-A


title: Exp-13F-Control-B


title: Control_Blood_Monocyte1


title: Control_MG3_brain

source_name: mouse brain

value: brain

value: microglia


title: rat_NPC_Day6_Rep2_RNA

value: Day 6


title: rat_DE_Day1_Rep1_RNA

value: Definitive Endoderm

value: Day 1


title: rat_NPC_Day6_Rep1_RNA


title: Control_MG2_brain

value: C57BL/6J (CRL)


title: FD_ProsB5_1TH

description: Mhc>ProsB5RNAi (muscle-specific ProsB5 RNAi) replicate 1

value: muscle


title: Exp-13F-500nM-dBET6-18h-A


title: rat_NPC_Day5_Rep2_RNA

value: Day 5


title: Exp-13F-100nM-dBET6-4h-B

value: 100nM dBET6


title: Control_MG1_brain


title: rat_NPC_Day5_Rep1_RNA


title: rat_NPC_Day4_Rep2_RNA

value: Day 4


title: FD_ProsB1_1TH

description: Mhc>ProsB1RNAi (muscle-specific ProsB1 RNAi) replicate 1

value: male

value: 10 days


title: rat_NPC_Day7_Rep1_RNA

value: Neural Progenitor Cells


title: RNAP2pSer5 ChIP-Seq Method 2

city: Davis

first: Commodore

middle: Perry

last: St. Germain

address: One Shields Avenue

department: Microbiology and Molecular Genetics

institute: University of California, Davis

data_processing:
Sequenced reads were trimmed using Trimmomatic v0.36, mapped to the mm10 whole genome using bowtie2 v2.2.8
Unpaired, unmapped, and PCR duplicates were removed with samtools v1.9, Converted to bedGraph and normalized to RPM using bedtools genomecov, and converted to bigwig using wigToBigWig
Peaks were called using macs2 callpeak v2.2.5 option --nomodel
Differential binding was measured between the experimental and control samples using DiffBind v2.16.0 with the option minOverlap=0
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs for each sample
Supplementary_files_format_and_content: called peaks for each sample in BED format
Supplementary_files_format_and_content: differential binding analysis for macs2 peaks in CSV
Supplementary_files_format_and_content: differential binding analysis for TSS in CSV
Supplementary_files_format_and_content: transcription-replication interaction regions with genes in CSV

source_name: Spleen

growth_protocol: B cells were isolated from mice spleen, stimulated with IL4, LPS, and anti-CD180 in B cell media and grown at 37C, 5% CO2 for 72 hours

extract_protocol:
Lysates were clarified from sonicated cells and RNAP2-DNA or RNA-DNA complexes were isolated with antibody. The crosslinks were reversed for the RNAP2 enriched material, purified, and for the TRIPn-Seq samples - sequencing adapters were ligated before the BrdU immunoprecipitation.
Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: The TRIPn-Seq experimental cells were treated with 10 uM BrdU for 30 minutes before harvesting, crosslinked with formaldehyde, quenched with glycine, washed, and snap frozen in EtOH/dry ice and stored at -80C. The DRIP-Seq samples were not crosslinked.

