title: G40G2D217V15_L8.D702

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: number of reads mapped to the genes in all samples

tag: subject

tag: day

value: M

tag: protectionstatus

tag: description of day

value: Day of Challenge

value: PBMC


title: A-83_V15_MP215A-83_L1.LB15

status: Public on Apr 21 2020

type: SRA

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

library_source: transcriptomic

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited normalized gene counts table

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: patient id

tag: gender

value: Female

tag: ethnicity

value: White - caucasian / european heritage

tag: treatment

tag: protection

value: NOT PROTECTED


title: A-41_V5_MP205A-41_L4.LB20

value: African heritage / african american


title: R-37_V21_MP221R-37_L3.LB10

value: RTSS+RTSS+RTSS


title: US-1473390_L7.LB7

value: Male


title: A-180_V5_MP205A-180_L3.LB18


title: A-35_V2_MP202A-35_L7.LB16


title: G40G2D199V11_L1.D711

value: Day 3 post VAC3

tag: cell type


title: G40G2D197V10_L7.D710

value: Day 1 post VAC3


title: I88G2D199V11_L5.D709


title: I88G2D217V15_L6.D711


title: G40G2D196V09_L7.D709

value: Day of VAC3


title: I88G2D197V10_L5.D708


title: I88G2D210V14_L6.D710

value: Day 14 post VAC3


title: W15G2D210V14_L4.D710


title: W15G2D197V10_L3.D708


title: W15G2D199V11_L3.D709


title: W15G2D217V15_L4.D711


title: W15G2D196V09_L3.D707


title: I88G2D140V02_L5.D706

value: PreVAC


title: W15G2D140V02_L3.D706


title: M92G2D210V14_L2.D703

value: F


title: M92G2D196V09_L2.D712


title: M92G2D199V11_L5


title: H61G2D199V11_L4.D701


title: H61G2D210V14_L4.D702


title: M92G2D140V02_L2.D711


title: G40G2D140V02_L7.D708


title: H61G2D196V09_L4.D711


title: X24G2D217V15_L1.D707


title: H61G2D197V10_L4.D712


title: X24G2D210V14_L5.D706


title: G40G2D210V14_L8.D712


title: X24G2D199V11_L5.D705


title: X24G2D197V10_L4.D704


title: X24G2D140V02_L4.D702


title: T69G2D217V15_L8.D710


title: X24G2D196V09_L4.D703


title: T69G2D199V11_L7.D708


title: T69G2D197V10_L7.D707


title: T69G2D196V09_L7.D706


title: K37G2D217V15_L3.D709


title: M92G2D197V10_L4


title: K37G2D199V11_L3.D707


title: H61G2D217V15_L4.D703


title: K37G2D196V09_L3.D705


title: K37G2D197V10_L3.D706


title: Y52G2D217V15_L7.D704


title: T69G2D140V02_L7.D705


title: K37G2D140V02_L2.D704


title: Y52G2D210V14_L6.D703


title: Y52G2D196V09_L6.D712


title: Y52G2D197V10_L6.D701


title: Y72G2D217V15_L8.D711


title: Y52G2D199V11_L6.D702


title: Y72G2D210V14_L8.D710


title: Y72G2D199V11_L7.D709


title: Y72G2D197V10_L7.D708


title: Y72G2D196V09_L7.D707


title: I45G2D217V15_L5.D709


title: I45G2D210V14_L5.D708


title: Y72G2D140V02_L7.D706


title: I45G2D199V11_L5.D707


title: K43G2D140V02_L3.D701


title: K43G2D196V09_L3.D702


title: K43G2D197V10_L3.D703


title: K43G2D217V15_L3.D706


title: I45G2D140V02_L4.D704


title: K43G2D210V14_L3.D705


title: E59G2D196V09_L1.D709


title: E59G2D199V11_L1


title: E59G2D217V15_L2.D701


title: K43G2D199V11_L3.D704


title: E59G2D140V02_L1.D708


title: Q64G2D217V15_L7.D707


title: Y47G2D197V10_L6.D701


title: Q64G2D210V14_L7.D706


title: Y47G2D140V02_L6.D711


title: Y47G2D196V09_L6.D712


title: Y47G2D199V11_L6.D702


title: E59G2D210V14_L2.D712


title: E59G2D197V10_L1.D710


title: Y47G2D210V14_L1.D703


title: Q64G2D197V10_L7.D704


title: Q64G2D140V02_L7.D702


title: Q64G2D196V09_L7.D703


title: F34G2D199V11_L4.D702


title: V44G1D217V17_L2.D703


title: F34G2D197V10_L4.D712


title: V44G1D210V16_L2.D702


title: F34G2D217V15_L5.D704


title: V44G1D199V13_L2.D701


title: N80G1D210V16_L1.D708


title: F34G2D196V09_L4.D711


title: V44G1D197V12_L2.D712


title: V44G1D196V11_L2.D711


title: V44G1D-07V02_L1.D710


title: N80G1D217V17_L1.D709


title: F34G2D140V02_L4.D710


title: N80G1D199V13_L1.D707


title: N80G1D196V11_L1.D705


title: F34G2D210V14_L4.D703


title: P50G1D217V17_L7.D705


title: P50G1D199V13_L6.D703


title: P50G1D196V11_L6.D701


title: P50G1D197V12_L6.D702


title: N80G1D197V12_L1.D706


title: N80G1D-07V02_L8.D704


title: C60G1D217V17_L2.D711


title: C60G1D210V16_L2.D710


title: P50G1D-07V02_L6.D712


title: P50G1D210V16_L7.D704


title: C60G1D197V12_L1.D708


title: C60G1D196V11_L1.D707


title: K37G2D210V14_L3.D708


title: Z38G1D217V17_L8.D701


title: C60G1D199V13_L1.D709


title: Z38G1D199V13_L8.D711


title: Z38G1D210V16_L8.D712


title: Z38G1D197V12_L8.D710


title: Z38G1D196V11_L8.D709


title: Z38G1D-07V02_L8.D708


title: R100G1D217V17_L7.D707


title: R100G1D210V16_L7.D706


title: R100G1D199V13_L1.D705


title: Q64G2D199V11_L7.D705


title: R100G1D197V12_L1.D704


title: R100G1D196V11_L1.D703


title: R100G1D-07V02_L6.D702


title: C60G1D-07V02_L1.D706


title: F25G1D217V17_L1.D706


title: F25G1D199V13_L1.D704


title: H61G2D140V02_L3.D710


title: F25G1D197V12_L1.D703


title: I88G2D196V09_L5.D707


title: F25G1D210V16_L1.D705


title: F25G1D196V11_L1.D702


title: F25G1D-07V02_L1.D701


title: P84G1D197V12_L8.D712


title: K97G1D217V17_L3.D703


title: HUVECs_Control gapmeR transfected_1

type: RNA

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-core
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuEx-1_0-st-v2
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: HUVEC human umbilical vein endothelial cells

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

growth_protocol: HUVECs were transfected at a confluency of 70% and harvested 48h after transfection.

extract_protocol: All samples were prepared using miRNeasy Kit (Qiagen) including DNase treatment. cDNA synthesis and amplification was performed using the Ambion WT Expression Kit (Affymetrix).

tag: tissue

tag: genotype/variation

value: Control gapmeR


title: HUVECs_LASSIE gapmeR transfected_2

value: HUVEC human umbilical vein endothelial cells

value: LASSIE gapmeR


title: T69G2D210V14_L2


title: HUVECs_Control gapmeR transfected_3


title: HUVECs_LASSIE gapmeR transfected_1


title: K97G1D210V16_L2.D702

value: M


title: HUVECs_LASSIE gapmeR transfected_3


title: K97G1D199V13_L2.D701

value: PBMC


title: P84G1D210V16_L8.D702


title: P4F

city: Beirut

first: Wassim

last: Abou-Kheir

address: Bliss St. DTS Bldg.

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

country: Lebanon

institute: American University of Beirut

description: Isolate from tumor tissue

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the  Homo sapiens GRCh37 (hg19)  genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis
Genome_build: Homo sapiens GRCh37 (hg19) genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Tumor - Organoid (3D) 5 Factors + bFGF2

extract_protocol:
Total RNA was extracted using TriZol LS and Rneasy Mini Kit (Qiagen) according to manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

tag: patient number

value: prostate

tag: patient age


title: P84G1D199V13_L8.D701


title: I45G2D197V10_L5.D706


title: P84G1D196V11_L8.D711


title: P3E

description: Isolate from tumor tissue

source_name: Tumor - Cell (2D)


title: P4E

description: Isolate from tumor tissue

source_name: Tumor - Organoid (3D) 5 Factors + FGF10


title: Y52G2D140V02_L6.D711


title: HUVECs_Control gapmeR transfected_2


title: P2F

description: Isolate from tumor tissue


title: K97G1D-07V02_L2.D710


title: P84G1D217V17_L8.D703

value: Day of Challenge


title: P3D

description: Isolate from non-tumor tissue

source_name: Unaffected - Cell (2D)


title: F99G1D217V17_L2.D712


title: P84G1D-07V02_L7.D710


title: F99G1D210V16_L2.D711


title: F99G1D196V11_L2.D708


title: P4D

description: Isolate from tumor tissue

source_name: Tumor - Organoid (3D)


title: P4C

description: Isolate from non-tumor tissue

source_name: Unaffected - Organoid (3D)


title: P2E

description: Isolate from non-tumor tissue


title: P2C

description: Isolate from non-tumor tissue


title: F99G1D199V13_L2.D710


title: K97G1D197V12_L2.D712


title: F99G1D197V12_L2.D709


title: F99G1D-07V02_L2.D707


title: P2D

description: Isolate from tumor tissue


title: P3B

description: Isolate from tumor tissue

source_name: Tumor Tissue


title: M92G2D217V15_L2.D704


title: N82G1D210V16_L5.D709


title: I45G2D196V09_L5.D705


title: N82G1D199V13_L5.D708


title: P4B

description: Isolate from tumor tissue


title: P4A

description: Isolate from non-tumor tissue

source_name: Unaffected Tissue


title: N82G1D197V12_L5.D707


title: K97G1D196V11_L2.D711


title: P2B

description: Isolate from tumor tissue


title: P3A

description: Isolate from non-tumor tissue


title: P2A

description: Isolate from non-tumor tissue


title: N82G1D196V11_L5.D706


title: N82G1D-07V02_L5.D705


title: H5G1D217V17_L4.D704


title: PARN mutant O68C4, BCH001 treated

city: Baltimore

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

description:
counts_matrix_Nagpal_Agarwal_2020.csv
TPM_matrix_Nagpal_Agarwal_2020.csv

data_processing:
Sequence reads were trimmed to a final length of 40 bases using Trimming software Cutadapt (Martin, 2011).
Salmon (Patro et al., 2017) was used to quasi-map trimmed reads to the reference transcriptome (ENSEMBL (Zerbino et al., 2018) GRCh38.80), including 6511 non-coding RNAs (scaRNAs, lincRNAs, snRNAs, and snoRNAs), to estimate transcript abundances. The number of reads mapping to the transcriptome ranged from 7.7 to 12.0 million. Read counts per gene were derived by summing the counts per transcript across all transcripts associated with the gene
For quality control measures, 0.1% of reads were randomly sampled from each FASTQ and directly aligned to ENSEMBL GRC Release 80 (ftp://ftp.ensembl.org/pub/release-80/gtf/) reference genomes using HISAT2 (Kim et al., 2015) to determine percentage alignment to H. Sapiens, M. Musculus, S. Cerevisiae, E. Coli, and D. Rerio genomes, as well as overlaps with genomic features (including rRNA, mtRNA, protein-coding regions), ambiguous and non-unique alignments, and unaligned reads.
Genome_build: GRCh38.80
Supplementary_files_format_and_content: .csv files containing gene expression matrices in raw counts and TPM formats

source_name: iPSC

growth_protocol: Derivation, characterization, and culture conditions of iPSCs from fibroblasts for patients 1 and 2 were performed as described (Moon et al., 2015). Patient 3 fibroblasts were reprogrammed using the 4-in-1-dTomato lentiviral reprogramming vector (Warlich et al., 2011). DKC1-mutant iPSCs were as described (Agarwal et al., 2010). For feeder-free culture, iPSCs were maintained in Essential 8 medium (Life Technologies) on hES-qualified Matrigel matrix (BD Biosciences) and subcultured using Accutase (Stem Cell Technologies).

