title: Flight-F03-qM20

city: Philadelphia

first: Yuanyuan

last: Wang

state: PA

address: 3720 Chestnut St, Apt 709

institute: UCLA

data_processing:
Raw sequencing reads were aligned to mm10 genome by STAR-2.7.1a using the followng parameters: --outSAMunmapped Within --outSAMattributes NH HI AS NM MD XS --twopassMode Basic --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignEndsType EndToEnd --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Gene expression TPM values were quantified by kallisto 0.46.0 using the following parameters: --single -l 50 -s 20 -b 100
Differential gene expression analysis were performed using DESeq2_1.26.0
Alternative splicing quantification and differential analysis were performed using rmats-turbo v4.1.0 with the following parameters: --anchorLength 1 --variable-read-length --readLength 50 -t single --libType fr-unstranded
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: tab-delimited text files include detailed information of splicing (exon skipping or mutual exclusive exons) events as well as differential splicing comparison results.

source_name: Quadriceps

extract_protocol:
Frozen carcasses were thawed on wet ice before tissue dissection. Skeletal muscles from the left hind limb of each carcass were individually dissected and preserved in RNAlater preservative solution. Total RNA was isolated using the acid guanidinium thiocyanate-phenol-chloroform extraction followed by silica-membrane purification. Briefly, frozen tissue samples were minced into small pieces (1mm x 1mm x 1mm). A homogeneous lysate was achieved by adding lysing buffer and gentle ultrasound vibration on ice. Tissue lysate was centrifuged and the supernatant was used for RNA phenol/chloroform extraction. After phase separation, the aqueous layer was transferred and mixed with an equal volume of 70% ethanol. Total RNA was then extracted using RNeasy spin columns from the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Quadriceps

tag: experimental group

value: Flight


title: yth1-1

status: Public on Jun 25 2021

type: SRA

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

library_source: transcriptomic

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 89
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis. primers.gff contains the primer sequences used in this analysis.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Saccharoymces cerevisiae in YPAD media at 37ºC

growth_protocol: Yeast cells were grown at 25ºC until an OD600 of 0.6 then switched to 37ºC for 1 hour. 2 biological replicates were included.

extract_protocol:
Samples were harvested at 37ºC. Cells were spun down by centrifugation and stored at -80ºC until mPAT analysis.
Libraries were prepared according to the mPAT approach (Beilharz et al. 2017)

tag: strain


title: TRIM28 ChIP-Seq, TNF treated for 4hr

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

library_source: genomic

data_processing:
Raw reads were mapped to the reference mouse (hg19) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using makeBigwig.pl script of HOMER suite.

molecule: genomic DNA

organism: Homo sapiens

source_name: HT29 cell line

growth_protocol: HT29 cell line was cultured in conditions as described in this study.

extract_protocol:
Lysates were prepared from ~5 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02;  PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: Treated with TNF or TSZ as indicated.

tag: antibody

value: anti-TIF1b (Cell signaling, #4123)

tag: treatment

value: TNF

tag: treatment time

value: 4 hr


title: SOX9 ChIP-Seq, TSZ treated for 4hr

value: anti-SOX9 (Merck, AB5535)

value: TSZ


title: SOX9 ChIP-Seq, Control

value: non-treated


title: Ground-G02-qM03

country: USA

organism: Mus musculus

tag: tissue

value: Ground


title: swd2-2


title: TRIM28 ChIP-Seq, TSZ treated for 4hr


title: B-ALL patient A97

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
The sequenced reads were aligned from raw sequence fastq data using STAR v2.5.2b software on UCSC hg19 reference genome.
The aligned reads were normalized, and log transformed using the R bioconductor package DEseq2 (http://bioconductor.org/packages/3.12/bioc/html/DESeq2.html).
Genome_build: hg19

molecule: total RNA

growth_protocol: Bone marrow aspiration was conducted at diagnosis. Mononuclear cells were enriched from BM samples by density gradient centrifugation with LymphoPrep™ Solution (Axis Shield PoC, Cat#1114547) and were stored at -80°C as dry pellets for further experimental analysis.

extract_protocol:
32 samples from  25 B-ALL patients’ bone marrow samples were processed for RNA extractions and sequencing. For 7 patients two independent RNAseq experiments were performed (duplicates).
For each sample, 1 µg RNA samples (RIN = 10) were used for libraries preparations with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Library prepared from B-ALL patients’ samples were sequenced on Hiseq 4000 (PE150) platform in Novagene company.

tag: gender

value: Female

tag: age

tag: wbc at diagnosis (x109/l)

tag: ph chromosome

value: Neg.

tag: dct(hadhb-gapdh)

tag: h4k5 cr/h3

tag: h4k5 bu/h3

tag: h4k5 cr high low

value: low

tag: h4k5 bu high low


title: set1


title: ref2-2


title: SVRS_2027 PATC53 polyA RNA-seq Inh 2day

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using HMM (Sanz et. al, 2016). For both, HTseq-count v0.6.0 was then used to count the total number of reads of each peak (sDRIP-seq) or genes (RNA-seq).
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). sDRIP-seq bed files were generated using HMM and converted into bigBed using bedToBigBed

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
RNA-seq: Total RNA was extracted using Trizol and poly(A) selected using poly(T) beads.
sDRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation, sonicated, and immunoprecipitated with S9.6 antibody.
RNA-seq: Standard paired-end TruSeq protocol.
sDRIP-seq: Enriched R-loop fragments were subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: Cells were subjected to either DMSO or PRMT inhibitor for 1, 2, or 3 days.

tag: disease state

value: PDAC

tag: cell line

value: Inh 2d


title: rna14-1


title: Flight-F02-qM12

tag: experimental group


title: SVRS_2026 PATC53 polyA RNA-seq Inh 2day


title: pti1-2

tag: strain


title: Flight-F01-qM11


title: SVRS_2032 PATC53 polyA RNA-seq Inh 3day

value: Inh 3d


title: sen1-1


title: TRIM28 ChIP-Seq, Control

tag: antibody


title: pfs2-1


title: p65 ChIP-Seq, TNF treated for 30min

value: anti-p65 (Cell signaling, #6956)

tag: treatment

value: 30 min


title: SVRS_2029 PATC53 polyA RNA-seq DMSO 3day

value: DMSO 3d


title: SVRS_2024 PATC53 polyA RNA-seq DMSO 2day

value: DMSO 2d


title: p65 ChIP-Seq, TSZ treated for 4hr

tag: treatment time


title: pcf11-13


title: p65 ChIP-Seq, TNF treated for 4hr


title: SVRS_2023 PATC53 polyA RNA-seq DMSO 2day


title: Ground-G03-qM08

tag: tissue

value: Quadriceps


title: SVRS_2028 PATC53 polyA RNA-seq DMSO 3day


title: SVRS_2021 PATC53 polyA RNA-seq Inh 1day

value: Inh 1d


title: Ground-G03-gM08

source_name: Gastrocnemius

value: Gastrocnemius


title: SVRS_2020 PATC53 polyA RNA-seq Inh 1day


title: Ground-G01-gM02


title: p65 ChIP-Seq, TSZ treated for 30min


title: Ground-G01-qM02


title: nab4-1


title: nab3-11


title: SVRS_2016 PATC53 polyA RNA-seq DMSO 1day

value: DMSO 1d


title: NRD1_R2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 89
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

source_name: Saccharoymces cerevisiae in YPAD media

extract_protocol:
Samples were harvested at 37ºC. Cells were spun down by centrifugation and stored at -80ºC until PAT-seq analysis.
Libraries were prepared according to the PAT-seq approach (Harrison et al. 2015)
Illumina directional RNA-seq on the Hiseq1500.

tag: strain/genotype


title: NRD1_R1


title: Flight-F03-gM20

value: Flight


title: single-cell RNA seq data of a patient with infectious endophthalmitis , patient#ctrl1

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.0.2)
Subsequent read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters.
The cellranger aggr pipeline was employed to generate a single cell-barcode matrix containing all the samples without normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

source_name: aqueous humor

extract_protocol:
AqH (100-150µl) was collected from each study subject using a 30G needle under local anesthesia, and immediately shipped at 4°C to the department of neurology at the University Clinic Muenster (Germany) for scRNA-seq and/or flow cytometry analysis. Freshly isolated cells were centrifuged once, counted and up to 5,000 of the input cells were used for scRNA-seq.
Freshly isolated single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 or v3 chemistry (both from 10X Genomics). Sample processing and library preparation was performed according to manufacturer's instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup.

value: intraokular leukocytes

tag: diagnosis

value: infectious endophthalmitis

tag: type of library

value: RNA expression

tag: subject id


title: pta1-1


title: SVRS_2025 PATC53 polyA RNA-seq Inh 2day


title: Flight-F02-gM12


title: p65 ChIP-Seq, Control

value: non-treated


title: Flight-F01-gM11


title: LS99G PATC53 sDRIP-seq Inh 1day

data_processing:
Library strategy: sDRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with tophat2 v2.1.0 (RNA-seq) or bowtie2 v2.2.6 (sDRIP-seq).
sDRIP-seq peaks were called using HMM (Sanz et. al, 2016). For both, HTseq-count v0.6.0 was then used to count the total number of reads of each peak (sDRIP-seq) or genes (RNA-seq).
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. DESeq2 was used to call differentially expressed regions.
Genome_build: hg19
Supplementary_files_format_and_content: Both sDRIP-seq and RNA-seq wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). sDRIP-seq bed files were generated using HMM and converted into bigBed using bedToBigBed

tag: ip antibody

value: S9.6 antibody


title: Ground-G02-gM03

value: Ground


title: pcf11-2


title: delta_syc1


title: pap1-1


title: SVRS_2022 PATC53 polyA RNA-seq DMSO 2day

value: PDAC


title: single-cell RNA seq data of a patient with HLA-B27pos acute anterior uveitis , patient#b27pos3

value: HLA-B27pos acute anterior uveitis


title: single-cell RNA seq data of a patient with HLA-B27pos acute anterior uveitis , patient#b27pos2


title: clp1-K136A-T137A


title: LS99E PATC53 sDRIP-seq DMSO 1day


title: nrd1-5


title: nrd1-DCID


title: SVRS_2019 PATC53 polyA RNA-seq Inh 1day


title: SEN1_R1


title: CLP1_25_R2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 93
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail-count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

extract_protocol:
Samples were harvested at both temperatures. Cells were spun down by centrifugation and stored at -80ºC until PAT-seq analysis.
Libraries were prepared according to the PAT-seq approach (Harrison et al. 2015)
Illumina directional RNA-seq on the Hiseq1500.