value: spleen

value: 4-6 months

value: wild type

tag: antibody


title: RNAP2pSer5 ChIP-Seq Method 1

tag: strain


title: rat_NPC_Day4_Rep1_RNA


title: FD_white_3TH

description: Mhc>whiteRNAi (control RNAi) replicate 3

tag: age

value: Mhc>whiteRNAi


title: Exp-13F-100nM-dBET6-18h-A


title: Exp-13F-100nM-dBET6-18h-B


title: rat_NPC_Day3_Rep2_RNA

value: Day 3


title: FD_ProsB5_2TH

description: Mhc>ProsB5RNAi (muscle-specific ProsB5 RNAi) replicate 2


title: TRI Cont Method 2

data_processing:
Library strategy: TRIPn-Seq
Sequenced reads were trimmed using Trimmomatic v0.36, mapped to the mm10 whole genome using bowtie2 v2.2.8
Unpaired, unmapped, and PCR duplicates were removed with samtools v1.9, Converted to bedGraph and normalized to RPM using bedtools genomecov, and converted to bigwig using wigToBigWig
Peaks were called using macs2 callpeak v2.2.5 option --nomodel
Differential binding was measured between the experimental and control samples using DiffBind v2.16.0 with the option minOverlap=0
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs for each sample
Supplementary_files_format_and_content: called peaks for each sample in BED format
Supplementary_files_format_and_content: differential binding analysis for macs2 peaks in CSV
Supplementary_files_format_and_content: differential binding analysis for TSS in CSV
Supplementary_files_format_and_content: transcription-replication interaction regions with genes in CSV


title: Exp-13F-500nM-dBET6-18h-B

value: 500nM dBET6


title: rat_NPC_Day3_Rep1_RNA


title: FD_white_2TH

description: Mhc>whiteRNAi (control RNAi) replicate 2


title: Exp-13E-Control-A


title: DRIP-Seq

data_processing:
Library strategy: DRIP-Seq
Sequenced reads were trimmed using Trimmomatic v0.36, mapped to the mm10 whole genome using bowtie2 v2.2.8
Unpaired, unmapped, and PCR duplicates were removed with samtools v1.9, Converted to bedGraph and normalized to RPM using bedtools genomecov, and converted to bigwig using wigToBigWig
Peaks were called using macs2 callpeak v2.2.5 option --nomodel
Differential binding was measured between the experimental and control samples using DiffBind v2.16.0 with the option minOverlap=0
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs for each sample
Supplementary_files_format_and_content: called peaks for each sample in BED format
Supplementary_files_format_and_content: differential binding analysis for macs2 peaks in CSV
Supplementary_files_format_and_content: differential binding analysis for TSS in CSV
Supplementary_files_format_and_content: transcription-replication interaction regions with genes in CSV

value: 8.5 months


title: Exp-13E-Control-B


title: FD_ProsB1_3TH

description: Mhc>ProsB1RNAi (muscle-specific ProsB1 RNAi) replicate 3


title: FD_ProsB1_2TH

description: Mhc>ProsB1RNAi (muscle-specific ProsB1 RNAi) replicate 2


title: FD_GFP_3TH

description: Mhc>GFPRNAi (control RNAi) replicate 3

value: Mhc>GFPRNAi


title: FD_white_1TH

description: Mhc>whiteRNAi (control RNAi) replicate 1


title: rat_NPC_Day2_Rep2_RNA

value: Day 2


title: TRI Cont Method 1 Rep 2

value: 6.5 months


title: rat_NPC_Day2_Rep1_RNA


title: Exp-13F-100nM-dBET6-4h-A


title: FD_GFP_2TH

description: Mhc>GFPRNAi (control RNAi) replicate 2

value: muscle


title: Exp-13E-500nM-JQ1-4h-A

value: 500nM JQ1


title: TRI Exp Method 1 Rep 2

value: 10 uM BrdU 30 mins


title: TRI Exp Method 2


title: rat_NPC_Day1_Rep2_RNA

value: Day 1


title: TRI Cont Method 1 Rep 1


title: FD_GFP_1TH

description: Mhc>GFPRNAi (control RNAi) replicate 1

value: male


title: rat_NPC_Day1_Rep1_RNA


title: Exp-13E-500nM-JQ1-18h-B


title: TRI Exp Method 1 Rep 1


title: rat_ESC_Day0_Rep2_RNA

value: Embryonic Stem Cells

value: Day 0


title: Exp-13E-500nM-JQ1-4h-B


title: Dmel_BG3-c2_rep1

description:
Dmel_anticodon_counts.csv
Dmel_isodecoder_counts.csv

source_name: BG3-c2 cells

tag: cell line

value: 42C, 75mM KCl, 16 hour primer-dependant RT reaction


title: Exp-13E-500nM-JQ1-18h-A


title: Exp-13E-500nM-dBET6-4h-B


title: Exp-13E-500nM-dBET6-4h-A


title: DpnII transcription block control Hi-C on coccoids cells clone D3 replicate 1 [Dino-HiC-cD3-DSG-DMSO-R1-T1]