extract_protocol:
Total RNA was isolated and RNA quality was checked by both fragment analyzer (Agilent Fragment Analyzer) and electrophoresis on 1.5% agarose/formaldehyde gel.
0.1-1 μg of total RNA was used as input for library preparation using TruSeq Stranded Total RNA with RiboZero Gold kit (Illumina- 20020599). Briefly, the total RNA was subjected to rRNA depletion and fragmentation followed by first and second strand cDNA synthesis. Further, second strand was removed after end repair and A-tailing. Finally, libraries were amplified for size selection and pooled at equimolar concentrations based on quantifications by Fragment Analyzer. The pooled libraries were sequenced on two lanes of HiSeq 2500 High Output V4 chemistry and single read 50 bases format.

tag: disease status

value: Dyskeratosis congenita (DC), PARN mutant

value: Skin fibroblast-derived iPSCs


title: PARN mutant O68C4, untreated


title: H5G1D210V16_L4.D703


title: WT NHSF, BCH001 treated

value: Normal


title: N82G1D217V17_L6.D710


title: H5G1D-07V02_L7


title: WT NFF1, untreated


title: WT G319A, BCH001 treated


title: WT NFF1, BCH001 treated


title: G54G1D210V16_L5.D705


title: H5G1D196V11_L4.D712


title: G54G1D217V17_L5.D706


title: PARN mutant BCH14, BCH001 treated


title: G54G1D196V11_L5.D702


title: G54G1D199V13_L5.D704


title: G54G1D197V12_L5.D703


title: PARN mutant BCH14, untreated


title: WT G319A, untreated


title: PARN mutant 130C1, untreated


title: G54G1D-07V02_L5.D701


title: bcCML shStaufen 2 shRNA input

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

library_source: genomic

data_processing:
Bowtie2-alignment tool
Macs2-peak calling
Genome_build: hg38

molecule: genomic DNA

source_name: K562 cells

extract_protocol:
Zymo ChIP DNA clean & concentrator
KAPA Hyper Prep Kit

tag: cell line

value: K562 cells

tag: condition

value: Stau2 shRNA

tag: antibody

value: input


title: A70G1D217V17_L1.D701

tag: subject

tag: day


title: bcCML Control shRNA input

value: Control shRNA


title: A70G1D210V16_L6.D712

tag: protectionstatus

tag: description of day

value: Day 14 post VAC3


title: bcCML shStaufen 2 H3K4me3


title: H5G1D199V13_L4.D702

tag: gender

value: Day 3 post VAC3


title: bcCML shStaufen 2 H3K4me2


title: WT NHSF, untreated


title: H5G1D197V12_L4.D701

value: Day 1 post VAC3


title: A70G1D197V12_L5.D710


title: bcCML shControl H3K4me3


title: A70G1D196V11_L5.D709

value: Day of VAC3


title: A70G1D-07V02_L5.D708

value: PreVAC


title: PARN mutant 130C1, BCH001 treated


title: bcCML shControl H3K4me2


title: Y85G1D217V17_L6.D703


title: Mut_NR2F1_input_2

city: Shanghai

first: Ke

last: Zhang

address: No.320 Yueyang Road

country: China

institute: SIBCB

data_processing:
For RNA-Seq, gene expression levels were calculated by HISAT2 (version 2.1.0) and FeatureCounts (version 1.5.3) (Sahraeian et al., 2017) with the reference hg19. The differentially expressed genes (DEGs) were identified by DESeq2 (version 1.16.1) (Love et al., 2014) (padj<0.05, foldchange>2).
For ChIP-Seq, clean reads were mapped with Bowtie2 (version 2.3.1), then the peaks were called using MACS2 (version 2.1.1) main program (q<0.05) (Zhang et al., 2008). MACS2 bdgcmp was used to generate the logLR track, then the bedGraph files for the logLR track were converted to bigWig files. Correlations between biological replicates were calculated with wigCorrelate, then the biological replicates were merged with MACS2. All the above were run with default parameters. Further analysis was performed with ChIPseek (Chen et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each sample in RNA-Seq; merged bigwig files for ChIP-Seq.

source_name: Human neuron progenitors

growth_protocol: The protocol for human ES cell differentiation was described previously. Briefly, human ES cell colonies were digested by collagenase IV (2 mg/ml, Gibco) and floated in the hESC growth medium without basic FGF. Embryonic bodies (EBs) were formed after 4 days' suspension and subsequently floated for 2 days in the neural induction medium consisting of DMEM/F12, 1% N2 supplement (Gibco), GlutaMAX, NEAA, and β-ME. The EBs then were adhered to a dish coated by Matrigel and cultured in the neuron differentiation medium consisting of 50% DMEM/F12 medium, 50% Neurobasal medium, 1% N2 supplement, 2% B27 without vitamin A (Gibco), GlutaMAX, NEAA and β-ME for additional 10 days. Then the attached EBs were dissociated into small patches by collagenase IV and cultured in neuron differentiation medium as suspended neural spheres for 4 days. Finally, these neural spheres were digested with Accutase (Gibco) into single cells and plated on Matrigel-coated dishes in the neuron differentiation medium.

extract_protocol:
For RNA-Seq, total RNA was extracted by TRIzol and subjected to quality control and quantification; For ChIP-Seq, cross-linked cells were lysed in lysis buffer, and the samples were sheared for 14 cycles (30s on/off) in a Bioruptor Pico (Diagenode, Belgium) to achieve an average fragment size of 200-300 bp. Solubilized fragmented chromatin was immunoprecipitated with Anti-FLAG® M2 Magnetic Beads (M8823, Sigma-Aldrich). Antibody-chromatin complexes were pulled down using a magnetic separation rack, washed several times, and then eluted from the magnetic beads. Reverse crosslink was performed subsequently under 65℃ for at least 4 hours. ChIP-DNA was treated with RNase A and Proteinase K, precipitated with ethanol. ChIP-DNA was finally solved in nuclease-free water and quantified using Qubit (Thermo).
For RNA-Seq, cDNA libraries were generated using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370S, NEB). High-throughput sequencing was performed on a HiSeq2500 instrument at the Berry Genomics Co, Ltd, using a 125 bp paired-end-reads setting; For ChIP-Seq, sequencing libraries were generated by using the NEBNext Ultra DNA library preparation kit (E7370, NEB). Libraries were quality-controlled and quantified using a Qubit 2.0 Fluorometer (Life Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies). High-throughput sequencing was performed on a Illumina HiSeq instrument at the Berry Genomics Co, Ltd.

treatment_protocol: For RNA-Seq, no treatment was done; For ChIP-Seq, H9 hESCs-derived neuron progenitors at D20 were overexpressed by an equal amount of pcDNA3.1-WT/Mut-NR2F1-Flag plasmids, and the samples were collected 24 hours after transfection.

value: hESC-derived neuron progenitors

tag: passages

tag: chip-antibody

value: pcDNA3.1-WT/Mut-NR2F1-Flag plasmids


title: Y47G2D217V15_L6.D704

value: M

value: PBMC


title: WT_NR2F1_input_2

value: WT


title: Y85G1D210V16_L6.D702


title: Y85G1D197V12_L1.D712


title: Y85G1D196V11_L6.D711


title: Mut_NR2F1_input_1


title: Y85G1D199V13_L6.D701


title: Mut_NR2F1_IP_2

value: Anti-FLAG M2 Magnetic Beads (M8826, Sigma-Aldrich)


title: Y85G1D-07V02_L5.D710


title: WT_NR2F1_IP_2

value: Anti-FLAG M2 Magnetic Beads (M8824, Sigma-Aldrich)


title: WT_NR2F1_input_1


title: A70G1D199V13_L6.D711


title: D81G1D217V17_L7.D709

value: F

value: Day of Challenge


title: D81G1D197V12_L7.D706


title: D81G1D199V13_L7.D707


title: D81G1D196V11_L7.D705


title: D81G1D-07V02_L3


title: WT_NPC_1


title: Mut_NPC_1

value: Mut NPCs


title: Mut_NPC_2


title: WT_NPC_2


title: LS01_relapse_AML

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
fastq conversion (bcl2fastq 1.8.4)
alignment: bowtie2 (2.1.0) using --very-sensitive-local
peak calling and depth coverage generation (bedGraph): MACS 1.4.1 using -g hs --keep-dup=all -w -S
Genome_build: hg19
Supplementary_files_format_and_content: wig format (coverages)

source_name: PBMC

growth_protocol: All patient samples were collected at the point of diagnosis, remission following treatment or relapse and stored with written informed consent for research in one of four centres (Newcastle Haematology Biobank, Newcastle, UK; University Hospital Schleswig-Holstein, Kiel, Germany; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Haematological Malignancy Diagnostic Service, Leeds, UK). Mononuclear cells were isolated from bone marrow or peripheral blood by density centrifugation followed by immediate extraction of DNA or RNA, or cryopreservation in the presence of 10% v/v DMSO.

extract_protocol:
DNase I (Worthington) digestion  was performed using ~5 million  patient sample cells using 8 units (presentation) or 14 units (relapse) for 3 min at 22 °C in a 1 mM CaCl2 supplemented buffer. Nuclear proteins were digested with 1 mg/ml Proteinase K overnight at 37 °C. DNaseI digestion products were size-selected on an agarose gel, cutting below 150 bp.
High-throughput sequencing libraries were prepared using 10 ng of size-selected material, using the Kapa Hyperprep kit as per manufacturer’s instruction. Libraries were sequenced with 50 bp single-end reads on an Illumina HiSeq 2500 sequencer according to manufacturer’s instructions

tag: dnase units

tag: disease state

value: relapse AML patient


title: O75G1D217V17_L2

tag: cell type


title: O75G1D210V16_L4.D712


title: Mut_NR2F1_IP_1

value: Anti-FLAG M2 Magnetic Beads (M8825, Sigma-Aldrich)

tag: genotype/variation


title: GHU-63: Pool9 of 11 genomic DNA sample from dcshA cold-suppressor strains

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
The source code use to process the data is available here: https://gitlab.unige.ch/LinderLab/evar
filter low quality reads and trim adapter sequence with "SGA preprocess"
filter reads containing sequencing errors with "SGA filter"
perfom k-mer counting with "SGA kmer-count" considering kmer size of 61nt
perform de novo assembly of contigs with "SGA fm-merge" considering kmer size of 61nt
compute assemlby graph with "SGA overlap"
identify contigs containing k-mers not seen in the reference genome. This are candidates containing mutations
map contigs onthe reference genome for annotation only (not for mutation detection)
Manual curration of the identified mutations
Genome_build: S. aureus strain SA564, Refseq assembly: GCF_001281145.1
Supplementary_files_format_and_content: A table in TSV format (Tab Separated Value) listing manualy curated mutations identified in the sequencing data

organism: Staphylococcus aureus

source_name: bacterial culture

growth_protocol: Suppressors strains where selected by platting 50 μl of ON cultures of DcshA strain grown at 37°C in MH medium on MH plate at 25°C

extract_protocol:
kit QIAGEN dnEasy blood and tissue kit
Genomic Library were prepared by the service provider Fasteris SA (Switzerland) following the protocol TruSeq Nano DNA Library Prep.