tag: temperature


title: nab4-7


title: LS72H PATC53 sDRIP-seq Inh 3day

value: Inh 3d


title: single-cell RNA seq data of a patient with HLA-B27neg anterior uveitis , patient#b27neg2

value: HLA-B27neg anterior uveitis


title: NAB3_R2


title: SVRS_2017 PATC53 polyA RNA-seq DMSO 1day


title: NAB3_R1


title: SVRS_2018 PATC53 polyA RNA-seq DMSO 1day


title: single-cell RNA seq data of a patient with HLA-B27neg anterior uveitis , patient#b27neg1


title: mpe1-1


title: SEN1_R2


title: LS72E PATC53 sDRIP-seq DMSO 1day


title: G-MDSCs, MS

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the hg38 version of the human genome as reference using STAR v2.6.1d after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the hg38-RefSeq Transcript Release 93 and normalized by TMM (+1/TMM/log2)
Normalized counts were used to determine differential gene expression between the Control group and the Covid-19 groups using DESEQ2
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: hg38
Supplementary_files_format_and_content: txt files contain raw counts and normalized counts

source_name: purified G-MDSC

extract_protocol:
RNA was isolated from purified g_MDSC using the Universal RNA/DNA Isolation kit (Qiagen, Germantown, MD) following the manufacturer's protocol
Paired-end libraries (2 x 75) were prepared (600ng per sample) using the TruSeq Stranded mRNA Library Prep kit

tag: cell type

value: G-MDSC purified from PBMC

tag: isolate

value: MS

tag: age

tag: Sex

value: female

tag: disease

value: Control

tag: bmi


title: W303_R2


title: PAP1_25_R2


title: single-cell RNA seq data of a patient with HLA-B27pos acute anterior uveitis , patient#b27pos4


title: W303_R1


title: fip1-1

tag: strain


title: glc7-5


title: LS99F PATC53 sDRIP-seq Inh 1day

tag: disease state

tag: cell line

value: Inh 1d


title: single-cell RNA seq data of a patient with HLA-B27pos acute anterior uveitis , patient#b27pos1


title: LS99I PATC53 sDRIP-seq Inh 3day

tag: treatment


title: LS99H PATC53 sDRIP-seq DMSO 3day

value: DMSO 3d


title: G-MDSCs, 072

value: Convalescent


title: YSH1_37_R2


title: W303


title: NAB4_25_R2


title: 12-C5-epithelial cell

type: genomic

city: Shihezi

first: Yan

last: Qi

state: Xinjiang province

address: North 2 road

department: Department of Pathology

country: China

institute: Shihezi University School of Medicine & the First Affiliated Hospital to Shihezi University School of Medicine

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 8

hyb_protocol: resuspended DNA samples were dispensed on BeadChips. The BeadChips were incubated in an Illumina Hybridization Oven for approximately 16-24 h in order to hybridize samples onto the BeadChips

scan_protocol: There are eight categories of internal controls per sample in an Illumina SNP microarray experiment: staining, extension, hybridization, stringency, target removal, recovery, nonspecific binding, and nonpolymorphic controls.

data_processing:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
Processed_data.txt reports genotypes: --(no call), II(Ins/Ins genotype), ID(Ins/Del genotype), DD(Del/Del genotype), DI(Del/Ins genotype), GG(G/G genotype), TG(T/G genotype), AC(A/C genotype), TT(T/T genotype), CC(C/C genotype), AA(A/A genotype), AG(A/G genotype),  TC(T/C genotype), GC(G/C genotype), AT(A/T genotype), CG(C/G genotype), TA(T/A genotype)

label: Cy3, Cy5

source_name: synovial sarcoma

label_protocol: The minimum amount of genomic DNA successfully subjected to genomic SNP microarray analysis was 1 ug, with quality metrics of A260/280 = 1.7–2.0 and A260/230 > 1.6

growth_protocol: Formalin-fixed paraffin-embedded (FFPE) samples of primary and recurrent SS

extract_protocol: Genomic DNA was isolated from four FFPE tumor samples using the QIAamp DNA Micro Kit (Qiagen Inc, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: According to the manufacturer's recommendation, the patient's DNA target was prepared and hybridized with Infinium HD analysis Superchip. CEL files were imported into Illumina Human Exome-12v1.1

tag: gender

value: Male

value: synovial sarcoma

tag: type

value: recurrent

value: epithelial cell


title: 15-C7-epithelial cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 9

value: Female

value: primary


title: NAB4-wt


title: LS72G PATC53 sDRIP-seq DMSO 3day

value: PDAC

value: S9.6 antibody


title: PAP1_37_R2

tag: strain/genotype


title: rpb1_slow_4tU_cordycepin_40mins_rep2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 93
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis. primers.gff contains the primer sequences used in this analysis.

source_name: Saccharoymces cerevisiae in SC media at 25ºC

growth_protocol: rpb1-1 yeast cells carrying plasmids with either RPB1 wild-type (pCK859) or the rpb1-H1085Y slow mutation were grown at 25ºC until an OD600 of 0.6. 2 biological replicates were included.

extract_protocol:
Cells were spun down by centrifugation and stored at -80ºC until mPAT analysis.
Libraries were prepared according to the mPAT approach (Beilharz et al. 2017) using a mTVN-PAT primer. This primer has an identical primer sequence to the mPAT reverse except for the addition of two 3’ variable bases, V (A, G or C) and N (any base).

treatment_protocol: An untreated sample was harvested, and the remaining cells were split into 4 flasks. 20µg/ml cordycepin or an equivalent volume of DMSO (control) was added to each flask along with 500µM 4tU or an equivalent volume of DMSO (unlabelled control). Samples were taken after 20 and 40 minutes.

tag: genotype

value: rpb1-1 yeast cells

tag: plasmid

value: rbp1 slow

tag: 4tu status

value: Cordycepin

tag: treatment time

value: 40 minutes


title: 16-C7-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 10

tag: cell type

value: spindle cell


title: NAB4_37_R2

tag: temperature


title: rpb1_slow_4tU_DMSO_40mins_rep2

value: DMSO


title: G-MDSCs, KR

value: G-MDSC purified from PBMC

tag: isolate

value: KR

tag: age

value: male

value: Control


title: FIP1_37_R2


title: FIP1_25_R2


title: G-MDSCs, 069

tag: Sex

tag: disease

value: Convalescent


title: BY4741

tag: strain


title: G-MDSCs, 067

value: female

tag: bmi


title: CLP1_37_R2


title: 8-C4-epithelial cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 4

tag: disease state

value: synovial sarcoma

value: epithelial cell


title: rpb1_slow_4tU_cordycepin_40mins_rep1

tag: treatment


title: 9-C4-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 5

tag: gender

value: Female

value: recurrent


title: rpb1_slow_4tU_DMSO_40mins_rep1


title: rpb1_slow_4tU_cordycepin_20mins_rep1

value: 20 minutes


title: rpb1_slow_4tU_cordycepin_20mins_rep2

value: rpb1-1 yeast cells


title: 10-C5-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 6

value: Male

tag: type

value: primary


title: G-MDSCs, 066


title: 7-C4-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 3


title: rpb1_slow_untreated_0mins_rep2

value: rbp1 slow

value: No 4tU

value: Untreated

value: 0 minutes


title: RNA14_37_R2

tag: strain/genotype


title: PCF11_25_R2


title: RNA14_25_R2


title: G-MDSCs, 059

value: G-MDSC purified from PBMC


title: 11-C5-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 7

value: spindle cell


title: 4-C2-spindle cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 2


title: rpb1_slow_untreated_0mins_rep1

tag: genotype


title: rpb1_slow_4tU_DMSO_20mins_rep1

tag: plasmid

value: DMSO


title: W303_37_R2


title: rpb1_slow_4tU_DMSO_20mins_rep2

tag: 4tu status


title: G-MDSCs, 061

value: male

value: Asymptomatic


title: PCF11_37_R2


title: G-MDSCs, 062

value: female


title: RPB1_wt_4tU_cordycepin_40mins_rep2

value: RBP1 wild-type

value: Cordycepin

tag: treatment time

value: 40 minutes


title: G-MDSCs, 058

tag: cell type

value: Severe


title: CLP1_37_R1

tag: temperature


title: W303_25_R2


title: G-MDSCs, 054

tag: isolate


title: G-MDSCs, 060

tag: age

value: Control


title: RPB1_wt_4tU_cordycepin_40mins_rep1

value: rpb1-1 yeast cells


title: G-MDSCs, 053

tag: Sex


title: RPB1_wt_4tU_DMSO_40mins_rep2


title: 317_SPO_T9_B1_IP

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Collected after 8h

data_processing:
Library strategy: m6Aseq2
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9

source_name: yeast strain, Collected after 8h

growth_protocol: All yeast strains used in this work were derived from the sporulation proficient SK1 strain background. S. cerevisiae cells (WT, PC: Ndt80Δ/Δ, NC: Ndt80Δ/Δ & Ime4Δ/Δ) were grown in YPD (2% dextrose) at 30C. To induce synchronous meiotic entry, cells were grown for 24 h in 1% yeast extract, 2% peptone, 4% dextrose at 30C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30C, 200 rpm. Cells were then washed once with water and re-suspended in SPO (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30C at 190 rpm. Cells were isolated from SPO at the indicated times and collected by 2 min centrifugation at 3000 g. Pellets were snap-frozen and stored at -80 for RNA extraction.