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

institute: University of Massachusetts Medical School

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-cD3-DSG-DMSO-R1-T1.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-DMSO-R1-T1.smic1.1N.mapq_30.1000.mcool

data_processing:
library strategy: In situ Hi-C
In situ Hi-C  FASTQ sequencing files were mapped to Smic1.0 and Smic1.1N
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
Genome_build: Smic1.0 and Smic1.1N
Supplementary_files_format_and_content: multitires cooler files '.mcool' of all interactions

organism: Symbiodinium microadriaticum

source_name: whole organism

growth_protocol: Cells were grown in F/2 medium with antibiotics cocktail as described in detail in supplemental methods.

extract_protocol:
For each In situ Hi-C library ~20 million cells were crosslinked.
In situ Hi-C was performed as described in detail in supplemental methods.

treatment_protocol: No special treatment

value: Symbiodinium microadriaticum Bigelow Laboratory for Ocean Sciences  (CCMP2467-SC)

tag: protocol

value: In situ Hi-C

tag: enzyme

value: DpnII


title: 33W_snATAC

city: Copenhagen

first: Tune

last: Pers

address: Blegdamsvej 3B

institute: University of Copenhagen

description:
snATAC_unnormdata.csv.gz
snATAC_normdata.csv.gz
snATAC_metadata.csv.gz

data_processing:
Read alignment of the snRNA-seq data: Raw sequencing reads were processed using the 10x Genomics Cell Ranger version 3.0 pipeline and aligned with default parameters. For each sample, a UMI count matrix was generated using both exonic and intronic reads.
Read alignment of the snATAC-seq data: Raw sequencing reads were processed using the Cell Ranger ATAC version 1.1.0 pipeline and aligned with default parameters.
Quality control of the snRNA-seq data: Cells with a mitochondrial RNA content >5% were discarded and doublets were removed using DoubletFinder version 2.0.0. Furthermore, cells that could not confidently be assigned to a cluster were removed using a multi-step procedure. See article for details.
Quality control of the snATAC-seq data: Fragments that were uniquely mapped (mapping quality score>30) and with proper length (50 bp<length<1000 bp) were kept. Based on visual inspection, high-quality cells were detected based on the number of unique fragments and fragments in promoter ratio (selecting cells with 1,000<unique fragments<100,000; 0.15<fragments in promoter ratio<0.6). Furthermore, cells that could not confidently be assigned to a cluster were removed using a multi-step procedure. See article for details.
Peak calling: Cells belonging to the same cluster were aggregated, and accessible peaks were called clusterwise using MACS2 version 2.2.6.
Normalization of the snRNA-seq data: Counts for each cell were normalized by the total gene expression of that cell, multiplied by 10,000 and log-transformed.
Normalization of the snATAC-seq data: Counts were normalized using term-frequency inverse-document-frequency normalization.
Genome_build: mm10
Supplementary_files_format_and_content: snRNA_unnormdata.csv.gz: comma-separated, gzip archived. Content: gene*cell matrix containing the filtered gene expression counts.
Supplementary_files_format_and_content: snRNA_normdata.csv.gz: comma-separated, gzip archived. Content: gene*cell matrix containing the filtered and normalized gene expression counts.
Supplementary_files_format_and_content: snRNA_metadata.csv.gz: comma-separated, gzip archived. Content: snRNA-seq metadata. Columns: nCount_RNA, nFeature_RNA, sample, percent.mito, percent.ribo, cell.type, neuronal.subtype.
Supplementary_files_format_and_content: snATAC_unnormdata.csv.gz: comma-separated, gzip archived. Content: peak*cell matrix containing the filtered peak counts.
Supplementary_files_format_and_content: snATAC_normdata.csv.gz: comma-separated, gzip archived. Content: peak*cell matrix containing the filtered and normalized peak counts.
Supplementary_files_format_and_content: snATAC_metadata.csv.gz: comma-separated, gzip archived. Content: snATAC-seq metadata. Columns: nCount_peaks, nFeature_peaks, nCount_activity, nFeature_activity, sample, cell.type, neuronal.subtype.