tag: strain

tag: tissue

value: bacterial culture


title: O75G1D196V11_L3.D709


title: O75G1D199V13_L4.D711

value: Day 3 post VAC3


title: O75G1D197V12_L3.D710

value: Day 1 post VAC3


title: GHU-62: Pool8 of 12 genomic DNA sample from dcshA cold-suppressor strains


title: LS01_pres_ALL

value: presentation ALL patient


title: L2G1D217V17_L8.D710


title: WT_NR2F1_IP_1

value: Anti-FLAG M2 Magnetic Beads (M8823, Sigma-Aldrich)


title: D81G1D210V16_L7.D708

value: Day 14 post VAC3


title: L2G1D210V16_L7.D709


title: O75G1D-07V02_L3.D708

value: PreVAC


title: GHU-56: Pool2 of 10 genomic DNA sample from dcshA cold-suppressor strains


title: GHU-58: Pool4 of 8 genomic DNA sample from dcshA cold-suppressor strains


title: GHU-60: Pool6 of 7 genomic DNA sample from dcshA cold-suppressor strains


title: GHU-57: Pool3 of 6 genomic DNA sample from dcshA cold-suppressor strains


title: GHU-55: Pool1 of 10 genomic DNA sample from dcshA cold-suppressor strains


title: L2G1D199V13_L8

value: M


title: L2G1D197V12_L7.D707

value: PBMC


title: L2G1D196V11_L7.D706

value: Day of VAC3


title: L2G1D-07V02_L7.D705


title: C32G1D217V17_L1.D704


title: GHU-59: Pool5 of 8 genomic DNA sample from dcshA cold-suppressor strains


title: C32G1D210V16_L8.D703


title: GHU-61: Pool7 of 10 genomic DNA sample from dcshA cold-suppressor strains


title: WT_75min_AAG1_rep2

city: Mainz

first: Helle

last: Ulrich

state: Germany

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Library strategy: GLOE-seq
Reads were filtered and trimmed based on quality and adapter inclusion using Trimmomatic (release 0.36; parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed and filtered reads were mapped to the yeast genome (sacCer3) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the dinucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
Genome_build: sacCer3
Supplementary_files_format_and_content: BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365).

organism: Saccharomyces cerevisiae

source_name: cultured yeast cells

growth_protocol: Yeast strains DF5 (wildtype) and its apn1Δapn2Δ derivative (yHU1905) were grown at 30° C in YP medium containing 2% (w/v) glucose.

extract_protocol:
Ca. 6×109 cells (300 OD600) were collected by centrifugation (2,000×g, 5 min), washed in 25 ml of 10 mM Tris-HCl, pH 8.5, resuspended in 4 ml of Y1 buffer (1 M sorbitol, 100 mM EDTA, pH 8.0, 14 mM ß-mercaptoethanol) and spheroplasted by addition of 400 µl of Zymolyase 20T (AMS Biotechnology, 10 mg/ml). Spheroplasts were harvested by centrifugation (2,000×g for 5 min), washed once with 4 ml of Y1 buffer without ß-mercaptoethanol, resuspended in 4.75 ml of lysis buffer (50 mM Tris-HCl, pH 8.0, 50 mM EDTA) and lysed by incubation at 37° C by with 250 µl of 20% SDS. After centrifugation at 5,000×g for 10 min, the supernatant was transferred to a fresh 50 ml tube, 1.666 ml of 5 M potassium acetate were added, and tubes were incubated on ice for 45 min. The suspension was cleared of debris by two rounds of centrifugation (17,000×g for 15 min), and DNA was precipitated by addition of 19.5 ml of 100% ethanol. After centrifugation at 8,000×g for 15 min, the pellet was washed twice with 70% (v/v) ethanol and distributed into two 2 ml microcentrifuge tubes. After air-drying, the DNA was resuspended in 245 µl of TE by incubation overnight at 4° C. After addition of 5 µl of 5 M NaCl, samples were treated with 2.5 µl of RNase A (Sigma-Aldrich, 10109169001) for 1 h at 37° C. DNA was again precipitated by addition of 1.5 ml of 100% ethanol and centrifugation at 21,100×g for 10 min. Pellets were rinsed once with 1 ml of 70% (v/v) ethanol, air-dried, and resuspended overnight at 4° C by gentle rocking in 250 µl of 10 mM Tris-HCl pH 8.5. The DNA was then purified using AMPure beads and eluted in 125 µl of 10 mM Tris-HCl, pH 8.5. Aliquots (2.5 µg) of genomic DNA were treated with 3.75 U/µg hAAG (NEB, 90 min at 37° C) followed by 2.5 U/µg APE1 (NEB, 90 min at 37° C). Control samples were left untreated. The treated samples were purified using AMPure beads.
Genomic DNA (2.5 µg) was incubated at 95° C for 10 min, followed by incubation on slushy ice for 5 min to denature the DNA. A ligation mix was set up by addition of 6.5 µl of 10× T4 DNA ligase buffer, 3.55 µl proximal adaptor (40 µM in 60 mM NaCl), 19.5 µl of 50% (w/v) PEG 8000, 3 µl of high-concentration T4 DNA ligase (NEB) and water up to a total volume of 65 µl. The reaction was incubated at 25° C for 1 h, followed by 2 h at 22° C. The reaction mix was supplemented with 35 µl of 5 M NaCl and 35 µl of water and bound to an equivalent of 100 µl AMPure beads. The beads were incubated at room temperature for 5 min and rinsed twice with 500 µl of 70% (v/v) ethanol, followed by elution of the DNA with 103 µl of water and incubation at room temperature for 5 min. This eluate (100 µl) was subjected to sonication to a fragment size of 200 nt, using a Bioruptor Pico (4 cycles, 30 s on/30 s off). The sonicated DNA was then transferred to a microfuge tube containing 20 µl Streptavidin MyOne C1 Dynabeads (ThermoFisher Scientific, prewashed once with 1 ml 10 mM Tris-HCl pH 8.5, 2 M NaCl) and incubated for 15 min at room temperature with rotation. The beads were washed on a rotating wheel at room temperature: twice with 50 µl 1× SSC buffer each for 5 min at room temperature, once with 25 µl 20 mM NaOH for 10 min and briefly with 100 µl water. The DNA was eluted in 16 µl of water by incubation at 95° C for 5 to 10 min. For second-strand synthesis, the eluted DNA (14.85 µl) was combined with 15 µl Phusion FLASH mix (ThermoFisher Scientific) and 0.15 µl 100 µM oligonucleotide 3790, and incubated at 95° C for 2 min, 60° C for 3 min and 72° C for 2 min. The resulting double-stranded DNA was purified with AMPure beads and eluted in 19 µl water. This eluate (17 µl) was A-tailed with 2.3 µl End Prep Reaction Buffer and 1 µl End Prep Enzyme Mix (NEBNext® Ultra™ II DNA Library Prep kit, NEB) for 20° C for 30 min, followed by inactivation at 65° C for 30 min. Distal adaptor (2.25 µl, 40 µM in 60 mM NaCl) was ligated to the A-tailed DNA in the presence of 13.5 µl Ligation Master Mix, 0.45 µl Ligation Enhancer (NEBNext® Ultra™ II DNA Library Prep kit, NEB) and 8.8 µl water at 20° C for 20 min. The ligated DNA was cleaned up twice with AMPure beads, before being eluted in 20 µl water. This DNA (7.25 µl) was mixed with 5 µl 5× Q5 reaction buffer, 2.5 µl 1 µM Illumina P5 primer, 2.5 µl 1 µM Illumina P7 primer, 0.5 µl 10 mM dNTPs, 0.25 µl Q5 DNA polymerase (NEB) and 7 µl water and amplified by PCR, using the following programme: 95° C for 2 min, 8× (95° C for 15 s, 60° C for 30 s, 72° C for 20 s). The amplified DNA was cleaned up twice with AMPure beads, before being eluted in 25 µl water and sequenced following the guidelines supplied by Illumina.   Oligonucleotides:   proximal adaptor: 3898/3899;   distal adaptor: 3791/3792;   3898: CTACACGACGCTCTTCCGATCTNNNNN*N-NH2 (*: phosphorothioate bond, IDT code *; NH2: 3’-amino modification, IDT code /3AmMO/);   3899: PO4-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGTTTT-Bio (PO4: 5’-phosphorylation, IDT code /5Phos/; T-Bio: 3’-biotin-dT, IDT code /3BiodT/);   3790: CGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   3791 GACTGGAGTTCAGACGTGTGCTCTTCCGATCT;   3792 GATCGGAAGAGCACACGTCTGAACTCCAGTC;   P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   P7 CAAGCAGAAGACGGCATACGAGAT(X)6GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

treatment_protocol: Cells were arrested in G1 phase with 5 µg/ml alpha-factor for 90 min, treated with 0.02% v/v MMS for 30 min, released into S phase and harvested at 0, 30 and 75 min.

value: DF5, wildtype

tag: treatment

tag: nuclease treatment

value: hAAG, followed by Ape1


title: WT_75min_rep1


title: WT_75min_AAG1_rep1


title: WT_75min_rep2


title: C32G1D197V12_L8.D701


title: L66G1D217V17_L4.D712


title: WT_30min_rep1


title: WT_30min_rep2


title: C32G1D196V11_L8.D712


title: WT_30min_AAG1_rep1


title: WT_30min_AAG1_rep2


title: WT_0min_rep2


title: L66G1D197V12_L4.D709


title: L66G1D210V16_L4.D711


title: L66G1D196V11_L4.D708


title: L66G1D199V13_L4.D710


title: WT_0min_AAG1_rep2


title: WT_0min_AAG1_rep1


title: Apn1Apn2_75min_rep2

value: DF5, apn1[delta],apn2[delta]


title: L66G1D-07V02_L4.D707


title: Q26G1D217V17_L3.D707

value: Day of Challenge


title: Apn1Apn2_75min_rep1


title: Apn1Apn2_75min_AAG1_rep2


title: Q26G1D210V16_L3.D706


title: Q26G1D199V13_L1.D705


title: C32G1D199V13_L8.D702


title: C32G1D-07V02_L8.D711


title: Apn1Apn2_30min_rep2


title: WT_0min_rep1


title: Apn1Apn2_75min_AAG1_rep1


title: Q26G1D196V11_L2.D703


title: Q26G1D197V12_L2.D704


title: T90G1D217V17_L1.D707

value: F


title: T90G1D199V13_L1.D705


title: Apn1Apn2_0min_rep1


title: Apn1Apn2_0min_rep2


title: Apn1Apn2_30min_AAG1_rep1


title: Apn1Apn2_30min_rep1


title: Q26G1D-07V02_L2.D702


title: T90G1D197V12_L8.D704


title: T90G1D210V16_L1.D706


title: Y33G1D217V17_L2.D709


title: T90G1D196V11_L8.D703


title: Apn1Apn2_0min_AAG1_rep2


title: T90G1D-07V02_L8.D702


title: Y33G1D199V13_L1.D707


title: Apn1Apn2_0min_AAG1_rep1


title: UD_WT_30min_rep2


title: UD_WT_75min_rep2


title: UD_WT_75min_AAG1_rep2


title: UD_WT_75min_AAG1_rep1


title: Y33G1D196V11_L1.D704


title: Y33G1D-07V02_L1.D703


title: UD_WT_30min_AAG1_rep2


title: Y33G1D210V16_L1.D708


title: Y33G1D197V12_L1


title: UD_WT_30min_AAG1_rep1


title: Apn1Apn2_30min_AAG1_rep2


title: H14G1D217V17_L5.D705


title: UD_WT_30min_rep1


title: UD_WT_0min_rep1


title: H14G1D210V16_L5.D704


title: H14G1D197V12_L4.D702


title: H14G1D-07V02_L4.D712


title: UD_WT_0min_AAG1_rep2


title: H14G1D199V13_L4.D703


title: UD_Apn1Apn2_75min_rep2


title: UD_WT_0min_rep2


title: UD_WT_75min_rep1


title: UD_WT_0min_AAG1_rep1


title: S7G1D217V17_L6.D701


title: S7G1D210V16_L6.D712


title: S7G1D199V13_L6.D711


title: UD_Apn1Apn2_75min_AAG1_rep2


title: S7G1D197V12_L6.D710


title: UD_Apn1Apn2_30min_rep2


title: S7G1D196V11_L6.D709


title: UD_Apn1Apn2_30min_rep1


title: I13G1D217V17_L5.D710


title: H14G1D196V11_L4.D701


title: UD_Apn1Apn2_30min_AAG1_rep2


title: I13G1D199V13_L5.D708


title: I13G1D210V16_L5.D709


title: UD_Apn1Apn2_30min_AAG1_rep1


title: UD_Apn1Apn2_0min_rep2


title: I13G1D197V12_L5.D707


title: S7G1D-07V02_L6.D708


title: UD_Apn1Apn2_0min_AAG1_rep2


title: UD_Apn1Apn2_0min_rep1


title: CDC9

data_processing:
Library strategy: GLOE-Seq
Reads were mapped to the yeast genome (sacCer3) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the nucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365).
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig files based on replication fork directionality (RFD) ratio (RFD = (REV – FWD)/(REV + FWD)) were generated using deepTools (version 3.1.0) bigwigCompare program (parameter: -bs 200).