extract_protocol:
Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit (Lucigen, MPY03100).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

tag: background

value: WT

tag: antibody

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: 317_SPO_T9_B2_Input

description: Collected after 8h


title: 317_SPO_T9_B2_IP

description: Collected after 8h

growth_protocol: Commonly used V6.5 51 mouse embryonic stem cell line was kept in DMEM (Gibco) supplemented with penicillin-streptomycin, 1 mM L-glutamin, 1% non-essential amino acids, 20% high-grade fetal bovine serum, beta-mercaptoethanol and 10 µg recombinant leukemia inhibiting factor (LIF). Cells were kept on tissue culture plates covered by 0.2% gelatin in co-culture with in-house generated, radiation-inactivated mouse embryonic fibroblasts (MEF). For ESCs cells, total RNA was extracted using Nucleozol and subsequent 2-time polyA-selection according to manufacturers protocol.  m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

extract_protocol:
For mESCs cells, total RNA was extracted using Nucleozol (Macherey-Nagel, 740404.200).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)


title: G-MDSCs, 050

tag: disease

tag: bmi


title: CLP1_25_R1


title: YSH1_25_R2


title: 3-C2-epithelial cell

description:
Genomic DNA extracted from synovial sarcoma was genotyped using Illumina HumanExome-12 v1.1 BeadChip
SAMPLE 1

value: Female

tag: disease state

value: synovial sarcoma

value: primary

value: epithelial cell


title: RPB1_wt_4tU_DMSO_40mins_rep1

tag: treatment


title: YSH1_37_R1


title: 317_SPO_T9_B1_Input

description: Collected after 8h


title: G-MDSCs, 048

value: G-MDSC purified from PBMC


title: G-MDSCs, 049


title: YSH1_25_R1


title: 317_SPO_T7_B2_Input

description: Collected after 6h

source_name: yeast strain, Collected after 6h


title: RPB1_wt_4tU_cordycepin_20mins_rep1

value: 20 minutes


title: abx04_abx-d30-pDC_A149

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings; v 0.7.12). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.
Peaks were identified using the MACS algorithm (v 2.1.0) at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: Hg38

source_name: cryopreserved pbmcs

extract_protocol:
Atac-seq was performed on purified innate immune cell subsets immediately after sorting based on the low-input Omni-Atac protocol described before (Corces et al., 2017). In brief, 1,500 – 5,500 cells were washed with ATAC resuspension buffer (10 mM Tris-HCl pH 7.5 [Invitrogen, 15567027], 10 mM NaCl [Invitrogen, AM9760G], 3 mM MgCl2 [Invitrogen, AM9530G], in water [Invitrogen, 10977015]) and supernatant was carefully aspirated, first using a P1000, then a P200 pipette. Next, 10 µL transposition mix (0.5 µL Tn5, 0.1 µL 10% Tween-20, 0.1 µL 1% Digitonin, 3.3 µL PBS, 1 µL water, and 5 µL tagmentation buffer) was added to the pellet and cells were resuspended by pipetting up and down 6 times. Tagmentation buffer was prepared locally by resuspending 20 mM Tris-HCl pH 7.5, 10 mM MgCl2, and 20% Dimethyl Formamide (Sigma Aldrich, D4551-250ML) in water. Cells were incubated at 37C for 30 minutes under constant mixing.
After tagmentation, the reaction was cleaned up using the MinElute PCR Purification Kit (Qiagen, 28006) according to manufacturer’s instructions. Cleaned DNA was eluted in 21 µL of elution buffer, stored at -20C, and shipped to Active Motif for sequencing library preparation. At Active Motif, tagmented DNA was amplified with 10 cycles of PCR using customized Nextera PCR Primers 1 and 2 (see Key Resource table), and purified using Agencourt AMPure SPRI beads (Beckman Coulter, A63882). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (Roche, 07960255001), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

tag: time

value: abx

tag: assay

value: bulk ATAC-seq

tag: cell

value: pDCs


title: PAP1_25_R1

tag: strain/genotype


title: 317_SPO_T7_B2_IP

description: Collected after 6h


title: RPB1_wt_4tU_DMSO_20mins_rep2

tag: genotype

tag: plasmid

value: RBP1 wild-type

tag: 4tu status

value: DMSO


title: abx04_abx-d0-mDC_A139

value: cd11c+ cDCs


title: NAB4_37_R1

tag: temperature


title: PAP1_37_R1


title: 317_SPO_T7_B1_Input

description: Collected after 6h


title: RPB1_wt_untreated_0mins_rep2

value: No 4tU

value: Untreated

tag: treatment time

value: 0 minutes


title: 317_SPO_T7_B1_IP

description: Collected after 6h

value: WT


title: NAB4_25_R1


title: abx04_abx-d0-MC_A137

value: cd14+ monocytes


title: RPB1_wt_untreated_0mins_rep1

value: rpb1-1 yeast cells


title: 4tU_cordycepin_40mins_rep2

source_name: Saccharoymces cerevisiae in SC media at 30ºC

growth_protocol: BY4741 cells were grown at 30ºC until an OD600 of 0.6. 2 biological replicates were included.

tag: strain

value: cordycepin

value: 40 minutes


title: FIP1_37_R1


title: 317_SPO_T5_B1_IP

description: Collected after 4h

source_name: yeast strain, Collected after 4h

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: FIP1_25_R1


title: RPB1_wt_4tU_cordycepin_20mins_rep2

value: Cordycepin


title: abx04_abx-bl-MC_A129

value: bl


title: abx07_abx-d30-mDC_A123

value: abx


title: RNA14_37_R1


title: abx04_abx-d30-mDC_A148

value: bulk ATAC-seq


title: DMSO_cordycein_40mins_rep2


title: 4tU_cordycepin_40mins_rep1


title: abx07_abx-d30-MC_A122


title: 317_SPO_T3_B2_IP

description: Collected after 2h

source_name: yeast strain, Collected after 2h


title: RNA14_25_R1


title: abx07_abx-d0-pDC_A117

value: pDCs


title: 317_SPO_T5_B2_IP

description: Collected after 4h


title: DMSO_cordycein_40mins_rep1


title: PCF11_37_R1


title: RPB1_wt_4tU_DMSO_20mins_rep1

value: RBP1 wild-type

value: 20 minutes


title: 4tU_DMSO_40mins_rep2

value: DMSO


title: 317_SPO_T3_B2_Input

description: Collected after 2h


title: 317_SPO_T5_B2_Input

description: Collected after 4h


title: abx07_abx-d0-mDC_A115

value: cd11c+ cDCs


title: abx04_abx-bl-mDC_A131


title: 317_SPO_T3_B1_IP

description: Collected after 2h


title: W303_37_R1


title: DMSO_40mins_rep2

value: No 4tU


title: abx07_abx-d0-MC_A113


title: 317_SPO_T1_B2__IP

description: Collected after 0h

source_name: yeast strain, Collected after 0h


title: abx07_abx-bl-mDC_A107


title: W303_25_R1


title: DMSO_40mins_rep1


title: abx07_abx-bl-MC_A106


title: 40_minutes_R2

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 82
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

source_name: Saccharomyces cerevisiae in SD media with Ura, His, Lys and Met

growth_protocol: Yeast cells were grown at 30ºC until an OD600 of 0.6. 2 biological replicates were included.

treatment_protocol: Cells were treated with 20µg/ml cordycepin for 0, 5, 10, 20 or 40 minutes.

tag: cordycepin treatment time


title: 4tU_cordycepin_20mins_rep2


title: PCF11_25_R1


title: abx20_ctrl-d30-pDC_A101

value: ctrl


title: 4tU_cordycepin_20mins_rep1


title: 40_minutes_R1


title: 317_SPO_T3_B1_Input

description: Collected after 2h

tag: background

value: WT


title: 4tU_DMSO_40mins_rep1


title: 317_SPO_966_IP

source_name: yeast strain

tag: antibody


title: 317_SPO_T1_B1_IP

description: Collected after 0h


title: 20_minutes_R2


title: 317_SPO_T1_B2__Input

description: Collected after 0h


title: 317_SPO_T5_B1_Input

description: Collected after 4h


title: DMSO_cordycein_20mins_rep1


title: 10_minutes_R2

value: 10 minutes


title: 20_minutes_R1


title: abx20_ctrl-d30-MC_A097

value: cd14+ monocytes


title: 4tU_DMSO_20mins_rep2


title: abx20_ctrl-d0-pDC_A093


title: abx20_ctrl-d0-mDC_A091


title: 317_SPO_841_Input


title: 10_minutes_R1


title: 5_minutes_R2

value: 5 minutes


title: 4tU_DMSO_20mins_rep1


title: DMSO_20mins_rep2


title: abx20_ctrl-d0-MC_A089


title: abx20_ctrl-d30-mDC_A099


title: DMSO_cordycein_20mins_rep2

value: cordycepin


title: Batch4_IP_6152_Gis2_Ndt80

description: degradation-induced, Gis2

source_name: yeast strain, degradation-induced, Gis2

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: 317_SPO_T1_B1_Input

description: Collected after 0h


title: Batch4_IP_6093_C_Not3_Ndt80

description: non-induced, Not3

source_name: yeast strain, non-induced, Not3

growth_protocol: Gene deletion strains were generated by a one-step promoter replacement protocol, and genetic crosses. For generating depletion alleles, we used the auxin-induced degron allele (AID) and a plasmid expressing Oryza sativa osTIR1 ligase from a CUP1 promoter (pCUP1-TIR1 (Chia et al. 2021)). All gene deletions and AID alleles were crossed into the ndt80-deletion background, which ensures that cells do not exit meiotic prophase. To induce depletion, AID tagged allele cells expressing pCUP-TIR1 were grown to BYTA as described above. Four hours after shifting to SPO, 50 µM CuSO4 was added to induce TIR1 expression from the CUP1 promoter and 500 µM indole-3-acetic acid (IAA) to induce degradation. Samples were harvested after 2 hours (thus 6 hours in SPO).


title: 0_minutes_R2

value: 0 minutes


title: 5_minutes_R1


title: Untreated_0mins_rep2

value: Untreated


title: abx26_ctrl-d30-pDC_A085


title: 0_minutes_R1


title: Batch4_IP_6093_A_Not3_Ndt80

description: degradation-induced, Not3

source_name: yeast strain, degradation-induced, Not3


title: abx26_ctrl-d30-mDC_A083


title: abx26_ctrl-d30-MC_A081


title: 317_SPO_966_Input


title: Batch4_IP_6088_C_Pan3_Ndt80

description: non-induced, Pan3

source_name: yeast strain, non-induced, Pan3


title: Untreated_0mins_rep1


title: Batch4_IP_6088_A_Pan3_Ndt80

description: degradation-induced, Pan3

source_name: yeast strain, degradation-induced, Pan3


title: abx26_ctrl-d0-pDC_A077


title: 10DKO

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description:
1dpiDKO_rawcounts.csv
1dpi_DeSeq2_result.csv

data_processing:
Illumina Pipeline  Casava 1.8.2
7dpi Raw fastq files were mapped using TopHat 2.1.1/HTSeq 0.10 (tophat -p 6 --min-intron-length 40 --max-intron-length 2000 --bowtie1 --no-novel-juncs --read-mismatches 2 -G /mnt/genomes/Mus_musculus/mm10/annotation/genes.gtf --transcriptome-index transcriptome_data --output-dir tophatFolder/ /mnt/genomes/Mus_musculus/mm10/bowtieIndex/genome /home/BIOTECH/sample.fastq.gz  )
1dpi Raw fastq files were mapped using Star-aligner 2.7.3a (STAR --runThreadN 12 --genomeDir mm10 --readFilesCommand zcat --readFilesIn RNAseq/inputFolder --outFileNamePrefix outputFolder --outSAMtype BAM SortedByCoordinate)
Data were analyzed using DEseq2
Genome_build: Genome_build: mm10

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water. Kdm6a/Kdm6b-floxed mice were mated to mP0TOTA-Cre (B6N.FVB-Tg(Mpz-cre)26Mes/J, obtained from Jackson Laboratory, RRID: IMSR_JAX:017927).