source_name: Single-nucleus ATAC-sequencing of the DVC

extract_protocol:
Libraries were prepared using the 10x Genomics Chromium single-cell ATAC reagent kits. Libraries were sequenced on an Illumina NovaSeq 6000.
Nuclei were purified with reagents from the Nuclei Pure Prep Nuclei Isolation Kit (Sigma-Aldrich, NUC-201). See article for details.

treatment_protocol: Amimals were weight-matched to the semaglutide-administered group. Animals were terminated by decapitation under CO2/O2 anaesthesia.

value: 26 weeks

tag: number of mice

value: DVC

tag: rna population


title: 34W_snATAC

tag: tissue


title: Exp-13E-500nM-dBET6-18h-B

tag: treatment

value: 500nM dBET6


title: Exp-13E-500nM-dBET6-18h-A


title: rat_ESC_Day0_Rep1_RNA


title: Dmel_BG3-c2_rep2

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v2.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline using the common parameters --snp-tolerance --cluster --min-cov 2000 --max-mismatches 0.1 --cca-analysis --remap --remap-mismatches 0.075 and unique options for --control-condition and --cluster-id (0.90 for budding yeast, 0.95 for fission yeast and Drosophila, and 0.97 for human samples). HEK293T samples were addiitonally aligned to a collapsed non-redundant reference with Bowtie (parameters -m 1 -v3 --best --strata) or Bowtie 2 in local mode (--local -k 100 --very-sensitive --ignore-quals --np 5 --reorder).
Genome_build: S288c, 972h, dm6, hg19