growth_protocol: Strain W303 cdc9AID (MATa, bar1Δ::hisG ade2‐1 can1‐100 his3‐11,15  leu2‐3,112 trp1‐1 ura3‐1 RAD5+ URA3::pRS306‐PGAL1‐10‐OsTIR1 codon plus cdc9-AID::kanMX) was from Anne Donaldson (doi: 10.1016/j.molcel.2013.02.012). Yeast cultures were grown at 30° C in YP medium containing 2% (w/v) glucose.

extract_protocol:
Ca. 6×10^9 cells (300 OD600) were collected by centrifugation (2,000×g, 5 min), washed in 25 ml of 10 mM Tris-HCl, pH 8.5, resuspended in 4 ml of Y1 buffer (1 M sorbitol, 100 mM EDTA, pH 8.0, 14 mM ß-mercaptoethanol) and spheroplasted by addition of 400 µl of Zymolyase 20T (AMS Biotechnology, 10 mg/ml). Spheroplasts were harvested by centrifugation (2,000×g for 5 min), washed once with 4 ml of Y1 buffer without ß-mercaptoethanol, resuspended in 4.75 ml of lysis buffer (50 mM Tris-HCl, pH 8.0, 50 mM EDTA) and lysed by incubation at 37° C by with 250 µl of 20% SDS. After centrifugation at 5,000×g for 10 min, the supernatant was transferred to a fresh 50 ml tube, 1.666 ml of 5 M potassium acetate were added, and tubes were incubated on ice for 45 min. The suspension was cleared of debris by two rounds of centrifugation (17,000×g for 15 min), and DNA was precipitated by addition of 19.5 ml of 100% ethanol. After centrifugation at 8,000×g for 15 min, the pellet was washed twice with 70% (v/v) ethanol and distributed into two 2 ml microcentrifuge tubes. After air-drying, the DNA was resuspended in 245 µl of TE by incubation overnight at 4° C. After addition of 5 µl of 5 M NaCl, samples were treated with 2.5 µl of RNase A (Sigma-Aldrich, 10109169001) for 1 h at 37° C. DNA was again precipitated by addition of 1.5 ml of 100% ethanol and centrifugation at 21,100×g for 10 min. Pellets were rinsed once with 1 ml of 70% (v/v) ethanol, air-dried, and resuspended overnight at 4° C by gentle rocking in 250 µl of 10 mM Tris-HCl pH 8.5. The DNA was then purified using AMPure beads and eluted in 125 µl of 10 mM Tris-HCl, pH 8.5.
Genomic DNA (2.5 µg) was incubated at 95° C for 10 min, followed by incubation on slushy ice for 5 min to denature the DNA. A ligation mix was set up by addition of 6.5 µl of 10× T4 DNA ligase buffer, 3.55 µl proximal adaptor (40 µM in 60 mM NaCl), 19.5 µl of 50% (w/v) PEG 8000, 3 µl of high-concentration T4 DNA ligase (NEB) and water up to a total volume of 65 µl. The reaction was incubated at 25° C for 1 h, followed by 2 h at 22° C. The reaction mix was supplemented with 35 µl of 5 M NaCl and 35 µl of water and bound to an equivalent of 100 µl AMPure beads. The beads were incubated at room temperature for 5 min and rinsed twice with 500 µl of 70% (v/v) ethanol, followed by elution of the DNA with 103 µl of water and incubation at room temperature for 5 min. This eluate (100 µl) was subjected to sonication to a fragment size of 200 nt, using a Bioruptor Pico (4 cycles, 30 s on/30 s off). The sonicated DNA was then transferred to a microfuge tube containing 20 µl Streptavidin MyOne C1 Dynabeads (ThermoFisher Scientific, prewashed once with 1 ml 10 mM Tris-HCl pH 8.5, 2 M NaCl) and incubated for 15 min at room temperature with rotation. The beads were washed on a rotating wheel at room temperature: twice with 50 µl 1× SSC buffer each for 5 min at room temperature, once with 25 µl 20 mM NaOH for 10 min and briefly with 100 µl water. The DNA was eluted in 16 µl of water by incubation at 95° C for 5 to 10 min. For second-strand synthesis, the eluted DNA (14.85 µl) was combined with 15 µl Phusion FLASH mix (ThermoFisher Scientific) and 0.15 µl 100 µM oligonucleotide 3790, and incubated at 95° C for 2 min, 60° C for 3 min and 72° C for 2 min. The resulting double-stranded DNA was purified with AMPure beads and eluted in 19 µl water. This eluate (17 µl) was A-tailed with 2.3 µl End Prep Reaction Buffer and 1 µl End Prep Enzyme Mix (NEBNext® Ultra™ II DNA Library Prep kit, NEB) for 20° C for 30 min, followed by inactivation at 65° C for 30 min. Distal adaptor (2.25 µl, 40 µM in 60 mM NaCl) was ligated to the A-tailed DNA in the presence of 13.5 µl Ligation Master Mix, 0.45 µl Ligation Enhancer (NEBNext® Ultra™ II DNA Library Prep kit, NEB) and 8.8 µl water at 20° C for 20 min. The ligated DNA was cleaned up twice with AMPure beads, before being eluted in 20 µl water. This DNA (7.25 µl) was mixed with 5 µl 5× Q5 reaction buffer, 2.5 µl 1 µM Illumina P5 primer, 2.5 µl 1 µM Illumina P7 primer, 0.5 µl 10 mM dNTPs, 0.25 µl Q5 DNA polymerase (NEB) and 7 µl water and amplified by PCR, using the following programme: 95° C for 2 min, 8× (95° C for 15 s, 60° C for 30 s, 72° C for 20 s). The amplified DNA was cleaned up twice with AMPure beads, before being eluted in 25 µl water and sequenced following the guidelines supplied by Illumina.   Oligonucleotides:   proximal adaptor: 3898/3899;   distal adaptor: 3791/3792;   3898: CTACACGACGCTCTTCCGATCTNNNNN*N-NH2 (*: phosphorothioate bond, IDT code *; NH2: 3’-amino modification, IDT code /3AmMO/);   3899: PO4-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGTTTT-Bio (PO4: 5’-phosphorylation, IDT code /5Phos/; T-Bio: 3’-biotin-dT, IDT code /3BiodT/);   3790: CGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   3791: GACTGGAGTTCAGACGTGTGCTCTTCCGATCT;   3792: GATCGGAAGAGCACACGTCTGAACTCCAGTC;   P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   P7: CAAGCAGAAGACGGCATACGAGAT(X)6GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT.

treatment_protocol: Cells were arrested in G1 phase with 5 µg/ml alpha-factor for 90 min, followed by a 60 min incubation with 1 mM auxin and release into S phase for 60 min.


title: cdc9_AID

value: W303 cdc9AID


title: Q11G1D217V17_L1.D710


title: I13G1D196V11_L1.D706


title: WT120J_withoutEndoVApe1_rep2

data_processing:
Library strategy: GLOE-seq
bed files were used directly to map the reads to the yeast genome and extract the frequencies of dinucleotide sequences immediately adjacent to the 5' end of the sequencing read. Therefore, we have not generated bigwig files to visualize these samples.

growth_protocol: Yeast cultures were grown at 30° C in YP medium containing 2% (w/v) glucose.

extract_protocol:
Genomic DNA was prepared using a spheroplast-based genomic DNA extraction kit (Qiagen, 10243) according to the instruction manual. Aliquots (2.5 µg) were treated with 5 U/µg T4 Endonuclease V (NEB, 30 min at 37° C) followed by 2 U/µg APE1 (NEB, 30 min at 37° C). Control samples were left untreated.
Genomic DNA (2.5 µg) was incubated at 95° C for 10 min, followed by incubation on slushy ice for 5 min to denature the DNA. A ligation mix was set up by addition of 6.5 µl of 10× T4 DNA ligase buffer, 3.55 µl proximal adaptor (40 µM in 60 mM NaCl), 19.5 µl of 50% (w/v) PEG 8000, 3 µl of high-concentration T4 DNA ligase (NEB) and water up to a total volume of 65 µl. The reaction was incubated at 25° C for 1 h, followed by 2 h at 22° C. The reaction mix was supplemented with 35 µl of 5 M NaCl and 35 µl of water and bound to an equivalent of 100 µl AMPure beads. The beads were incubated at room temperature for 5 min and rinsed twice with 500 µl of 70% (v/v) ethanol, followed by elution of the DNA with 103 µl of water and incubation at room temperature for 5 min. This eluate (100 µl) was subjected to sonication to a fragment size of 200 nt, using a Bioruptor Pico (4 cycles, 30 s on/30 s off). The sonicated DNA was then transferred to a microfuge tube containing 20 µl Streptavidin MyOne C1 Dynabeads (ThermoFisher Scientific, prewashed once with 1 ml 10 mM Tris-HCl pH 8.5, 2 M NaCl) and incubated for 15 min at room temperature with rotation. The beads were washed on a rotating wheel at room temperature: twice with 50 µl 1× SSC buffer each for 5 min at room temperature, once with 25 µl 20 mM NaOH for 10 min and briefly with 100 µl water. The DNA was eluted in 16 µl of water by incubation at 95° C for 5 to 10 min. For second-strand synthesis, the eluted DNA (14.85 µl) was combined with 15 µl Phusion FLASH mix (ThermoFisher Scientific) and 0.15 µl 100 µM oligonucleotide 3790, and incubated at 95° C for 2 min, 60° C for 3 min and 72° C for 2 min. The resulting double-stranded DNA was purified with AMPure beads and eluted in 19 µl water. This eluate (17 µl) was A-tailed with 2.3 µl End Prep Reaction Buffer and 1 µl End Prep Enzyme Mix (NEBNext® Ultra™ II DNA Library Prep kit, NEB) for 20° C for 30 min, followed by inactivation at 65° C for 30 min. Distal adaptor (2.25 µl, 40 µM in 60 mM NaCl) was ligated to the A-tailed DNA in the presence of 13.5 µl Ligation Master Mix, 0.45 µl Ligation Enhancer (NEBNext® Ultra™ II DNA Library Prep kit, NEB) and 8.8 µl water at 20° C for 20 min. The ligated DNA was cleaned up twice with AMPure beads, before being eluted in 20 µl water. This DNA (7.25 µl) was mixed with 5 µl 5× Q5 reaction buffer, 2.5 µl 1 µM Illumina P5 primer, 2.5 µl 1 µM Illumina P7 primer, 0.5 µl 10 mM dNTPs, 0.25 µl Q5 DNA polymerase (NEB) and 7 µl water and amplified by PCR, using the following programme: 95° C for 2 min, 8× (95° C for 15 s, 60° C for 30 s, 72° C for 20 s). The amplified DNA was cleaned up twice with AMPure beads, before being eluted in 25 µl water and sequenced following the guidelines supplied by Illumina.   Oligonucleotides:   proximal adaptor: 3898/3899;   distal adaptor: 3791/3792;   3898: CTACACGACGCTCTTCCGATCTNNNNN*N-NH2 (*: phosphorothioate bond, IDT code *; NH2: 3’-amino modification, IDT code /3AmMO/);   3899: PO4-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGTTTT-Bio (PO4: 5’-phosphorylation, IDT code /5Phos/; T-Bio: 3’-biotin-dT, IDT code /3BiodT/);   3790: CGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   3791 GACTGGAGTTCAGACGTGTGCTCTTCCGATCT;   3792 GATCGGAAGAGCACACGTCTGAACTCCAGTC;   P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   P7 CAAGCAGAAGACGGCATACGAGAT(X)6GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

treatment_protocol: Exponentially growing cells were exposed to UV irradiation (254 nm, 20 or 120 J/m2) or left unirradiated.