extract_protocol:
Total RNA was purified using Qiagen Rneasy Lipid Kit
Libraries were prepared using the Illumina TruSeq Stranded total RNA sample preparation kit V2

treatment_protocol: The sciatic nerves of adult mice at the age of 2 months were exposed and transected at the sciatic notch (Hung et al., 2015). As a control, the contralateral limb also rece a sham operation consisting of only a skin incision. The nerve tissues distal to the transection and contralateral (sham) nerves were isolated.

tag: age

value: Injury 1 dpi, ipsilateral

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: 317_SPO_841_IP


title: PUF6-dataset-II

city: Edinburgh

first: Sander

last: Granneman

address: Max Born Crescent, CH Waddington Building

department: Centre for Synthetic and Systems Biology (SynthSys)

country: United Kingdom

institute: University of Edinburgh

data_processing:
demultiplexing and adapter removal with flexbar
collapsing cDNA-duplicates with pyFastqDuplicateRemover.py from pyCRAC (pypi.org) package
mapping of collapsed reads to Saccharomyces_cerevisiae.R64-1-1.75 using novoalign
reads were counted with pyReadCounters.py and converted to bedgraph files
outputs from novoalign and pyReadCounters.py were used for further analysis with pyPileUp.py
Genome_build: Saccharomyces_cerevisiae.R64-1-1.75.3.gtf
Supplementary_files_format_and_content: bedgraph (txt) with readcounts/per nucleotide for visualisation in genome browsers, xlsx with pileup output analysis used for the figure

source_name: cells

extract_protocol:
Growing yeast cells expressing a His6-TEV-ProtA (HTP)-tagged Puf6 protein were irradiated with UV in a Vari-X-linker, collected by filtration and stored at -80oC. Cells were washed from filters in PBS, pelletted and broken with zirconia beads in extraction buffer. After clearing of the extracts by centrifugation, Puf6 with crosslinked RNA was purified on IgG beads, washed under high salt conditions and released from the TAP-tag by TEV protease; non-protected RNA was then removed by RNAse digestion and the resulting RNA/His6-tagged protein hybrid was bound to NTA-beads under denaturing conditions.
RNA, while crosslinked to NTA-bound Puf6, was radio-labelled and ligated to adapters (with the 5'-adaptor containing a sample-specific barcode), after which the hybrid was eluted with imidazole, size-selected by gel electrophoresis and isolated from gel. Upon its release from Puf6 by ProtK digestion and phenol/chloroform extraction, the RNA with attached adapters was converted into cDNA by reverse transcription. The cDNA-library was amplified with illumina primers and submitted for HTS.

tag: expression


title: abx26_ctrl-d0-mDC_A075

value: bulk ATAC-seq


title: PUF6-dataset-I

value: His6-TEV-ProtA (HTP)-tagged Puf6 protein


title: abx26_ctrl-d0-MC_A074


title: Batch4_IP_6080_C_Rat1_Ndt80

description: non-induced, Rat1

source_name: yeast strain, non-induced, Rat1


title: 7DKO


title: P3F_high_U23674_ATACSeq

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

institute: Medical Center - University of Freiburg

description:
Tn5 accessible chromatin
mouse primary rhabdomyosarcoma tumor cells

data_processing:
FASTQ files were processed by trimming Illumina adapters and Tn5 sequences with trimmomatic, then aligned to mouse genome (build mm10) using bowtie2. Duplicate reads and mitochondrial reads were removed and HOMER pipeline was used to determine transcription factor motifs enriched specific for each cell type (Heinz S et al 2010 PMID: 20513432). Gene Set Enrichment Analysis (GSEA) was performed according to previous reports (Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273).
Genome_build: mm10
Supplementary_files_format_and_content: Annotated Peak file as outputted by Homer

source_name: Mouse U23674 Rhapdomyosarcoma cell line with high expression of YFP (P3F) (126)

growth_protocol: U23674  cells were grown in Dulbecco´s modified Eagle´s medium (DMEM, Gibco, 41965-039), supplemented with 10% Fetal Bovine Serum (FBS, Sigma, F7524) and 1% Penicillin/ Streptomycin (PS, Gibco, 15140-122).

extract_protocol:
FACS-sorted cells were centrifuged at 500g for 5 min at 4oC. Supernatant was carefully removed and discarded without disturbing the cell pellet. Cell pellets were then resuspended in 50l cold lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40) and immediately centrifuged at 500g for 5 min at 4oC. Supernatant was removed carefully and then resuspended in freshly prepared Tn5 reaction buffer (12.5ml 1X TD buffer (Illumina), 1ml Tn5 Transposase, 11.5ml nuclease-free water). Transposition reaction was incubated at 37oC for 30min and then purified using Zymo ChIP clean up kit.
Transposed DNA was subjected to 5 cycles of indexed PCR amplification using NEBNext Ultra II Q5 Master mix and custom indexed primers. Quantitative real time PCR was performed to determine optimal PCR cycles for linear amplification without saturating ATAC-Seq libraries. ATAC-Seq libraries were then quantified using Qubit (Invitrogen

treatment_protocol: Cells were suspended in Hank’s balanced salt solution (HBSS) with 2% FBS. Prior to FACS sorting, cells were labeled with 7AAD (BD Biosciences, 559925) to exclude dead cells. Cells were sorted twice using a MoFlo Astrios flow cytometer. Purity checks were performed to confirm that the sorted YFPpos and YFPneg cell subsets had a purity of >98% using a YFP expression threshold determined by the background fluorescence of YFP- C2C12 cells.

tag: cell line

tag: origin

value: Myf6Cre,Pax3:Fkhr,p53 RMS cells

tag: tumor stage

value: localized

tag: tissue

value: soft tissue sarcoma tissue


title: DMSO_20mins_rep1

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: s. cerevisiae ensembl version 89
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis. primers.gff contains the primer sequences used in this analysis.

value: No 4tU

tag: treatment

value: DMSO

value: 20 minutes


title: Batch4_IP_6080_A_Rat1_Ndt80

description: degradation-induced, Rat1

source_name: yeast strain, degradation-induced, Rat1


title: P3F_Low_U23674_ATACSeq

source_name: Mouse U23674 Rhapdomyosarcoma cell line with low expression of YFP (P3F) (124)


title: abx27_ctrl-d30-pDC_A069

source_name: cryopreserved pbmcs

tag: time

value: ctrl

tag: assay

tag: cell

value: pDCs


title: 6WT

tag: genotype

value: Kdm6a fl/wt, Kdm6b fl/fl


title: abx27_ctrl-d30-mDC_A067

value: cd11c+ cDCs


title: Batch4_IP_6060_C_Ime4_Ndt80

description: non-induced, Ime4

source_name: yeast strain, non-induced, Ime4

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: 5DKO


title: 4WT

value: Kdm6a fl/fl, Kdm6b fl/fl


title: abx27_ctrl-d0-pDC_A061


title: hiPSC_F2, scRNA-seq

city: Charlestown

first: Mutsumi

last: Kobayashi

state: Massachusetts

address: Building 147, 13th street, Rm# 7103

institute: MGH, center for cancer reserch

data_processing:
Illumina Casava1.7 software used for basecalling.
Demultiplexed, adaptor trimming, quality control, mapping to hg38, and counting reads mapped on genes were performed by Cell Ranger v6.0.1.
Filtering by cell barcode via unique molecular identifiers, and analysisng were perfoemed by Scanpy Python pcakage v.1.7.2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cells

source_name: human iPSC

growth_protocol: Human iPSCs were maintained in the mTeSR plus medium and converted to hPGCLCs. LTC-hPGCLCs were cultured in the hPGCLC maintenance media.

extract_protocol: Synthesis of cDNA and library preparation were performed by Chromium Next GEM Single Cell 5' Reagent Kits v2 - Dual Index

treatment_protocol: Cells were harvested from dishes dilectly.

tag: Sex

value: female

tag: cell id

tag: cell type

value: human iPSC


title: 3WT

value: Injury 1 dpi, ipsilateral


title: abx27_ctrl-d30-MC_A065

value: bulk ATAC-seq

value: cd14+ monocytes


title: Batch4_IP_4911_C_Ndt80

description: non-induced

source_name: yeast strain, non-induced


title: LTC-hPGCLC_A5, scRNA-seq

source_name: human PGCLC

value: male

value: human PGCLC


title: LTC-hPGCLC_F2, scRNA-seq


title: hiPSC_A5, scRNA-seq


title: Batch4_Input_6093_C_Not3_Ndt80

description: non-induced, Not3


title: 2DKO

value: Kdm6a fl/y, Kdm6b fl/fl Cre


title: abx27_ctrl-d0-MC_A057


title: abx27_ctrl-d0-mDC_A059


title: Batch4_Input_6152_Gis2_Ndt80

description: degradation-induced, Gis2


title: 1WT

value: Kdm6a wt/y, Kdm6b fl/fl


title: 8DKO

value: Kdm6a fl/fl, Kdm6b fl/fl Cre


title: Batch4_Input_6093_A_Not3_Ndt80

description: degradation-induced, Not3


title: Batch4_Input_6088_C_Pan3_Ndt80

description: non-induced, Pan3


title: abx14_ctrl-d30-pDC_A053


title: abx14_ctrl-d30-MC_A049


title: Batch4_Input_6080_C_Rat1_Ndt80

description: non-induced, Rat1


title: Batch4_Input_6080_A_Rat1_Ndt80

description: degradation-induced, Rat1


title: abx14_ctrl-d0-pDC_A045


title: Batch4_Input_6060_C_Ime4_Ndt80

description: non-induced, Ime4


title: abx14_ctrl-d0-mDC_A043


title: Batch4_Input_4911_C_Ndt80

description: non-induced


title: abx14_ctrl-d0-MC_A041


title: abx14_ctrl-d30-mDC_A051


title: Batch3_IP_6100_C_TIR_Ndt80

description: non-induced, TIR

source_name: yeast strain, non-induced, TIR


title: abx10_abx-bl-MC_A033

value: bl

value: abx


title: Batch3_IP_6100_A_TIR_Ndt80

description: degradation-induced, TIR

source_name: yeast strain, degradation-induced, TIR


title: abx10_abx-d30-pDC_A029

value: pDCs


title: Batch3_IP_6075_C_Lsm1_Ndt80

description: non-induced, Lsm1

source_name: yeast strain, non-induced, Lsm1


title: Batch3_IP_6075_A_Lsm1_Ndt80

description: degradation-induced, Lsm1

source_name: yeast strain, degradation-induced, Lsm1


title: ChIP antiBRD4 REH FASTKD1 ko1 2

data_processing:
Raw fastq files were processed by 5 prime trimming, keeping 30 bp-length fragments, using `fastx_trimmer` (with options -l 30 -Q33). The trimmed fastq files were aligned on the USCS human hg38 genome using the Bowtie2 aligner (Langmead and Salzberg, 2012), with options –end-to-end, –no-mixed, –no-discordant. The aligned reads were filtered according to alignment quality (mapping quality score > 30).
The aligned read counts were converted into a 10 bp bin matrix of the signal 2Kb upstream and downstream genes TSS, using computeMatrix (from the package deepTools2, Ramírez et al., 2016), heatmaps and profiles were generated using the respective deepTools2 packages, plotHeatmap and plotProfile.
Genome_build: hg38

source_name: REH

growth_protocol: Human lymphoblastic leukemia cell line REH (Female, CVCL_1650) was obtained from National Collection of Authenticated Cell Cultures and was authenticated by STR analysis prior to use. REH and the derivative cells were maintained in RPMI-1640 (Gibco) supplemented with 10% FBS (Dominique DUTSCHER), 4mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
For sequencing, ChIP libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
ChIP libraries against H4K5bu and BRD4 were sequenced using the NovaSeq 6000 in PE150 mode according to manufacturer’s instructions at the Novogene company.