extract_protocol:
RNA from Drosophila BG3-c2, HEK293T, and human iPS cells was isolated with Trizol (Sigma Aldrich) according to the manufacturer’s instructions. For total RNA isolation from yeast, frozen cells were resuspended in 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0, 1% SDS (1 ml per 50 OD600 units). An equal volume of hot acid phenol (pH=4.3) was added, and the cell suspension was vortexed vigorously followed by incubation at 65℃ for 5 min with intermittent mixing. After addition of 1/10 volume 1-Bromo-3-chloropropane (BCP, Sigma Aldrich), samples were centrifuged at 10,000 x g for 5 min and the aqueous phase was transferred to a new tube. Following an additional round of hot acid phenol/BCP and a round of BCP only extraction, RNA was precipitated from the aqueous phase by the addition of 3 volumes of ethanol. For RNA isolation from yeast under conditions that preserve tRNA charging, frozen cells were resuspended in ice-cold 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0. One volume of cold acid phenol (pH=4.3) was added and cells were lysed with glass beads. One-tenth volume of BCP was then added and the samples were centrifuged at 10,000 x g/4℃ for 5 min, followed by a second round of cold phenol-BCP and one round of BCP-only extraction. RNA was ethanol-precipitated from the aqueous phase and pellets were washed in 80% ethanol containing 50 mM sodium acetate, pH=4.5, briefly air-dried, and resuspended in 50 mM sodium acetate pH=4.5, 1 mM EDTA pH=8.0. Two synthetic standards corresponding to E.coli tRNALys(UUU) with intact 3’-CCA (5’-GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA-3’) or a 3’-CC (5’- GGGTCGTTAGCTCAGTTGGTAG AGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACC-3’) were added to 5 - 10 µg of total RNA in a 3:1 molar ratio at 0.06 pmol/µg, followed by incubation at 37oC in 50 mM Tris-HCl pH=9.0 to deacylate tRNAs. Deacylation was omitted for samples subjected to oxidation and β-elimination. Total RNA was subsequently dephosphorylated and purified by ethanol precipitation in 0.3M sodium acetate pH=4.5 with 25 µg glycogen (Ambion) as a carrier. RNA was resolved on a denaturing 10% polyacrylamide/7M urea/1xTBE gel and species migrating at the size range of mature tRNAs (60 – 90 nt) were excised and gel slices were crushed with disposable pestles. Following addition of 400 µl gel elution buffer (0.3M sodium acetate pH=4.5, 0.25% SDS, 1mM EDTA pH=8.0), the gel slurry was incubated at 65℃ for 10 min, snap-frozen on dry ice, and thawed at 65℃ for 5 min. RNA was eluted overnight at room temperature with continuous mixing. Gel pieces were removed with Costar Spin-X centrifuge tube filters and RNA was recovered from the flow-through by ethanol precipitation in the presence of 25 µg of glycogen.
50 to 200 ng of gel-purified tRNA was ligated to one of four adapters with distinct barcodes.Ligation was performed for 3 hours at 25°C in a 20-µl reaction volume containing pre-adenylated adapter and RNA substrate in a 4:1 molar ratio, 1x T4 RNA Ligase Reaction Buffer, 200 U of T4 RNA ligase 2 (truncated KQ; NEB), 25% PEG 8000, and 10 U SUPERase In (Ambion). Ligation products were separated from excess adapter on denaturing 10% polyacrylamide/7M urea/1xTBE gels. Bands migrating at 95-125 nt were excised and ligation products were recovered from crushed gel slices. Reverse transcription reactions contained 125 nM adapter-ligated tRNA pool, 125 nM primer(5’pRNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’) and 500 nM TGIRT (InGex) in a final volume of 20 µl. Reactions were performed in 50 mM Tris-HCl pH=8.3, 75 mM KCl, 3 mM MgCl2, 5 mM DTT (from a freshly made 100 mM stock), and 10 U SUPERase In. After TGIRT addition, reactions were pre-incubated at 42℃ for 10 min, initiated by addition of dNTPs to a final concentration of 1.25 mM, and incubated at 42℃ for 16 hours in a Themrocycler. For Superscript III RT, template and primer were denatured at 75℃ for 5 min and chilled on ice, and reverse transcription was performed in the presence of 1X First-Strand Buffer, 5 mM DTT, 0.5 mM dNTPs, 10 U SUPERase In, and 200 U Superscript III (Invitrogen) at 57℃ for 60 min. Template RNA was hydrolyzed by the addition of 1 µl 5M NaOH and incubation at 95℃ for 3 min. cDNA between 60 and 150 nt was excised and cDNA was eluted from crushed gel slices in 400 µl 10 mM Tris-HCl pH=8.0, 1 mM EDTA at 70℃/2000 rpm for 1 hour in a Thermoblock, followed by ethanol precipitation. Purified cDNA was circularized with CircLigase ssDNA ligase (Lucigen) in 1x reaction buffer supplemented with 1 mM ATP, 50 mM MgCl2, and 1M betaine for 3 hours at 60℃, followed by enzyme inactivation for 10 min at 80℃. One-fifth of circularized cDNA was directly used for library construction PCR. Amplification was performed with KAPA HiFi Polymerase in 1x GC buffer with initial denaturation at 95℃ for 3 min, followed by five to six cycles of 98℃ for 20 sec, 62℃ for 30 sec, 72℃ for 30 sec. PCR products were purified with DNA Clean&Concentrator (Zymo Research) and resolved on 8% polyacrylamide/1xTBE gels alongside pBR322 DNA-MspI Digest (NEB). The 130-220 bp region of each lane was excised and DNA was eluted from crushed gel slices in 400 µl water with continuous mixing at room temperature overnight. After ethanol precipitation in 0.3M sodium acetate pH=5.5 and 25 µg glycogen, libraries were dissolved in 10 µl 10 mM Tris-HCl pH=8.0, quantified with Qubit, and sequenced for 150 cycles on an Illumina NextSeq platform.