tag: uv irradiation


title: WT120J_withoutEndoVApe1_rep1


title: UD_Apn1Apn2_75min_rep1


title: Q11G1D210V16_L1.D709


title: I13G1D-07V02_L5.D705


title: Q11G1D199V13_L1.D708


title: WT120J_withEndoVApe1_rep2

value: Endonuclease V / APE1


title: WT120J_withEndoVApe1_rep1


title: UD_Apn1Apn2_75min_AAG1_rep1


title: WT20J_withoutEndoVApe1_rep1


title: Q11G1D-07V02_L1.D705


title: Q11G1D196V11_L1.D706


title: U95G1D217V17_L4.D709


title: Q11G1D197V12_L1.D707


title: WT20J_withEndoVApe1_rep2


title: U95G1D210V16_L3.D708


title: WT0J_withoutEndoVApe1_rep2


title: WT20J_withEndoVApe1_rep1


title: U95G1D197V12_L3.D706


title: U95G1D199V13_L3.D707


title: U95G1D196V11_L3.D705


title: UD_Apn1Apn2_0min_AAG1_rep1


title: U95G1D-07V02_L3.D704


title: F18G1D217V17_L3.D705


title: WT0J_withEndoVApe1_rep1


title: WT_GAL_rep2

data_processing:
Library strategy: GLOE-seq
Reads were filtered and trimmed based on quality and adapter inclusion using Trimmomatic (release 0.36; parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed and filtered reads were mapped to the yeast genome (sacCer3) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the nucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
Genome_build: sacCer3
Supplementary_files_format_and_content: BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365).

growth_protocol: Strain JKM179 (hoΔ MATα hmlΔ::ADE1 hmrΔ::ADE1 ade1-100 leu2-3,112 lys5 trp1::hisG′ ura3-52 ade3::GAL::HO) was from Jim Haber (doi: 10.1016/S0092-8674(00)81482-8). Yeast cultures were pre-grown at 30° C in YP medium containing 2% (w/v) raffinose.

treatment_protocol: Cultures were shifted to YP medium containing 2% (v/v) galactose for 1 h (samples 3 and 4). Control cultures (samples 1 and 2) were kept in raffinose medium.

value: growth in galactose


title: WT0J_withEndoVApe1_rep2


title: F18G1D199V13_L2.D703

value: Day 3 post VAC3


title: F18G1D197V12_L2.D702

value: Day 1 post VAC3


title: WT_GAL_rep1


title: WT_RAF_rep2

value: growth in raffinose


title: WT20J_withoutEndoVApe1_rep2


title: NbBtsI_rep2

description: Sample 22

data_processing:
Library strategy: GLOE-seq
Reads were filtered and trimmed based on quality and adapter inclusion using Trimmomatic (release 0.36; parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed and filtered reads were mapped to the yeast genome (sacCer3) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the nucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
Genome_build: sacCer3
Supplementary_files_format_and_content: BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365). BigWig files based on replication fork directionality (RFD) ratio (RFD = (Crick – Watson)/(Crick + Watson)) were generated using deepTools (version 3.1.0) bigwigCompare program (parameter: -bs 1000).

extract_protocol:
Genomic DNA was prepared using a spheroplast-based genomic DNA extraction kit (Qiagen, 10243) according to the instruction manual. Isolated DNA was treated with restriction or nicking endonucleases, left untreated (samples 1 and 2) or subjected to random fragmentation to an average size of ca. 300 bp by sonication (samples 19 and 20).
EndoSeq libraries (samples 9 and 10) were prepared according to a published protocol (doi: 10.1038/nprot.2015.099).   GLOE-Seq libraries (all other samples) were prepared as follows:   Genomic DNA (2.5 µg) was incubated at 95° C for 10 min, followed by incubation on slushy ice for 5 min to denature the DNA. A ligation mix was set up by addition of 6.5 µl of 10× T4 DNA ligase buffer, 3.55 µl proximal adaptor (40 µM in 60 mM NaCl), 19.5 µl of 50% (w/v) PEG 8000, 3 µl of high-concentration T4 DNA ligase (NEB) and water up to a total volume of 65 µl. The reaction was incubated at 25° C for 1 h, followed by 2 h at 22° C. The reaction mix was supplemented with 35 µl of 5 M NaCl and 35 µl of water and bound to an equivalent of 100 µl AMPure beads. The beads were incubated at room temperature for 5 min and rinsed twice with 500 µl of 70% (v/v) ethanol, followed by elution of the DNA with 103 µl of water and incubation at room temperature for 5 min. This eluate (100 µl) was subjected to sonication to a fragment size of 200 nt, using a Bioruptor Pico (4 cycles, 30 s on/30 s off). The sonicated DNA was then transferred to a microfuge tube containing 20 µl Streptavidin MyOne C1 Dynabeads (ThermoFisher Scientific, prewashed once with 1 ml 10 mM Tris-HCl pH 8.5, 2 M NaCl) and incubated for 15 min at room temperature with rotation. The beads were washed on a rotating wheel at room temperature: twice with 50 µl 1× SSC buffer each for 5 min at room temperature, once with 25 µl 20 mM NaOH for 10 min and briefly with 100 µl water. The DNA was eluted in 16 µl of water by incubation at 95° C for 5 to 10 min. For second-strand synthesis, the eluted DNA (14.85 µl) was combined with 15 µl Phusion FLASH mix (ThermoFisher Scientific) and 0.15 µl 100 µM oligonucleotide 3790, and incubated at 95° C for 2 min, 60° C for 3 min and 72° C for 2 min. The resulting double-stranded DNA was purified with AMPure beads and eluted in 19 µl water. This eluate (17 µl) was A-tailed with 2.3 µl End Prep Reaction Buffer and 1 µl End Prep Enzyme Mix (NEBNext® Ultra™ II DNA Library Prep kit, NEB) for 20° C for 30 min, followed by inactivation at 65° C for 30 min. Distal adaptor (2.25 µl, 40 µM in 60 mM NaCl) was ligated to the A-tailed DNA in the presence of 13.5 µl Ligation Master Mix, 0.45 µl Ligation Enhancer (NEBNext® Ultra™ II DNA Library Prep kit, NEB) and 8.8 µl water at 20° C for 20 min. The ligated DNA was cleaned up twice with AMPure beads, before being eluted in 20 µl water. This DNA (7.25 µl) was mixed with 5 µl 5× Q5 reaction buffer, 2.5 µl 1 µM Illumina P5 primer, 2.5 µl 1 µM Illumina P7 primer, 0.5 µl 10 mM dNTPs, 0.25 µl Q5 DNA polymerase (NEB) and 7 µl water and amplified by PCR, using the following programme: 95° C for 2 min, 8× (95° C for 15 s, 60° C for 30 s, 72° C for 20 s). The amplified DNA was cleaned up twice with AMPure beads, before being eluted in 25 µl water and sequenced following the guidelines supplied by Illumina.   Oligonucleotides:   proximal adaptor: 3898/3899;   distal adaptor: 3791/3792;   3898: CTACACGACGCTCTTCCGATCTNNNNN*N-NH2 (*: phosphorothioate bond, IDT code *; NH2: 3’-amino modification, IDT code /3AmMO/);   3899: PO4-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGTTTT-Bio (PO4: 5’-phosphorylation, IDT code /5Phos/; T-Bio: 3’-biotin-dT, IDT code /3BiodT/);   3790: CGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   3791: GACTGGAGTTCAGACGTGTGCTCTTCCGATCT;   3792: GATCGGAAGAGCACACGTCTGAACTCCAGTC;   P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   P7: CAAGCAGAAGACGGCATACGAGAT(X)6GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT.

treatment_protocol: Cultures were left untreated.

tag: protocol

value: GLOE-Seq


title: M51G1D217V17_L3.D710

tag: subject


title: NbBtsI_rep1

description: Sample 21


title: WT_RAF_rep1


title: M51G1D199V13_L3.D708

tag: day


title: Random_rep2

description: Sample 20

value: sonicated to ca 300 bp


title: WT0J_withoutEndoVApe1_rep1


title: M51G1D210V16_L3.D709

tag: protectionstatus

value: Day 14 post VAC3


title: NbBsrDI_NotI_1_10_rep2

description: Sample 18

value: 1:10 dilution of Nb.BsrDI/NotI-treated with NotI-treated DNA


title: M51G1D196V11_L3.D706

tag: description of day

value: PBMC


title: M51G1D197V12_L3.D707

tag: gender


title: M51G1D-07V02_L6

value: PreVAC


title: NbBsrDI_NotI_1_100_rep2

description: Sample 16

value: 1:100 dilution of Nb.BsrDI/NotI-treated with NotI-treated DNA


title: NbBsrDI_NotI_1_100_rep1

description: Sample 15


title: NbBsrDI_NotI_1_1000_rep1

description: Sample 13

value: 1:1000 dilution of Nb.BsrDI/NotI-treated with NotI-treated DNA


title: NbBsrDI_NotI_1_1000_rep2

description: Sample 14


title: NbBsrDI_NotI_1_10000_rep2

description: Sample 12

value: 1:10000 dilution of Nb.BsrDI/NotI-treated with NotI-treated DNA


title: NbBsrDI_after_fragmentation

description: Sample 10

data_processing:
Library strategy: Endo-seq
Reads were filtered and trimmed based on quality and adapter inclusion using Trimmomatic (release 0.36; parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, SLIDINGWINDOW:4:15, MINLEN:36).
Trimmed and filtered reads were mapped to the yeast genome (sacCer3) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the nucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
Genome_build: sacCer3
Supplementary_files_format_and_content: BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365). BigWig files based on replication fork directionality (RFD) ratio (RFD = (Crick – Watson)/(Crick + Watson)) were generated using deepTools (version 3.1.0) bigwigCompare program (parameter: -bs 1000).

value: Nb.BsrDI-treated during EndoSeq

value: EndoSeq


title: NbBsrDI_NotI_1_10_rep1

description: Sample 17


title: NbBsrDI_NotI_1_10000_rep1

description: Sample 11


title: Random_rep1

description: Sample 19


title: NbBsrDI_rep4

description: Sample 8


title: F18G1D-07V02_L2.D712

value: M


title: NbBsrDI_before_fragmentation

description: Sample 9

value: Nb.BsrDI-treated before EndoSeq


title: F18G1D210V16_L3.D704


title: NbBsrDI_rep1

description: Sample 5


title: NbBsrDI_rep2

description: Sample 6


title: NbBsrDI_rep3

description: Sample 7


title: Undigested_rep2

description: Sample 2


title: BsrDI_rep2

description: Sample 4

value: BsrDI-treated


title: BsrDI_rep1

description: Sample 3


title: Undigested_rep1

description: Sample 1


title: MYOG Venus 3wks_biological rep2

city: Boston

first: Olivier

last: Pourquie

state: MASSACHUSETTS

address: 60 Fenwood Road

department: Department of Pathology

institute: Brigham and Women’s Hospital

description:
Gene expression data from iPS-derived myogenic cells
MYOGVenus_3wks-2 RMA Signal

hyb_protocol: Following fragmentation, cRNAs were hybridized on GeneChip Human Gene 2.0ST Arrays. Each microarray was then washed and stained on a GeneChip fluidics station 450 and further scanned with a GeneChip Scanner 3000 7G.