treatment_protocol: Immunoprecipitations were carried out as follows: 5 μg anti-H4K5cr (PTM biolabs, Cat#PTM-521), anti-H4K5bu (PTM biolabs, Cat#PTM-310), anti-H4K5ac (abcam, Cat#ab51997), anti-BRD4 (Bethyl lab, Cat#A301-985A100) antibodies were coupled with 50 µl Dynabeads protein G (Thermo Fisher, Cat#10007D) respectively according to the manufacturer’s instructions. Digested mononucleosomes solutions were diluted with LSDB500 buffer (50 mM HEPES pH 7.0, 3mM MgCl2, 500 mM KCl, 20% glycerol, protease cocktail inhibitors) with 10 mM sodium butyrate to achieve the final KCl concentration of 350 mM. For each reaction, around 100 μg chromatin was incubated with antibody-coupled beads at 4°C for 16 hours. Immunoprecipitated beads were then washed three times with LSDB350 buffer (50 mM HEPES pH 7.0, 3 mM MgCl2, 350 mM KCl, 20% glycerol, protease cocktail inhibitors) with 10 mM sodium butyrate and one time with elution buffer (10 mM Tris-HCl pH 8.5, 1 mM EDTA). ChIP samples were eluted from beads with elution buffer containing 1%SDS at 65°C for 15 min and were purified by phenol-chloroform extraction and ethanol precipitation in parallel with input samples.

value: REH

value: FASTKD1 ko1

tag: chip antibody

value: ChIP antiBRD4


title: ChIP antiH4K5bu REH FASTKD1 ko1

value: ChIP antiH4K5bu


title: ChIP antiH4K5bu REH FASTKD1 ko2

value: FASTKD1 ko2


title: ChIP antiH4K5bu REH WT

value: WT


title: ChIP antiBRD4 REH FASTKD1 ko2 2


title: abx10_abx-d30-mDC_A027

value: cd11c+ cDCs


title: Batch3_IP_6060_C_Ime4_Ndt80

description: non-induced, Ime4

tag: background

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: ChIP antiBRD4 REH WT 2


title: abx10_abx-d30-MC_A025

value: bulk ATAC-seq

value: cd14+ monocytes


title: Batch3_IP_6048_C_Dcp2_Ndt80

description: non-induced, Dcp2

source_name: yeast strain, non-induced, Dcp2

tag: antibody


title: Batch4_Input_6088_A_Pan3_Ndt80

description: degradation-induced, Pan3

source_name: yeast strain, degradation-induced, Pan3


title: input MNase REH FASTKD1 ko2 3

value: input MNase


title: abx10_abx-d0-pDC_A021


title: Batch3_IP_6048_A_Dcp2_Ndt80

description: degradation-induced, Dcp2

source_name: yeast strain, degradation-induced, Dcp2


title: Batch3_IP_6043_C_Nrd1_Ndt80

description: non-induced, Nrd1

source_name: yeast strain, non-induced, Nrd1


title: abx10_abx-d0-mDC_A019


title: input MNase REH FASTKD1 ko1 3


title: input MNase REH WT 3


title: abx10_abx-d0-MC_A017


title: Batch3_IP_6043_A_Nrd1_Ndt80

description: degradation-induced, Nrd1

source_name: yeast strain, degradation-induced, Nrd1


title: abx23_ctrl-d30-pDC_A013

value: ctrl


title: abx10_abx-bl-mDC_A035


title: abx-04_d30_abx_MC

data_processing:
Alignment was performed using STAR version 2.7.3a
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Genome_build: GRCh38

extract_protocol:
Bulk RNA-seq was performed on purified CD14+ monocytes after sorting. In brief, after sorting, 5,500 cells were washed, resuspended in 350 µL chilled Buffer RLT (Qiagen, 79216) supplemented with 1% beta-Mercaptoethanol (Sigma, M3148-25ML), vortexed for 1 minute, and immediately frozen at -80C.
RNA was isolated using the RNeasy Micro kit (Qiagen, 74004) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer and total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio, 634894) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina, FC-131-1096). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20-25 million reads per sample.

tag: time after vaccination

value: antibiotics


title: abx-04_d0_abx_MC


title: Batch3_IP_4911_C_Ndt80

description: non-induced


title: abx23_ctrl-d30-mDC_A011


title: Batch3_Input_6100_C_TIR_Ndt80

description: non-induced, TIR


title: abx23_ctrl-d0-pDC_A006


title: Batch3_Input_6100_A_TIR_Ndt80

description: degradation-induced, TIR


title: Batch3_Input_6075_A_Lsm1_Ndt80

description: degradation-induced, Lsm1


title: abx-20_d0_ctrl_MC

value: control


title: abx23_ctrl-d0-mDC_A004


title: abx-20_d30_ctrl_MC


title: abx23_ctrl-d0-MC_A002


title: Batch3_Input_6060_C_Ime4_Ndt80

description: non-induced, Ime4


title: Batch3_Input_6075_C_Lsm1_Ndt80

description: non-induced, Lsm1


title: abx-26_d0_ctrl_MC


title: REH WT JQ1 500nM replicate3

data_processing:
The sequenced reads were aligned from raw sequence fastq data using STAR v2.5.2b software on UCSC hg19 reference genome.
The aligned reads were normalized, and log transformed using the R bioconductor package DEseq2 (http://bioconductor.org/packages/3.12/bioc/html/DESeq2.html).
Genome_build: hg19

extract_protocol:
5x106 cells were harvested and yielded to RNA extraction with 500 μl TRIzol reagent (Invitrogen, Cat#15596018) according to the provider’s protocol. Precipitated RNA was dissolved in DEPC-treated water and used for RNA-sequencing. Three independent RNA extractions from solvent and JQ1 treated WT cells samples were sequenced.
For each sample, 1 µg RNA samples (RIN = 10) were used for libraries preparations with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Libraries prepared from solvent and JQ1 treated cells samples were sequenced on Illumina NS500 (PE75) at the TGML Platform of Aix-Marseille Université

treatment_protocol: REH WT cells were exposed to 0.1 μM or 0.5 μM JQ1 or DMSO as control respectively for 24 hours.

tag: replicate


title: Batch3_Input_6048_C_Dcp2_Ndt80

description: non-induced, Dcp2


title: abx-26_d30_ctrl_MC


title: Batch3_Input_6048_A_Dcp2_Ndt80

description: degradation-induced, Dcp2


title: REH WT JQ1 100nM replicate3

tag: cell line


title: Batch3_Input_6043_C_Nrd1_Ndt80

description: non-induced, Nrd1


title: REH WT ctrl replicate3


title: abx-27_d0_ctrl_MC


title: Batch3_Input_6043_A_Nrd1_Ndt80

description: degradation-induced, Nrd1


title: Batch3_Input_4911_C_Ndt80

description: non-induced


title: abx-07_d30_abx_MC


title: abx23_ctrl-d30-MC_A009


title: REH WT JQ1 100nM replicate2


title: REH WT JQ1 500nM replicate2


title: Batch2_IP_6070_C_Not5_Ndt80

description: non-induced, Not5

source_name: yeast strain, non-induced, Not5


title: REH WT ctrl replicate2


title: 1A8: Abx-15_d30_L2

city: Palo Alto

first: Florian

last: Wimmers

address: 1651 Page Mill Road

department: School of Medicine

institute: Stanford University

data_processing:
CellRanger-ATAC (v1.1.0) count functionality was used for alignment, deduplication, demultiplexing, and identification of cut sites.
CellRanger-ATAC (v1.1.0)'s aggr function was then used to aggregate samples without depth normalization (--normalize=none)
The resulting fragment file was read into SnapATAC (v1.0). Cells were called as barcodes with at least 1000 UMIs and a promotor ratio (defined as: (fragments in promoter regions + 1) / (total fragments + 1)) of at least 0.1. Reads were mapped into 5kb bins to create a bin-by-cell matrix.
average of 1500 fragments per barcode by randomly removing counts from these samples at a probability p=1500/(mean fragments per cell in the sample).
SnapATAC was then used to identify clusters from the cell-by-bin matrix, then peaks were called (MACS2 v2.2.7.1) separately for each cluster and joined for a joined set of peaks.
Fragments were mapped to the joined set of peaks for each cell barcode to create the peak-by-cell matrix.
Genome_build: hg38
Supplementary_files_format_and_content: TIV_scATAC_counts.mtx.gz: raw count matrix
Supplementary_files_format_and_content: TIV_scATAC_meta.tsv: tab-seperated cell annotations
Supplementary_files_format_and_content: TIV_scATAC_peaks.bed: peaks in bed format

source_name: monocytes and dendritic cells

extract_protocol:
Cryopreserved PBMCs were thawed and innate immune cell subsets were isolated using FACS. Within the live gated cells, CD14+ monocytes were identified as CD14+ (fraction A) while a mixture of the remaining monocyte and dendritic cell subsets was identified as CD14-CD56-HLA-DR+ (fraction B). After sorting and depending on the number of isolated cells, fraction A and B were mixed at a 2:1 ratio to yield a solution of monocytes and dendritic cells enriched for CD14- cells.
FACS-purified cells were processed for single nuclei ATAC-seq according to the manufacturer’s instructions (10x Genomics, CG000168 Rev D). Briefly, nuclei were obtained by incubating PBMCs for 3.20 minutes in freshly prepared Lysis buffer following manufacturer’s instructions for Low Cell Input Nuclei Isolation (10x Genomics, CG000169 Rev C). Nuclei were washed and resuspended in chilled diluted nuclei buffer (10x Genomics, 2000153). Next, nuclei were subjected to transposition for 1h at 37C on the C1000 touch PCR instrument (BioRad) prior to single nucleus capture on the 10x Chromium instrument. Samples were subjected to post GEM cleanup, sample index PCR, cleanup and library QC prior to sequencing according to the protocol. Samples were pooled, quantified and sequenced on NovaSeq 6000 instrument (Illumina) with at least minimum recommended read depth (25000 read pairs/nucleus).