title: Panobinostat treatment, biological replicate 3

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

country: Australia

institute: The University of New South Wales

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: The probes from the Clariom D microarray were assigned to Ensembl Genes using custom chip definition file (CDF) clariomdhumanhsensgcdf (version 22.0.0) from (http://mbni.org/customcdf/22.0.0/ensg.download/clariomdhumanhsensgcdf_22.0.0.tar.gz) (PMID 16284200). The array data were analysed using Bioconductor/R andhe Robust MultiArray (RMA) pipeline (PMID 21070630), and batch effects were removed using the remove unwanted variation (ruv) R library and the RUVIII function (PMID 31114909) with one unwanted factor (k=1).

label: biotin

source_name: DIPG neurospheres, panobinostat treatment

label_protocol: As per Affymetrix protocol

growth_protocol: HSJD-DIPG007 cells were cultured in DMEM/F12 and Neurobasal media (1:1) supplemented with HEPES, non-essential amino acids, antibiotic/antimycotic, pyruvate, glutamax, heparin, B27, human EGF, human FGF, PDGF-AA and PDGF-BB for 72 hours to form neurospheres.

extract_protocol: RNA was extracted using the RNeasy extraction kit (Qiagen; Cat No./ID: 74106) according to the manufacturer’s instruction.

treatment_protocol: 72 hours after incubation, cells were treated for 24 hours with DMSO, 0.6μM CBL0137, 20nM panobinostat and the combination of the two agents.

value: Diffuse intrinsic pontine glioma (DIPG) neurospheres

value: panobinostat


title: DpnII transcription block Hi-C on coccoids cells clone D3 replicate 1 [Dino-HiC-cD3-DSG-TPL50uM-DRB400uM-R1-T1]

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-cD3-DSG-TPL-DRB.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL-DRB.smic1.1N.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL50uM-DRB400uM-R1-T1.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL50uM-DRB400uM-R1-T1.smic1.1N.mapq_30.1000.mcool


title: DpnII transcription block Hi-C on coccoids cells clone D3 replicate 1 [Dino-HiC-cD3-DSG-TPL25uM-DRB200uM-R1-T1]

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-cD3-DSG-TPL-DRB.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL-DRB.smic1.1N.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL25uM-DRB200uM-R1-T1.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD3-DSG-TPL25uM-DRB200uM-R1-T1.smic1.1N.mapq_30.1000.mcool


title: 20W_snATAC

department: Novo Nordisk Foundation Center for Basic Metabolic Research

growth_protocol: Animals were single-housed with ad libitum access to 60% HFD (#12492 Research Diets) and tap water in controlled environment (temperature 22 ± 2°C; relative humidity 50 ± 10%; 12-hour light/dark cycle).


title: DpnII Hi-C on mastigotes cells clone D7 replicate 2

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD7plus-R2.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD7plus-R2.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool

data_processing:
In situ Hi-C  FASTQ sequencing files were mapped to Smic1.0 and Smic1.1
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
Genome_build: Smic1.0 and Smic1.1
Supplementary_files_format_and_content: multitires cooler files '.mcool' of all interactions

value: Bigelow Laboratory for Ocean Sciences  (CCMP2467-SC)


title: Exp-13E-100nM-dBET6-4h-A

value: 100nM dBET6


title: 7W_snATAC


title: Panobinostat treatment, biological replicate 1


title: Panobinostat treatment, biological replicate 2


title: DpnII Hi-C on mastigotes cells clone D4 replicate 2

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD4plus-R2.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD4plus-R2.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: 37W_snATAC