scan_protocol: Raw data (CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip Command Console (AGCC) version 1.4.1.46

data_processing: Initial filtering and preprocessing, including background correction, quantile normalization and summarization, was performed using both RMA and MAS with the R Bioconductor package (R version 2.12.1, Bioconductor version 2.8). Expression sets were then filtered according to Calls information. Probe sets expression fold changes between conditions (biological triplicates) were calculated using the “Comparative Marker Selection” module of GenePattern (Reich et al., 2006). Volcano and FcFc scatter plots were generated using the Multiplot application of GenePattern. Histogram expression profiles of gene probe sets were generated from MAS values. Further analysis was performed using the Manteia database (Tassy and Pourquie, 2014) and DAVID Functional Annotation tools (Huang da et al., 2009). Hierarchical clustering was performed on Microarray RMA data. Clustering was computed with an Average linkage method and Euclidean distances. Both an Approximately unbiased (AU) and Bootstrap probability (BP) P values were calculated (pvclust, R package).

source_name: FASC sorted MYOG-Venus cells at 3 weeks of myogenic differentiation

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: iPS cells were cultured on Matrigel (BD Biosciences)-coated dishes in mTesR1 media (Stem Cell Technologies). Cells were passaged as aggregates or as single cells.

extract_protocol: Cells were purified by FACS from differentiated cultures using an Aria (BD Biosciences) or a S3 cell sorter (Bio-Rad). Gating was determined for each reporter line using corresponding undifferentiated culture as a baseline control.

treatment_protocol: Serum-free myogenic differentiation of human iPS lines was performed as described previously (Chal et al., 2016; Chal et al., 2015)

value: human iPS-derived MYOG


title: hiPS undif_biological rep3

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-3 RMA Signal

source_name: Undifferentiated iPS cells (Pluripotent)

value: human iPS (NCRM-1, RUCDR)


title: hiPS undif_biological rep1

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-1 RMA Signal


title: Huh-106 rep1

city: Strasbourg

first: Thomas

last: Baumert

address: 3 Rue Koeberle

country: France

institute: INSERM U1110

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Gene 2.0 ST arrays (Affymetrix) interrogating over 40 0000 RefSeq transcripts and ~ 11000 LncRNAs.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings. Modulated molecular pathways were determined by using GSEA 63. Individual differential gene expression of the selected candidates was evaluated through the Z score transformation.

source_name: RNA from Huh106 cells

label_protocol: Biotinylated single strand cDNA targets were prepared from 200 ng of total RNA using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Cell lines were grown in DMEM supplemented with 10% FBS. For HepG2-NTCP cells were supplemented with puromycine and with G418 for Huh-106

extract_protocol: RNA was isolated using  Promega Relia Prep kit according to the manufacture's instructions

tag: cell line


title: MYOG Venus 3wks_biological rep3

description:
Gene expression data from iPS-derived myogenic cells
MYOGVenus_3wks-3 RMA Signal


title: hiPS undif_biological rep2

description:
Gene expression data from undifferentiated iPS cells (Pluripotent)
hiPS_undif-2 RMA Signal


title: Huh-106 rep3


title: NCBP3_rep2

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT2 against hg38.
Uniquely mapped and properly paired reads were used for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from bam files using genomecov from the bedtools suite, scaled for library size, and converted to bigwig format bedGraphtoBigWig. The score represents strand specific library-size normalized per base genome coverage.

source_name: NCBP3 total RNA replicate 2

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual.
Libraries were prepared, after rRNA-depletion using Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat; Illumina), using Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: siRNA transfections were performed targeting EGFP(control), ARS2, ZC3H18

value: HeLa Kyoto


title: NCBP3_rep3

source_name: NCBP3 total RNA replicate 3


title: HepG2-NTCP rep2

source_name: RNA from HepG2-NTCP cells


title: MYOG Venus 3wks_biological rep1

description:
Gene expression data from iPS-derived myogenic cells
MYOGVenus_3wks-1 RMA Signal


title: Fis1-/- ESCs

city: seoul

first: bong jong

last: seo

address: neung-dong ro

department: Stem cell and regenerative biotechnology

country: South Korea

institute: Konkuk university

data_processing:
The validity of sequenced reads was accessed with FastQC (v0.11.5) and the reads were aligned with STAR (v2.5.2b) to UCSC mouse mm10 genome assembly.
StringTie (v1.3.3b) was used to process STAR results in transcript assemblies. Results from StringTie were used to calculate average expression of each gene in FPKM and the acquired values were used for drawing scatter plots in R (v3.6.1).
For heatmaps, the FPKM value of individual samples and heatmap2 function of R’s gplots (v3.0.1.1) package were used.
In all cases, DEGs were identified with the aforementioned cutoff value using calculations with R.
With the resulting DEGs from scatter plot and heatmap, gene ontology and KEGG pathway analysis were conducted through DAVID (v6.8).
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

organism: Mus musculus

source_name: knockout in e14tg2a ESCs

growth_protocol: Control ESC and Knockout ESC lines were maintained on a dish layered with MEF in the Mouse Embryonic Stem Cell (mESC) medium, consisting of Dulbecco’s modified Eagle’s medium (DMEM) low glucose (Hyclone, 11885-084, GE Healthcare, Melbourne, VIC, Australia) supplemented with 15% heat-inactivated fetal bovine serum (FBS; Hyclone), 1x penicillin/streptomycin/glutamine (P/S/G; Gibco, 10378-016, Grand Island, NY, USA), 0.1 mM nonessential amino acids (NEAA; Gibco, 11140- 050), 1 mM β-mercaptoethanol (Gibco, 21985-023), and 103 U/mL leukemia inhibitory factor (ESGRO, Merck Millipore).

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cells

tag: genotype

tag: passages


title: Pax7 GFP 3wks_biological rep3

description:
Gene expression data from mouse ES-derived myogenic cells
Pax7GFP_3wks-3 RMA Signal

hyb_protocol: Mouse ESCs samples were hybridized on GeneChip Mouse Genome 430 2.0 arrays as described previously (Chal et al., 2015).

source_name: Mouse ES-derived Pax7

growth_protocol: Mouse ES cell lines were cultured  as described previously (Chal et al., 2015).

extract_protocol: Cells were purified by FACS from differentiated cultures using an Aria (BD Biosciences) cell sorter. Gating was determined for each reporter line using corresponding undifferentiated culture as a baseline control.

treatment_protocol: Mouse ES cell lines were differentiated according to previously described protocol (Chal et al., 2015).

value: FASC sorted PAX7-GFP cells at 3 weeks of myogenic differentiation


title: NCBP3_rep1

source_name: NCBP3 total RNA replicate 1


title: Pax7 GFP 3wks_biological rep1

description:
Gene expression data from mouse ES-derived myogenic cells
Pax7GFP_3wks-1 RMA Signal


title: ES undif_biological rep2

description:
Gene expression data from undifferentiated mouse ES cells (Pluripotent)
ES_undif-2 RMA Signal

source_name: Mouse ES cells

value: Undifferentiated ES cells (Pluripotent)


title: ES undif_biological rep1

description:
Gene expression data from undifferentiated mouse ES cells (Pluripotent)
ES_undif-1 RMA Signal


title: Mff-/- ESCs

value: Mff-/-


title: ES undif_biological rep3

description:
Gene expression data from undifferentiated mouse ES cells (Pluripotent)
ES_undif-3 RMA Signal


title: HepG2-NTCP rep1


title: Input NT shRNA H9 hESCs (replicate 1)[Input_NT_1]

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

institute: CECAD - Cluster of Excellence

description:
Input control of H9 hESCs NT shRNA (replicate 1). 75 μl was not subject to immunoprecipitation, thus representing total input control for the ChIP reactions.
PEAKS_ChIP_NT1_Input_NT1.xls

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were aligned to the  homo sapiens
peaks were called using macs version 2
Genome_build: homo_sapiens – Ensembl build 87 (hg38)
Supplementary_files_format_and_content: ChIP-Seq

source_name: H9 hESCs (WA09)

growth_protocol: hESCs were grown on Geltrex (ThermoFisher Scientific) using mTeSR1 media (Stem Cell Technologies) after passaged using a solution of dispase (2 mg ml-1), and scraping the colonies with a glass pipette.

extract_protocol: Illumina ChIP Seq library Protocol

treatment_protocol: To obtain shRNA stable lines, hESC colonies growing on Geltrex were incubated with mTesR1 medium containing 10 μM ROCK inhibitor for 1 h and individualized using Accutase. Fifty thousand cells were infected with 20 µl of concentrated lentivirus in the presence of 10 μM ROCK inhibitor for 1 h. Cell suspension was centrifuged to remove virus, passed through a mesh of 40 μM to obtain individual cells, and plated back on a feeder layer of mitotically inactive mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% knockout serum replacement (ThermoFisher Scientific), 0.1 mM non-essential amino acids, 1 mM L-glutamine, β-mercaptoethanol and 10 ng ml−1 bFGF (Joint Protein Central) supplemented with 10 μM ROCK inhibitor. After several days in culture, small hESC colonies arose. Then, we performed 1 µg ml−1 puromycin selection during 2 days and colonies were manually passaged onto fresh MEFs to establish new hESC stable lines.

tag: shRNA

value: H9 hESCs expressing NT shRNA as a control to compare with UBE2K shRNA-treated cells

tag: antibody


title: ChIP experiment with H3K9me3 antibody of NT shRNA H9 hESCs (replicate 1)[ChIP_NT_1]

description:
Chromatin of H9 hESCs NT shRNA (replicate 1) was incubated with 10 μg of anti-H3K9me3 antibody (Abcam, #8898)
PEAKS_ChIP_NT1_Input_NT1.xls

value: anti-H3K9me3 antibody (Abcam, #8898)


title: Lung_neonatal_male_mice_DMA-treated

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

description: Gene expression data from lung of transplacental DMA treated neonatal male mice

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: lung, transplacental DMA-treated neonatala male mice

label_protocol: Not provided

growth_protocol: Male and female 10-week-old CD-1 mice were mated.

extract_protocol: RNeasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: Mice were given 0 (control) or 200 ppm DMA for 10 days in the drinking water at the 8 days after mating. After parturition, the offspring were sacrificed on postnatal day 0.

value: lung

tag: age

value: neonatal

value: male


title: e14tg2a ESCs

source_name: e14tg2a ESCs

tag: cell type

tag: strain


title: Input NT shRNA H9 hESCs (replicate 2)[Input_NT_2]

description:
Input control of H9 hESCs NT shRNA (replicate 2). 75 μl was not subject to immunoprecipitation, thus representing total input control for the ChIP reactions.
PEAKS_ChIP_NT2_Input_NT2.xls


title: peritoneal macrophage from Ninjurin1 KO mouse 3

city: Incheon

first: Hyun Jin

last: Jung

address: 317 College of Pharmacy, 191 Hambangmoe-ro,  Yeonsu-gu

institute: Seoul National University

description: Gene expression data from peritoneal macrophages from Ninjurin1 knockout mouse

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

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

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: Ninjurin1 KO (knockout) mouse peritoneal macrophage

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Peritoneal macrophages were harvested from the peritoneal cavity using a syringe. The cells were incubated at 37°C for 40 min in cell culture plates. After non-adherent cells were washed, the adherent cells were collected.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment

value: Female

tag: cell

value: peritoneal macrophages


title: ChIP experiment with H3K9me3 antibody of NT shRNA H9 hESCs (replicate 2)[Chip_NT_2]

description:
Chromatin of H9 hESCs NT shRNA (replicate 2) was incubated with 10 μg of anti-H3K9me3 antibody (Abcam, #8898)
PEAKS_ChIP_NT2_Input_NT2.xls


title: peritoneal macrophage from Ninjurin1 KO mouse 2


title: C10

city: MEXICO CITY

first: TZVETANKA

middle: DIMITROVA

last: DINKOVA

state: DISTRITO FEDERAL

address: CIRCUITO EXTERIOR, CIUDAD UNIVERSITARIA DELEGACION COYOACAN

department: BIOCHEMESTRY

country: Mexico

institute: UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO, FACULTAD DE QUIMICA