tag: subject

tag: time point

tag: experiment

tag: lane

value: monocytes and dendritic cells


title: abx-07_d0_abx_MC

source_name: cryopreserved pbmcs

tag: treatment


title: 6A: Abx-02_d30_L2

tag: tissue


title: Batch2_IP_6070_A_Not5_Ndt80

description: degradation-induced, Not5

source_name: yeast strain, degradation-induced, Not5


title: 1A9: Abx-20_d30_L2


title: Batch2_IP_6065_C_Pat1_Ndt80

description: non-induced, Pat1

source_name: yeast strain, non-induced, Pat1


title: REH WT JQ1 100nM replicate1


title: 4A8: Abx-15_d1_L2


title: REH WT ctrl replicate1


title: REH WT JQ1 500nM replicate1


title: abx-27_d30_ctrl_MC


title: REH FASTKD1 ko2 replicate3

extract_protocol:
Three independent RNA extractions from FASTKD1 WT and two ko clones (ko-1, ko-2) samples were sequenced.
For each sample, 1 µg RNA samples (RIN = 10) were used for libraries preparations with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Library prepared from WT and knockout cells samples were sequenced on Hiseq 4000 (PE150) platform in Novagene company


title: Batch2_IP_6065_A_Pat1_Ndt80

description: degradation-induced, Pat1

source_name: yeast strain, degradation-induced, Pat1


title: 2A9: Abx-20_d0_L2


title: 3A: Abx-02_d1_L2


title: Batch2_IP_6060_C_Ime4_Ndt80

description: non-induced, Ime4

source_name: yeast strain, non-induced, Ime4


title: Batch2_IP_6060_A_Ime4_Ndt80

description: degradation-induced, Ime4

source_name: yeast strain, degradation-induced, Ime4


title: 5A8: Abx-15_d0_L2


title: REH FASTKD1 ko1 replicate3


title: REH WT replicate3


title: Batch2_IP_5961_C_Caf40_Ndt80

description: non-induced, Caf40

source_name: yeast strain, non-induced, Caf40


title: 5A: Abx-02_d0_L2


title: Batch2_IP_5961_A_Caf40_Ndt80

description: degradation-induced, Caf40

source_name: yeast strain, degradation-induced, Caf40


title: REH FASTKD1 ko2 replicate2


title: REH FASTKD1 ko1 replicate2


title: 1A9: Abx-20_d30_L1


title: Batch2_IP_4911_C_Ndt80

description: non-induced

source_name: yeast strain, non-induced


title: 4A9: Abx-20_d1_L2


title: 1A8: Abx-15_d30_L1


title: Batch2_Input_6070_C_Not5_Ndt80

description: non-induced, Not5


title: REH FASTKD1 ko2 replicate1

source_name: REH


title: 6A: Abx-02_d30_L1


title: 4A9: Abx-20_d1_L1


title: Batch2_Input_6070_A_Not5_Ndt80

description: degradation-induced, Not5


title: REH FASTKD1 ko1 replicate1


title: 4A8: Abx-15_d1_L1


title: SN1

city: Hongkong

first: Taida

last: Huang

address: 39 Area

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The sequencing results were first analysed by FastQC software for quality control. Sequenced reads were trimmed for adaptor sequence with Fastp software, then mapped to mm10 whole genome using Bowtie2 software.
Normalized FPKM were calculated and compared between samples by using Cufflink software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: sacral neural crest cell

growth_protocol: Neural tube explant were isolated from E9.0 mouse embryos at the somate level from 1 to 7 (vagal) and E9.5 mouse embryos at distal end to somate 24 (sacral). The explants were cultured in fibronectin coated 4-well plate containing DMEM/F12 based culture medium.

extract_protocol:
Total RNA from the NCC cultures was extracted using RNeasy Micro Kit following with the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24 hours, the emigrated neural crest cells were harvested for RNA extraction.

tag: strain

tag: age

value: wild type

value: sacral neural crest cell


title: SN2

tag: genotype


title: Batch2_Input_6065_C_Pat1_Ndt80

description: non-induced, Pat1


title: REH WT replicate1

value: REH


title: VN2

source_name: vagal neural crest cell

value: vagal neural crest cell


title: 3A: Abx-02_d1_L1


title: Batch2_Input_6065_A_Pat1_Ndt80

description: degradation-induced, Pat1


title: VN3


title: Batch2_Input_6060_C_Ime4_Ndt80

description: non-induced, Ime4


title: VN1


title: 2A9: Abx-20_d0_L1


title: 520DD_mESC_24_IP_85_3

source_name: mus musculus

value: 15 % Mettl3 KO, 85% WT


title: SN3


title: ChIP antiBRD4 REH FASTKD1 ko2

data_processing:
alignment and filtering: Raw fastq files were processed by 5 prime trimming, keeping 30 bp-length fragments, using `fastx_trimmer` (with options -l 30 -Q33). The trimmed fastq files were aligned on the USCS human hg38 genome using the Bowtie2 aligner (Langmead and Salzberg, 2012), with options –end-to-end, –no-mixed, –no-discordant. The aligned reads were filtered according to alignment quality (mapping quality score > 30).
normalization: For the anti-BRD4 ChIPseq, scaling factors were computed according to the Spike in free method (Jin et al. Bioinformatics 2020), and accordingly the respective scaling factors 4.25, 3.58 and 5.81 were applied when calculating the BRD4 ChIPseq read counts in WT, ko1 and ko2 cells.
read counts analysis: The aligned read counts were converted into a 10 bp bin matrix of the signal 2Kb upstream and downstream genes TSS, using computeMatrix (from the package deepTools2, Ramírez et al., 2016), heatmaps and profiles were generated using the respective deepTools2 packages, plotHeatmap and plotProfile.
Genome_build: hg38

extract_protocol:
For sequencing, ChIP libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Libraries were then sequenced on a High-output flow cell (400M clusters) using the NextSeq® 500/550 High Output v2.5 150 cycles kit (Illumina), in paired-end 75/75nt mode, according to manufacturer’s instructions at the TGML Platform of Aix-Marseille Université.

treatment_protocol: ChIP assays for H4K5cr, H4K5ac and BRD4 were carried out as follows. Around 5 -10 x107 REH WT, ko-1 and ko-2 cells were harvested and lysed in 1.5 ml lysis buffer (0.05% Triton-X 100, 15 mM Tris-HCl pH 7.4, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 2 mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.65 mM spermidine, 1x protease cocktail inhibitors) with 10 mM sodium butyrate and incubated for 5 minutes at 4°C. Cell nuclei were pelleted by centrifugation at 250 g for 5 min at 4°C and resuspended in MNase buffer (10 mM Tris-HCl pH 7.5, 10 mM KCl, 2 mM CaCl2) with10 mM sodium butyrate. Then the cell nuclei solution was subjected to micrococcal nuclease S7 (Sigma-Aldrich, Cat#10107921001) digestion (5U MNase per 100μg nuclei) at 37°C for 20 min to obtain mononucleosomes. Small aliquots of mononucleosomes solutions were collected for input and used to check the efficiency of digestion before immunoprecipitation.   Immunoprecipitations were carried out as follows: 5 μg anti-H4K5cr (PTM biolabs, Cat#PTM-521), anti-H4K5ac (abcam, Cat#ab51997), anti-BRD4 (Bethyl lab, Cat#A700-004) antibodies were coupled with 50 µl Dynabeads protein G (Thermo Fisher, Cat#10007D) respectively according to the manufacturer’s instructions. Digested mononucleosomes solutions were diluted with LSDB500 buffer (50 mM HEPES pH 7.0, 3mM MgCl2, 500 mM KCl, 20% glycerol, protease cocktail inhibitors) to achieve the final KCl concentration of 350 mM. For each reaction, around 100 μg chromatin was incubated with antibody-coupled beads at 4°C for 16 hours. Immunoprecipitated beads were then washed three times with LSDB350 buffer (50 mM HEPES pH 7.0, 3 mM MgCl2, 350 mM KCl, 20% glycerol, protease cocktail inhibitors) with 10 mM sodium butyrate and one time with elution buffer (10 mM Tris-HCl pH 8.5, 1 mM EDTA). ChIP samples were eluted from beads with elution buffer containing 1%SDS at 65°C for 15 min and were purified by phenol-chloroform extraction and ethanol precipitation in parallel with input samples.

value: ChIP antiBRD4


title: Batch2_Input_6060_A_Ime4_Ndt80

description: degradation-induced, Ime4


title: 520DD_mESC_24_IP_85_2


title: Batch2_Input_5961_C_Caf40_Ndt80

description: non-induced, Caf40


title: ChIP antiBRD4 REH FASTKD1 ko1

value: FASTKD1 ko1


title: ChIP antiBRD4 REH WT

value: WT


title: REH WT replicate2


title: 5A: Abx-02_d0_L1


title: 4R9: Abx-20_d1_L2

data_processing:
Alignment, demultiplexing, cell-calling and filtering were performed using the count pipeline from 10x Genomics' CellRanger (v3.1.0) on each sample
Filtered count matrices were aggregated using CellRanger's aggr functionality, without depth normalization (--normalize=none)
Genome_build: hg38
Supplementary_files_format_and_content: TIV_scrna_matrix.mtx.gz: Matrix with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: TIV_scrna_features.tsv.gz: gene identifiers
Supplementary_files_format_and_content: TIV_scrna_cell_meta.csv: cell annotations

extract_protocol:
Cryopreserved PBMCs were thawed and innate immune cell subsets were isolated using FACS. Within the live gated cells, CD14+ monocytes were identified as CD14+ (fraction A) while a mixture of the remaining monocyte and dendritic cell subsets was identified as CD14-CD56-HLA-DR+ (fraction B). After sorting and depending on the number of isolated cells, fraction A and B were mixed at a 2:1 ratio to yield a solution of monocytes and dendritic cells enriched for CD14- cells.
FACS-purified cells were resuspended in PBS supplemented with 1% BSA (Miltenyi), and 0.5 U/μL RNase Inhibitor (Sigma Aldrich). About 9,000 cells were targeted for each experiment. Cells were mixed with the reverse transcription mix and subjected to partitioning along with the Chromium gel-beads using the 10X Chromium system to generate the Gel-Bead in Emulsions (GEMs) using the 3' V3 chemistry (10X Genomics). The RT reaction was conducted in the C1000 touch PCR instrument (BioRad). Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was subjected to 0.6x SPRI beads cleanup (Beckman, B23318). 25% of the amplified cDNA was subjected to enzymatic fragmentation, end-repair, A tailing, adapter ligation and 10X specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. Libraries were pooled and sequenced on an NovaSeq 6000 instrument (Illumina) using the recommended sequencing read lengths of 28 bp (Read 1), 8 bp (i7 Index Read), and 91 bp (Read 2).