title: 40S_snATAC


title: 39S_snATAC


title: DpnII Hi-C on mastigotes cells clone D4 replicate 1

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD4plus-R1.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD4plus-R1.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: Exp-13E-100nM-dBET6-18h-A


title: Control (DMSO), biological replicate 2

source_name: DIPG neurospheres, control without treatment

value: control without treatment


title: DpnII Hi-C on mastigotes cells clone D7 replicate 1

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD7plus-R1.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD7plus-R1.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: Exp-13D-Control-B


title: Exp-13E-100nM-dBET6-4h-B


title: DpnII Hi-C on mastigotes cells clone D3 replicate 2

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD3plus-R2.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD3plus-R2.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: DpnII Hi-C on mastigotes cells clone D3 replicate 1

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD3plus-R1.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD3plus-R1.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: 30S_snATAC


title: Exp-13D-Control-A


title: Exp-13E-100nM-dBET6-18h-B


title: DpnII Hi-C on mastigotes cells clone D1 replicate 2

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD1plus-R2.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD1plus-R2.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: Control (DMSO), biological replicate 1


title: 5S_snATAC


title: Combined CBL0137 and Panobinostat treatment, biological replicate 3

source_name: DIPG neurospheres, treated with a combination of CBL0137 andPanobinostat


title: Control (DMSO), biological replicate 3


title: 32V_snATAC


title: Combined CBL0137 and Panobinostat treatment, biological replicate 2

value: a combination of CBL0137 andPanobinostat


title: CBL0137 treatment, biological replicate 3

source_name: DIPG neurospheres, treated with CBL0137


title: Exp-13D-500nM-JQ1-4h-A

value: 500nM JQ1


title: Exp-13D-500nM-JQ1-18h-B


title: Combined CBL0137 and Panobinostat treatment, biological replicate 1


title: 25V_snATAC

value: male


title: Dino-PacBio-mD7plus-R1

description: symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.

data_processing:
Library strategy: Genomic DNA extraction for PacBio Sequencing
PacBio data is used for gapclosing for Smic1.0
publicly available LR_Gapcloser (https://github.com/CAFS-bioinformatics/LR_Gapcloser)
Genome_build: Smic1.0 and Smic1.1
Supplementary_files_format_and_content: fasta file Smic1.1

source_name: Genomic DNA extraction of mastigotes cells clone D7 replicate 1 for PacBio sequencing

extract_protocol:
QIAGEN DNeasy Plant Mini Kits
PacBio Express 2.0 Kit according to the manufacturer’s instructions as described in detail in supplemental methods.

value: Genomic DNA extraction


title: 31S_snATAC


title: DpnII Hi-C on mastigotes cells clone D1 replicate 1

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-mD1plus-R1.smic1.0.mapq_30.1000.mcool
Dino-HiC-mD1plus-R1.smic1.1N.mapq_30.1000.mcool
HiC-mDplus.smic1.0.mapq_30.1000.mcool
HiC-mDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: DpnII Hi-C on coccoids cells clone D7 replicate 2

description:
symbiodinium microadriaticum whole organism from Gulf of Aqaba near Asia.
processed data file:
Dino-HiC-cD7plus-R2.smic1.0.mapq_30.1000.mcool
Dino-HiC-cD7plus-R2.smic1.1N.mapq_30.1000.mcool
HiC-cDplus.smic1.0.mapq_30.1000.mcool
HiC-cDplus.smic1.1N.mapq_30.1000.mcool
HiC-Dplus.smic1.0.mapq_30.1000.mcool
HiC-Dplus.smic1.1N.mapq_30.1000.mcool


title: 23V_snATAC


title: Exp-13D-500nM-dBET6-4h-B


title: Exp-13D-500nM-JQ1-18h-A