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor null reads, insert null reads, adaptor contaminants were filtered and the adaptor sequences were trimmed with  fastx_artifacts_filter | fastq_quality_filter -q 30 | fastx_clipper -l 18 -c
Reads shorter than 18 and longer than 27 nt were discarded. Custom python script.
Sequences not mapping to the reference Z. mays genome (AGPv4.32) or mapping to tRNA, rRNA, snRNA and snoRNA databases were excluded from further analysis. Bowtie version 1.1.2 parameters -v 1 and custom python scripts.
The ShortStack 3.4 parameters –nostitch was used to identify known and novel miRNAs and for the discovery of pha-siRNAs.
Sequences were classified according on its mapping to ta-siRNAs, lincRNAs, CDS-derived RNAs,  hc-siRNAs, databases. Bowtie version 1.1.2 parameters -v 1 and custom python scripts.
Genome_build: AGPv4.32
Supplementary_files_format_and_content: Clean_sizes.csv: SmRNAs size abundances
Supplementary_files_format_and_content: Clean_RPM_sizes.csv: SmRNAs size abundances normalized
Supplementary_files_format_and_content: Results.txt: ShortStack output core results
Supplementary_files_format_and_content: ShortStack_D.gff3: ShortStack output likely RNAi-related
Supplementary_files_format_and_content: mature_miRNAs_table.csv: miRNA abundances
Supplementary_files_format_and_content: mature_miRNA_table_RPM.csv: miRNA abundances normalized
Supplementary_files_format_and_content: RNA_types.csv: Different types of smRNAs abundances
Supplementary_files_format_and_content: RNA_types_PC.csv: Different types of smRNAs abundances percentage

organism: Zea mays

source_name: Embryogenic callus subcultured for 10 months

extract_protocol:
Total RNA was isolated separately from each sample (IE, immature embryos; C1, one month; C4, four months and C10, ten months subcultured callus) using the TRIzol reagent (Thermofischer Scientific) according to the manufacturer’s instructions. For sRNA purification, the step of 70% ethanol wash was substituted by 96% ethanol wash. The quality of the total RNA was tested by 1% agarose-gel electrophoresis and the concentration was measured using the Agilent 2100 Bioanalyzer.
Small RNAs ranging between 18–30 nt were isolated from total RNA on 15% TBE-urea denaturing polyacrylamide gel, and then ligated to a 3' DNA adaptor (IE and C4 libraries: CTGTAGGCACCATCAAT; C1 and C10 libraries: ATCTCGTATGCCGTCTTCTGCTTG). Then, ligated to a 5' RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUC). It was reverse-transcribed using the RT primer (IE and C4 libraries: CAAGCAGAAGACGGCATACGAATTGATGGTGCCTACAG; C1 and C10 libraries: CAAGCAGAAGACGGCATACGA). Subsequently, a PCR reaction was performed using. The forward primer was (AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA) and as the reverse primer (CAAGCAGAAGACGGCATACGA). The amplified cDNA constructs were purified and mixed as follows: (IE + C1) and (C4 + C10) for multiplexed sequencing by UUSMD (UNAM-IBT, Mexico) using the Genome Analyzer IIx from Illumina.

tag: cultivar

value: 10 months subculture


title: Huh-106 rep2


title: C4

source_name: Embryogenic callus subcultured for 4 months

value: 4 months subculture


title: ChIP experiment with H3K9me3 antibody of UBE2K  shRNA H9 hESCs (replicate 2)[Chip_Ube2]

description:
Chromatin of H9 hESCs HTT shRNA (replicate 2) was incubated with 10 μg of anti-H3K9me3 antibody (Abcam, #8898)
PEAKS_ChIP_Ube2_Input_Ube2.xls

value: H9 hESCs expressing UBE2K shRNA to silence the expression of UBE2K


title: Pax7 GFP 3wks_biological rep2

description:
Gene expression data from mouse ES-derived myogenic cells
Pax7GFP_3wks-2 RMA Signal


title: Dnm1l-/- ESCs


title: peritoneal macrophage from Ninjurin1 KO mouse 1


title: HepG2-NTCP rep3


title: D164A4dpi

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zurich

data_processing:
FastQC
zUMIs pipeline
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: count matrix

molecule: polyA RNA

source_name: small intestinal crypts

growth_protocol: All animals were kept on a C57BL/6 background. Mice were 8-12 weeks old at the time of treatments and cell isolations. Mice of both sexes were used in all experiments and littermates were used as controls.

extract_protocol:
Control (n=3) and D164A (n=3) mice were sacrificed 0, 2 or 4d post injection, crypts were isolated as described (Sato and Clevers, 2013). Crypt fractions 3 and 4 were pooled and dissociated to single cells by incubating them with 5 mL pre-warmed TripLE Express Enzyme (ThermoFischer) in a 37 °C water bath for 5 min with frequent agitation. TripLE was inactivated with 50% FBS in Advanced DMEM/F12 (ThermoFischer). Single cells were pelleted at 180 g for 3 min and resuspended in 2 mL cold Intesticult (Stemcell Technologies Inc). Clumps were dissolved by pipetting up and down with a 1mL pipet before filtering twice through a 40 micron filter. Cell viability and number were quantified in automatically with a Countess (Thermo Scientific).
DropSeq workflow was performed as described (Macosko et al, 2015) on a Nadia Instrument (Dolomite Bio). Sequencing was performed on the Illumina NovaSeq6000 with an SP Reagent Kit.
single cell RNASeq

treatment_protocol: To induce Cre-ERT2-mediated recombination, tamoxifen (Sigma, 80 mg/kg) was injected intraperitoneally on two consecutive days. Mice were sacrificed 48 hours after the first tamoxifen injection. Alternatively, mice were injected on 4 consecutive days and sacrificed 96 hours after the first injection.

tag: tissue

value: small intestinal crypts

tag: strain/genotype

value: Tg(Vil1-cre/ERT2); Ctnnb1-D164A/flox

tag: days post cre induction

tag: background strain


title: Sample 99: Monocyte from TB

city: Medellín

first: LELIA

last: LAVALETT

state: Antioquia

department: Antioquia

country: Colombia

institute: Universidad de antioquia

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were extracted with Illumina GenomeStudio v2011.1  software. Probes signal value was transformed by logarithm and normalized by Z-ratio method. The data were normalised using quantile normalisation with Lumi package in R

source_name: Human monocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Peripheral blood

tag: agent

value: Mtb UT205

tag: disease state

value: Mycobacterium tuberculosis Infection


title: Sample 39: Monocyte from TB

description: replicate 1


title: Input UBE2K shRNA H9 hESCs (replicate 2)[Input_Ube2]

description:
Input control of H9 hESCs HTT shRNA (replicate 2). 75 μl was not subject to immunoprecipitation, thus representing total input control for the ChIP reactions.
PEAKS_ChIP_Ube2_Input_Ube2.xls


title: peritoneal macrophage from WT mouse 1

description: Gene expression data from peritoneal macrophages from wild-type mouse

source_name: WT (wild-type) mouse peritoneal macrophage

tag: gender


title: Sample 98: Monocyte from TB

description: replicate 3

value: Mtb UT127


title: Sample 48: Monocyte from TB

description: replicate 2


title: Sample 97: Monocyte from TB

description: replicate 4

value: TB control


title: Sample 34: Monocyte from TB

description: replicate 1


title: Sample 37: Monocyte from TB

description: replicate 2


title: Sample 93: Monocyte from healthy

description: replicate 5


title: Sample 47: Monocyte from TB

description: replicate 2


title: Sample 38: Monocyte from TB

description: replicate 1


title: Sample 46: Monocyte from TB

description: replicate 3


title: IE

source_name: Immature embryos 15 dap

value: 0 day subculture


title: ChIP experiment with H3K9me3 antibody of UBE2K shRNA H9 hESCs (replicate 1)[Chip_Ube1]

description:
Chromatin of H9 hESCs HTT shRNA (replicate 1) was incubated with 10 μg of anti-H3K9me3 antibody (Abcam, #8898)
PEAKS_ChIP_Ube1_Input_Ube1.xls

value: anti-H3K9me3 antibody (Abcam, #8898)


title: C1

source_name: Embryogenic callus subcultured for 1 month

value: 1 month subculture


title: Ube2k1.3

data_processing:
Illumina Casava software used for basecalling
Sequenced reads mapped to homo sapiens
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Homo sapiens(Ensembl 87) / hg38
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample

source_name: Embryonic stem cells H9

growth_protocol: iPSCs and hESCs were grown on Geltrex (ThermoFisher Scientific) using mTeSR1 media (Stem Cell Technologies) after passaged using a solution of dispase (2 mg ml-1), and scraping the colonies. We induced neural differentiation of hESCs/iPSCs with STEMdiff Neural Induction Medium (Stem Cell Technologies) following the monolayer culture method as previously described (97). Undifferentiated cells were rinsed once with PBS and then we added 1 ml of Gentle Dissociation Reagent (Stem Cell Technologies) for 10 min. After the incubation period, we gently dislodged hESCs/iPSCs and add 2 ml of Dulbecco’s Modified Eagle Medium (DMEM)-F12 (ThermoFisher Scientific) + 10 μM ROCK inhibitor (Abcam). Then, we centrifuged cells at 300g for 10 min. hESCs/iPSCs were resuspended on STEMdiff Neural Induction Medium + 10 μM ROCK inhibitor and plated on polyornithine (15 μg ml−1)/laminin (10 μg ml−1)-coated plates at a density of 200,000 cells cm−2 with a glass pipette.

extract_protocol:
Total RNA was extracted using RNAbee (Tel-Test Inc.).
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit. Library preparation started with 1 µg total RNA. After selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (20 µl template, 14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent 2100 Bioanalyzer), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced on an Illumina HiSeq 4000 sequencer with a paired- end (2 × 75bp) protocol.

treatment_protocol: To obtain shRNA stable lines, iPSCs/hESC colonies growing on Geltrex were incubated with mTesR1 medium containing 10 μM ROCK inhibitor for 1 h and individualized using Accutase. Fifty thousand cells were infected with 20 µl of concentrated lentivirus in the presence of 10 μM ROCK inhibitor for 1 h. Cell suspension was centrifuged to remove virus, passed through a mesh of 40 μM to obtain individual cells, and plated back on a feeder layer of mitotically inactive mouse embryonic fibroblasts (MEFs) in DMEM/F12, 20% knockout serum replacement (ThermoFisher Scientific), 0.1 mM non-essential amino acids, 1 mM L-glutamine, β-mercaptoethanol and 10 ng ml−1 bFGF (Joint Protein Central) supplemented with 10 μM ROCK inhibitor. After several days in culture, small hESC colonies arose. Then, we performed 1 µg ml−1 puromycin selection during 2 days and colonies were manually passaged onto fresh MEFs to establish new hESC stable lines.

value: H9 ES cells expressing Ube2k  shRNA


title: Sample 96: Monocyte from healthy

description: replicate 6


title: a6A-IP mRNA

city: Hangzhou

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang University

data_processing:
adapter, low quality reads and short reads were trimed with fastp v0.19.7 with following parameters: -f 10 -F 10 -x --detect_adapter_for_pe -l 25
clean reads were aligned with GRCh38 genome using hisat2 v2.1.0 with parameters: --rna-strandness RF
a6A peaks were called following Ma et al., Genome Research. 2017, in short: to call a6A peaks, the longest isoform of each human gene was scanned using a 100-bp sliding window with 10-bp steps. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package (Robinson et al. 2010), combining information from all replicates in the two groups. The window was called as positive if the FDR < 1% and Fold Change ≥ 1.5. Overlapping positive windows were merged.
mutation was called by samtools mpileup v1.9 with parameters:  -BQ 0 -d 10000000 -l se.allyl.peaks.bed
Genome_build: GRCh38
Supplementary_files_format_and_content: bed file contains a6A peak regions in a6A-IP product relative to input samples in our method, excel file contains mutations called from a6A-IP-cyclized samples using samtools