title: input MNase REH FASTKD1 ko2 2

value: FASTKD1 ko2


title: 520DD_mESC_24_IP_85_1

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: Batch2_Input_5961_A_Caf40_Ndt80

description: degradation-induced, Caf40


title: Batch2_Input_4911_C_Ndt80

description: non-induced


title: 2R9: Abx-20_d0_L2


title: 520DD_mESC_24_IP_71_2

value: 29 % Mettl3 KO, 71% WT


title: input MNase REH WT 2


title: Batch1_IP_6060_C_Ime4_Ndt80

description: non-induced, Ime4


title: input MNase REH FASTKD1 ko1 2


title: 1R9: Abx-20_d30_L2


title: 5R8: Abx-15_d0_L2


title: 520DD_mESC_24_IP_71_1


title: 520DD_mESC_24_IP_57_3

value: 43 % Mettl3 KO, 57% WT


title: 5A8: Abx-15_d0_L1


title: Batch1_IP_5964_A_Xrn1_Ndt80

description: degradation-induced, Xrn1

source_name: yeast strain, degradation-induced, Xrn1


title: ChIP antiH4K5cr REH FASTKD1 ko2

data_processing:
alignment and filtering: Raw fastq files were processed by 5 prime trimming, keeping 30 bp-length fragments, using `fastx_trimmer` (with options -l 30 -Q33). The trimmed fastq files were aligned on the USCS human hg38 genome using the Bowtie2 aligner (Langmead and Salzberg, 2012), with options –end-to-end, –no-mixed, –no-discordant. The aligned reads were filtered according to alignment quality (mapping quality score > 30).
read counts analysis: The aligned read counts were converted into a 10 bp bin matrix of the signal 2Kb upstream and downstream genes TSS, using computeMatrix (from the package deepTools2, Ramírez et al., 2016), heatmaps and profiles were generated using the respective deepTools2 packages, plotHeatmap and plotProfile.
Genome_build: hg38

value: ChIP antiH4K5cr


title: ChIP antiH4K5cr REH FASTKD1 ko1


title: 520DD_mESC_24_IP_57_2


title: 4R8: Abx-15_d1_L2


title: 1R8: Abx-15_d30_L2


title: ChIP antiH4K5cr REH WT


title: Batch1_IP_5956_C_Pop2_Ndt80

description: non-induced, Pop2

source_name: yeast strain, non-induced, Pop2


title: 520DD_mESC_24_IP_57_1


title: ChIP antiH4K5ac REH FASTKD1 ko2

value: ChIP antiH4K5ac


title: Batch1_IP_5956_A_Pop2_Ndt80

description: degradation-induced, Pop2

source_name: yeast strain, degradation-induced, Pop2


title: 5R: Abx-02_d0_L2

source_name: monocytes and dendritic cells


title: 520DD_mESC_24_IP_71_3


title: Batch1_IP_5880_C_Rrp6_Ndt80

description: non-induced, Rrp6

source_name: yeast strain, non-induced, Rrp6


title: 3R: Abx-02_d1_L2


title: ChIP antiH4K5ac REH FASTKD1 ko1


title: ChIP antiH4K5ac REH WT


title: 520DD_mESC_24_IP_42_3

value: 58 % Mettl3 KO, 42% WT


title: 4R9: Abx-20_d1_L1


title: Batch1_IP_5964_C_Xrn1_Ndt80

description: non-induced, Xrn1

source_name: yeast strain, non-induced, Xrn1


title: 520DD_mESC_24_IP_42_1


title: Batch1_IP_5828_C_Rpb3_Ndt80

description: non-induced, Rpb3

source_name: yeast strain, non-induced, Rpb3


title: input MNase REH FASTKD1 ko2

value: input MNase


title: Batch1_IP_5880_A_Rrp6_Ndt80

description: degradation-induced, Rrp6

source_name: yeast strain, degradation-induced, Rrp6


title: 2R9: Abx-20_d0_L1

value: monocytes and dendritic cells


title: 1R9: Abx-20_d30_L1


title: 520DD_mESC_24_IP_28_3

value: 72 % Mettl3 KO, 28% WT


title: Batch1_IP_5828__A_Rpb3_Ndt80

description: degradation-induced, Rpb3

source_name: yeast strain, degradation-induced, Rpb3


title: 520DD_mESC_24_IP_28_2


title: input MNase REH WT


title: 5R8: Abx-15_d0_L1


title: Batch1_IP_4911_C_Ndt80

description: non-induced


title: 520DD_mESC_24_IP_28_1


title: Batch1_IP_4911_A_Ndt80

description: degradation-induced

source_name: yeast strain, degradation-induced


title: Batch1_Input_6060_C_Ime4_Ndt80

description: non-induced, Ime4

source_name: yeast strain, non-induced, Ime4


title: 4R8: Abx-15_d1_L1


title: 520DD_mESC_24_IP_14_3

value: 86 % Mettl3 KO, 14% WT


title: 520DD_mESC_24_IP_14_2


title: Batch1_Input_5964_C_Xrn1_Ndt80

description: non-induced, Xrn1


title: 1R8: Abx-15_d30_L1


title: 520DD_mESC_24_IP_42_2


title: 520DD_mESC_24_IP_14_1


title: 5R: Abx-02_d0_L1


title: input MNase REH FASTKD1 ko1

value: REH


title: Batch1_Input_5964_A_Xrn1_Ndt80

description: degradation-induced, Xrn1


title: 520DD_mESC_24_IP_100_3

value: 0 % Mettl3 KO, 100% WT


title: Batch1_Input_5956_C_Pop2_Ndt80

description: non-induced, Pop2


title: 9A: vax010_063_d42_L8

data_processing:
CellRanger-ATAC (v1.1.0) count functionality was used for alignment, deduplication, demultiplexing, and identification of cut sites. All lanes related to each sample were analyzed jointly.
CellRanger-ATAC (v1.1.0)'s aggr function was then used to aggregate samples without depth normalization (--normalize=none)
The resulting fragment file was read into SnapATAC (v1.0). Cells were called as barcodes with at least 1000 UMIs and a promotor ratio (defined as: (fragments in promoter regions + 1) / (total fragments + 1)) of at least 0.1. Reads were mapped into 5kb bins to create a bin-by-cell matrix.
SnapATAC was then used to identify clusters from the cell-by-bin matrix, then peaks were called (MACS2 v2.2.7.1) separately for each cluster and joined for a joined set of peaks.
Fragments were mapped to the joined set of peaks for each cell barcode to create the peak-by-cell matrix.
deeply-sequenced libraries were downsampled to an average of 1500 fragments per barcode by randomly removing counts from these samples at a probability p=1500/(mean fragments per cell in the sample)
Genome_build: hg38
Supplementary_files_format_and_content: TIV_scATAC_counts.mtx.gz: raw count matrix
Supplementary_files_format_and_content: TIV_scATAC_meta.tsv: tab-seperated cell annotations
Supplementary_files_format_and_content: TIV_scATAC_peaks.bed: peaks in bed format

tag: vaccine group


title: 3R: Abx-02_d1_L1


title: 520DD_mESC_24_IP_100_2

data_processing:
Library strategy: m6Aseq2
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9


title: Dacarbazine Malme 3 MvsNano-Control Malme 3M

type: RNA

city: Boston

first: Jean-Bosco

last: Tagne

state: MA

address: 72 East Concord

department: Medicine/Pulmonary

institute: Boston University

hyb_protocol: standard protocol

scan_protocol: Micoarrays were scanned on axon scanner to detect Cy3 and Cy5 fluorescence. Gridding and analysis of images is performed with genepix

data_processing: Background substracted and Lowess normalized data. Normalized log2 ratios (Numerator is Cy5 and Denominator is Cy3)

source_name: Breast Cancer HTB-20/Skin Cancers Malme and CRL

label_protocol: First strand cDNA was generated by oligo-dT primed reverse transcription (Superscript II) and labeled with Cy3 or Cy5 dyes

growth_protocol: Primary non-metastatic and metastatic tumor HTB-20 breast ductal carcinoma cells were cultured in Hybricare Culture Medium 46-X preparation supplemented with 19.98 ml of sodium bicarbonate solution [7.5% w/v] as indicated by the manufacturer’s instructions, supplemented with 10% fetal calf serum, 100 Units penicillin, and 100 μg streptomycin per ml and 1 mM sodium pyruvate, cultured at 37°C in 5% CO2 incubator after subculture steps as indicated by the manufacturer GlutaMAX -1 (1X) (Gibco for Life Technologies REF: 61870-036).

extract_protocol: Total mRNA was extracted from various human cancer cells by using an RNA isolation kit (Invitrogen, Inc. San Diego, CA, USA), which utilizes a modification of the method of Chomczynski and Sacchi(21), for rapid isolation of total RNA from tissue culture cells by using Phenol and Guanidine Thiocyanate.

treatment_protocol: The cells were grown in culture medium to reach 40-50% confluency before treatment with 10 µl of 50 nM Nano-miR-200c, miR-200c, empty Nano Control (same composition as the suspension or vehicle with no miRs), antago-miR or control untreated plates before harvesting after 48 hours to study the effect of our treatment.