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high-glucose media(HyCloneSH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco 10270) and 1% 100× Pen Strep (HyClone SV30010) at 37 °C with 5 % CO2

extract_protocol:
RNA was extracted with Triozl Reagent(invitrogene), mRNA was extracted with GenElute™ Direct mRNA Miniprep Kits(sigma), IP and cyclized products were precipitated with isopropanol
Libraries were constructed following illumina's instructions except using HIV/M-Mulv for reverse transcription instead of superscript Ⅱ

treatment_protocol: HeLa cells were starved in methionine deficient medium supplemented with 1 mM L-cysteine for 30min then treated with 1mM allyl-L-selenohomocysteine for 16h

tag: reverse transcriptase

value: RevertAid Reverse Transcriptase


title: control4dpi

value: Tg(Vil1-cre/ERT2); Ctnnb1-wt/flox


title: Input UBE2K shRNA H9 hESCs (replicate 1)[Input_Ube1]

description:
Input control of H9 hESCs HTT shRNA (replicate 1). 75 μl was not subject to immunoprecipitation, thus representing total input control for the ChIP reactions.
PEAKS_ChIP_Ube1_Input_Ube1.xls


title: input mRNA


title: D164A2dpi


title: Ube2k1.2


title: control2dpi


title: control0dpi


title: NT1

value: H9 ES cells expressing Nt shRNA


title: Ube2k1.1


title: NT2


title: IFNg2LPS1_PMA_HDAC1

type: protein

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

hyb_protocol: Microarray DNA double stranding and PBM protocols are as previously described (Berger et al., 2006, Siggers et al., 2015, and Mohaghegh et al., 2019).

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing:
Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006).
Processed data corresponds to z-scores normalized against the fluorescence distribution obtained  at sets of random background probes

label: alexa fluor conjugated antibody

molecule: protein

label_protocol: The array was incubated with nuclear extract for one hour in the dark in a binding reaction buffer (20mM HEPES, pH 7.9, 100mM NaCl, 1mM DTT, 0.2mg/mL BSA, 0.02% Triton X-100, 0.4mg/mL salmon testes DNA (Sigma-Aldrich, Catalogue #D7656). The array was then rinsed in a HBS bath containing 0.1% Tween-20 and subsequently de-wetted in a HBS bath. After the protein incubation, the array was incubated for 20 minutes in the dark with 20ug/mL primary antibodies for the TF or COF of interest. The primary antibodies were diluted in 2% milk in HBS. After the primary antibody incubation, the array was first rinsed in a HBS bath containing 0.1% Tween-20 and subsequently de-wetted in a HBS bath. Microarrays were then incubated with 10ug/mL of either alexa488 or alexa647 conjugated secondary antibody for 20 minutes in the dark. The secondary antibody was diluted in 2% milk in HBS. Excess antibody was removed by washing the array twice for 3 minutes in 0.05% Tween-20 in HBS and once for 2 minutes in HBS in coplin jars as described above. After the washes, the array was de-wetted in a HBS bath.

growth_protocol: THP-1 cells, a human monocyte cell line, were obtained from ATCC (TIB-202). The cells were grown in suspension in RPMI 1640 Glutamax media (Thermofisher Scientific, Catalogue #72400120) with 10% heat-inactivated fetal bovine serum (Thermofisher Scientific, Catalogue #11360070) and 1mM sodium pyruvate (Thermofisher Scientific, Catalogue #16140071). T175 (Thermofisher Scientific, Catalogue #132903) non-treated flasks were used when culturing THP-1 cells for experiments.Cells were grown in 50mL of media when being cultured in T175 flasks. To differentiate THP-1 cells into adherent macrophages, cells were grown to a density of 8.0 x 105 cells/mL and treated with 25ng/mL Phorbol 12-Myristate 13-Acetate (PMA) (Sigma-Aldrich, Catalogue #P8139) for 4 days. Following the 4 days of PMA treatment, the media was replaced with fresh RPMI media with 10% heat-inactivated fetal bovine serum and 1mM sodium pyruvate. The cells rested for two days in the fresh media before being stimulated with various reagents.

extract_protocol: To harvest nuclear extracts from THP-1 cells, the media was aspirated off and the cells were washed once with 1X PBS (Thermofisher Scientific, Catalogue #100010049). Once the 1X PBS used to wash the cells was aspirated off, enough 1X PBS was mixed with 1X Protease Inhibitor (Sigma-Aldrich, Catalogue #P8340) to cover the cells was added to each flask. A cell scraper was then used to dislodge the cells from the flask. The cells were collected in a falcon tube and placed on ice. To pellet the cells, the cell volume was centrifuged at 500xg for 5 minutes at 4°C. Once the cells were pelleted, the supernatant was aspirated off. The pellet was resuspended in Buffer A and incubated for 10 minutes on ice (10mM HEPES, pH 7.9, 1.5mM MgCl, 10mM KCl, 0.1mM Protease Inhibitor, Phosphatase Inhibitor (Santa-Cruz Biotechnology, Catalogue #sc-45044), 0.5mM DTT (Sigma-Aldrich, Catalogue #4315) to lyse the plasma membrane. After the 10 minute incubation, a final concentration of 0.1% Igepal detergent was added to the cell and Buffer A mixture and vortexed for 10 seconds. To separate the cytosolic fraction from the isolated nuclei, it was centrifuged at 500xg for 5 minutes at 4°C. The cytosolic fraction was collected into a separate eppendorf tube. The pelleted nuclei were then resuspended in Buffer C (20mM HEPES, pH 7.9, 25% Glycerol, 1.5mM MgCl, 0.2mM EDTA, 0.1mM Protease Inhibitor, Phosphatase Inhibitor, 0.5mM DTT, and 420mM NaCl) and then vortexed for 30 seconds. The nuclei are incubated in Buffer C while mixing at 4°C. To separate the nuclear extract from the nuclear debris, the mixture was centrifuged at 21,000xg for 20 minutes at 4°C. The nuclear extract was collected in a separate eppendorf tube and flash frozen using liquid nitrogen. Nuclear extracts were stored at -80°C until being used for experiments.

treatment_protocol: THP-1 cells differentiated with PMA were treated with either Lipopolysaccharide (LPS) (Sigma-Aldrich, L3024), Interferon gamma (IFN-γ) (Thermofisher Scientific, Catalogue #PHC4031), or IFN-γ in combination with LPS. PMA treated THP-1 cells were left untreated (UT), treated with 1ug/mL of LPS for 45 minutes (LPS45), or with 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1). For each condition, nuclear lysates were harvested. For all nuclear lysates assayed using PBM experiments, the expression levels of COFs and TFs profiled with CASCADE were confirmed with western blot.

tag: treatment

tag: target protein

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)

tag: secondary antibody concentration


title: D164A0dpi


title: cyclized a6A-IP mRNA

value: HIV


title: WGBS_ESC_DKO_P4

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw sequencing reads were trimmed using cutadapt and aligned against human or mouse genome using BSMAP.
Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: mm9
Supplementary_files_format_and_content: Bed format, columns: chr, start, end, ratio (0 to 1), number of reads.

source_name: ESCs

extract_protocol:
DNA was extracted using the Zymo Quick-DNA Universal Kit following the manufacturer's instructions.
DNA was sonicated, bisulfite converted using the Qiagen Epitect Fast kit and prepped using the Swift Accel-NGS Methyl-seq DNA library kit.

tag: knockout

value: DNMT3A, DNMT3B

tag: cell type

value: ESCs


title: IFNg2LPS1_PMA_PU1

value: 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1)


title: IFNg2LPS1_PMA_p65


title: KI-FL rep4

city: Guangzhou

first: Su

last: Yang

address: Huangpu Avenue

institute: Jinan University

data_processing:
Sequencing adapters were trimmed by BBduk (minlen=100 ktrim=r k=23 mink=11 hdist=1 tpe tbo; http://jgi.doe.gov/data-and-tools/bb-tools/). Reads with length under 100 bp after trimming were discarded.
lipped reads were aligned to mouse genome GRCm38 (primary assembly) by STAR aligner with default settings. Read counts for genes were obtained by using HTSeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for all samples

extract_protocol:
Mice were sacrificed and decapitated. Striatal tissues were dissected from the brain. RNAs were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: CRISPR-Cas9 to truncate full-length mutant Htt in HD140Q knock-in (KI)

tag: strain background

tag: age

tag: genotype/variation

value: KI-FL

value: striatum


title: Sample 90: Monocyte from healthy

description: replicate 4

tag: tissue

value: Peripheral blood

value: Mtb UT205

value: Mycobacterium tuberculosis Infection


title: peritoneal macrophage from WT mouse 3

value: Female

tag: cell

value: peritoneal macrophages


title: RNA_HUES64_DKO_cloneA_P27_rep2

data_processing:
Data was aligned using STAR aligner followed by stringtie v1.3 to the hg19 genome.
Genome_build: hg19
Supplementary_files_format_and_content: *_abundance.txt: Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM.

growth_protocol: HUES 64 and HUES8 cells were grown in feeder-free conditions using Geltrex (Thermo Fisher Scientific) and mTeSR (STEMCELL Technologies).

extract_protocol: Libraries were prepared using the TruSeq RNA Sample Prep v2 HS Protocol.

tag: cell line


title: RNA_HUES64_DKO_cloneA_P27_rep1


title: Sample 33: Monocyte from healthy

description: replicate 1

tag: agent

tag: disease state


title: RNA_HUES64_DKO_cloneA_P27_rep3


title: KI-FL rep3


title: Sample 84: Monocyte from healthy

description: replicate 2


title: Lung_neonatal_male_mice_Control

description: Gene expression data from lung of Control neonatal male mice

source_name: lung, control neonatala male mice

value: lung

value: neonatal

tag: gender

value: male


title: IFNg2LPS1_PMA_RBBP5

tag: treatment

tag: target protein


title: Sample 89: Monocyte from healthy

description: replicate 4

value: Mtb UT127


title: Sample 95: Monocyte from healthy

description: replicate 3


title: NT3

tag: shRNA

value: H9 ES cells expressing Nt shRNA


title: Sample 87: Monocyte from healthy

description: replicate 3


title: KI-FL rep2


title: RNA_HUES64_DKO_cloneA_P6_rep2


title: IFNg2LPS1_PMA_TBL1XR1

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: IFNg2LPS1_PMA_GCN5

tag: secondary antibody concentration


title: Sample 32: Monocyte from healthy

description: replicate 1


title: RNA_HUES64_DKO_cloneA_P6_rep3

tag: knockout

value: DNMT3A, DNMT3B

tag: cell type


title: KI-FL rep1

tag: strain

tag: strain background

tag: age


title: IFNg2LPS1_PMA_SMARCA4

value: SMARCA4 (sc17796)


title: KI-571 rep4

tag: genotype/variation

value: KI-571 (expressing an N-terminal Huntingtin fragment)

tag: tissue


title: IFNg2LPS1_PMA_p300

value: 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1)


title: Sample 92: Monocyte from healthy

description: replicate 2

tag: agent


title: RNA_HUES64_DKO_cloneA_P6_rep1

value: ESCs

tag: cell line


title: KI-571 rep3

value: CRISPR-Cas9 to truncate full-length mutant Htt in HD140Q knock-in (KI)

value: striatum


title: KI-571 rep2


title: HUES64_WT_RNA_rep2


title: KI-571 rep1