tag: cell type/treatment

value: Dacarbazine Malme 3 M

value: Nano-Control Malme 3M


title: Batch1_Input_5956_A_Pop2_Ndt80

description: degradation-induced, Pop2


title: 520DD_mESC_24_IP_100_1


title: Nano-Dacarbazine Malme 3MvsControl Malme 3 M

value: Nano-Dacarbazine Malme 3M

value: Control Malme 3 M


title: Nano-Dacarbazine CRL-1555vsNano-Control Malme 3M

value: Nano-Dacarbazine CRL-1555


title: 520DD_mESC_24_IP_0_3

value: 100 % Mettl3 KO, 0% WT

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: Batch1_Input_5880_A_Rrp6_Ndt80

description: degradation-induced, Rrp6


title: Nano-Control CRL-1555vsNano-Control Malme 3M

value: Nano-Control CRL-1555


title: Control Malme 3 MvsDacarbazine Malme 3 M


title: 9A: vax010_063_d42_L5


title: Control Malme 3 MvsNano-Control Malme 3M


title: 9A: vax010_063_d42_L4


title: 9A: vax010_063_d42_L7


title: Nano-Control Malme 3MvsNano-Dacarbazine Malme 3M


title: Batch1_Input_5828_C_Rpb3_Ndt80

description: non-induced, Rpb3


title: 9A: vax010_063_d42_L3


title: 520DD_mESC_24_Input_85_3

value: 15 % Mettl3 KO, 85% WT


title: Batch1_Input_5828__A_Rpb3_Ndt80

description: degradation-induced, Rpb3


title: Nano-Tam HTB-20vsControl HTB-20

value: Nano-Tam HTB-20

value: Control HTB-20


title: 9A: vax010_063_d42_L2


title: 9A: vax010_063_d42_L6


title: Nano-Control HTB-20vsNano-Tam HTB-20

value: Nano-Control HTB-20


title: Batch1_Input_4911_A_Ndt80

description: degradation-induced


title: Control HTB-20vsTam HTB-20

value: Tam HTB-20


title: 9A: vax010_063_d42_L1

value: monocytes and dendritic cells


title: Control HTB-20vsNano-Control HTB-20


title: 520DD_mESC_24_Input_85_1


title: Tech_m6A_Rep12_IP

source_name: yeast strain

growth_protocol: Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit and subsequent 2-time polyA-selection according to manufacturers protocol. m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)


title: 520DD_mESC_24_Input_85_2


title: Batch1_Input_5880_C_Rrp6_Ndt80

description: non-induced, Rrp6


title: 11A: vax010_062_d42_L8


title: 520DD_mESC_24_IP_0_2


title: 520DD_mESC_24_Input_71_3

value: 29 % Mettl3 KO, 71% WT


title: Tech_m6A_Rep11_IP


title: Tech_m6A_Rep12_Input


title: 11A: vax010_062_d42_L7


title: Batch1_Input_4911_C_Ndt80

description: non-induced

source_name: yeast strain, non-induced


title: 520DD_mESC_24_Input_71_1


title: 520DD_mESC_24_Input_71_2


title: Tam HTB-20vsNano-Tam HTB-20


title: 11A: vax010_062_d42_L5


title: 11A: vax010_062_d42_L6


title: 520DD_mESC_24_Input_57_3

value: 43 % Mettl3 KO, 57% WT


title: Tech_m6A_Rep10_IP


title: Tech_m6A_Rep10_Input


title: 520DD_mESC_24_Input_57_2


title: 11A: vax010_062_d42_L4


title: 11A: vax010_062_d42_L3


title: BMSC_T7_TET1_CHIP

city: Taichung City

first: Chun-Te

last: Ho

address: 7F, No. 6, Xueshi Rd., North Dist.

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

data_processing:
Illumina RTA v1.17.21.3 software used for basecalling, and CASAVA V1.8.2 software used for demultiplex and data converstion
Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 75bp, or have one or more ambiguous base.
The alignment, quantiﬁcation, normalization, and differential expression analysis were performed by STAR 2.5.3a49 through Partek Flow (Partek Inc., St. Louis, MO, USA), htseq-count 0.6.050, TMM51, and edgeR 3.18.152, respectively.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include overlapping features for each Sample

source_name: bone marrow-derived mesenchymal stem cell

growth_protocol: The isolation of human BMSCs has been described previously which was originally derived from the iliac crest of donors (Tsai et al. 2011). Briefly, mononuclear cells were isolated from heparinized bone marrow by density gradient centrifugation using Ficoll-Hypaque of a density of 1.077 g/L, followed by seeding into 6-well plate with complete medium [CM: low glucose DMEM (Gibco, Grand Island, NY), supplemented with 10 % fetal bovine serum (FBS; Gibco), 100 units/mL penicillin G, 100 μg/mL streptomycin sulfate and 25 μg/mL amphotericin B (Antibiotic Antimycotic Solution, Sigma-Aldrich, St. Louis, MO)] at 37°C under 5% CO2 atmosphere. At 9 days after seeding, BMSCs were recovered and reseeded in 10-cm plastic dishes at an initial density of 4×10^3 cells/cm^2 and the culture medium was changed twice per week. The medium was changed twice a week and a subculture is performed at 1:3 to 1:5 split every week.

extract_protocol: Aliquots of purified genomic DNA from each situation of MSCs were first sonicated to ∼250 bp using Bioruptor (Diagenode, Seraing, Belgium), then end-repaired and ligated to Illumina PE adaptors using NEB Next DNA Library Prep Master Mix Set (New England Biolabs, Beverly, MA, USA). In DIP assays, 10 μg of the adaptor-ligated genomic DNA was used as input, and 5 μl of anti-5-methylcytosine antibody、anti-TET1 or anti-PARP1 antibodies was added to immunoprecipitate modified DNA. Each of the immunoprecipitated DNA was amplified with forward primer and reverse primers in a 50 μl PCR reaction with 0.2× Sybr-Green I and 1× Phusion High-fidelity PCR Master Mix (New England Biolabs, Beverly, MA, USA). PCR products that contain barcodes were sequenced after the standard first read using N2IndSeq primer. After base-calling, each sequence was decoded using an in-house Perl script which required at least five out of six matching positions in the barcode sequence. All sequencing reads were trimmed from 5’ end to obtain final 37 bases in length for further analysis.

tag: donor

tag: cell type


title: BMSC_T7_PARP1_CHIP

value: bone marrow-derived mesenchymal stem cell


title: 520DD_mESC_24_Input_57_1

tag: background

tag: antibody


title: Tech_m6A_Rep9_IP

extract_protocol:
Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit (Lucigen, MPY03100).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)


title: 11A: vax010_062_d42_L2


title: BMSC_T7L_IP_MC

value: bone marrow-derived mesenchymal stem cell [Late passage (10~13)]


title: BJ4 KO_BI1 WT Replicate 4

city: Taipei

first: Meng-Chun

middle: Monica

last: Shih

address: Building G, No. 99, Lane 130, Section 1, Academia Road, Nangang District

institute: NLAC

description: Biological replicate 1 of 4

hyb_protocol: Agilent Gene Expression Hybridization Kits and wash kit were  used for hybridization according to the manufacturer’s instruction.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the AgilentG3_GX_2 Color scan protocol for 4x44K high densitiy Micorarray Formats (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red and Green PMT is set to 100%, the resulting file is a 20 bit tiff image).

data_processing:
Agilent Feature Extraction Software (v 10.5.1.1) was used to quanitify the image intensity , background subtraction and LOWESS normalization.
Normalized log2 ratio (Alexa Fluor 647/Alexa Fluor 555) representing infected sample/mock control using Gene spring GX

label: Alexa 647 (red)

source_name: E18.5 knockout pancreas

label_protocol: 20 µg of total RNA were primed with  anchored Oligo-(dT) at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen).  After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min to hydrolysis RNA followed by neutralization with addition of 25μL 1M HEPES pH 7.4. Then purified using QIAquick(Qaigen) kit, aa-cDNA was eluted from column with 60 μl 0.1M NaHCO3 pH 9.0.  The elute was added into a tube containing  Alexa 555 or Alexa 647 NHS ester. Coupled the dye at room temperature in the dark for 60-90 min.  The reaction was stopped by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Labeled cDNA was purified through QIAquick column.

extract_protocol: Total RNA was extracted using the RNeasy® kit from QIAGEN.

value: Pancreas

value: knockout

tag: development stage

label: Alexa 555 (green)

source_name: E18.5 wildtype pancreas

value: wildtype


title: 520DD_mESC_24_Input_42_3

source_name: mus musculus

extract_protocol:
For mESCs cells, total RNA was extracted using Nucleozol (Macherey-Nagel, 740404.200).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)

value: 58 % Mettl3 KO, 42% WT


title: Tech_m6A_Rep9_Input


title: 520DD_mESC_24_Input_42_2


title: Tech_m6A_Rep11_Input


title: BMSC_T8_TET1KD

data_processing:
Illumina RTA v1.17.21.3 software used for basecalling, and CASAVA V1.8.2 software used for demultiplex and data converstion
Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 75bp, or have one or more ambiguous base.
The alignment, quantiﬁcation, normalization, and differential expression analysis were performed by STAR 2.5.3a49 through Partek Flow (Partek Inc., St. Louis, MO, USA), htseq-count 0.6.050, TMM51, and edgeR 3.18.152, respectively.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of 13326 genes for each Sample

extract_protocol:
Total RNA was isolated with the GeneAll Hybrid-R RNA purification kit
RNA libraries were prepared for sequencing using Illumina TruSeq RNA sample Prep kit


title: Tech_m6A_Rep8_IP


title: BB5 KO_BG5 WT Replicate 2

description: Biological replicate 1 of 4


title: BF1 KO_BF6 WT Replicate 3

description: Biological replicate 1 of 4


title: 520DD_mESC_24_Input_42_1


title: BB2 KO_BF4 WT Replicate 1

description: Biological replicate 1 of 4


title: 4A: vax010_061_d42_L8


title: Tech_m6A_Rep8_Input


title: BMSC_T7E_IP_MC

value: bone marrow-derived mesenchymal stem cell [Early passage (1~4)]


title: 520DD_mESC_24_Input_28_3

value: 72 % Mettl3 KO, 28% WT


title: 520DD_mESC_24_IP_0_1

value: 100 % Mettl3 KO, 0% WT

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: BMSC_T8_PARP1KD


title: BMSC_T8L


title: BMSC_T7E_INPUT


title: 4A: vax010_061_d42_L6


title: 520DD_mESC_24_Input_28_2


title: BMSC_T8E


title: 520DD_mESC_24_Input_28_1


title: 4A: vax010_061_d42_L5


title: 11A: vax010_062_d42_L1


title: Tech_m6A_Rep7_Input


title: Tech_m6A_Rep6_IP


title: BMSC_T7_TET1KD


title: 4A: vax010_061_d42_L4


title: Tech_m6A_Rep6_Input


title: 4A: vax010_061_d42_L3


title: BMSC_T7_PARP1KD


title: 520DD_mESC_24_Input_14_3

value: 86 % Mettl3 KO, 14% WT


title: 520DD_mESC_24_Input_14_2


title: Tech_m6A_Rep5_IP


title: Tech_m6A_Rep7_IP


title: 520DD_mESC_24_Input_14_1


title: 4A: vax010_061_d42_L1


title: 4A: vax010_061_d42_L2


title: BMSC_T7E


title: 5A: vax010_012_d42_L8


title: Tech_m6A_Rep4_IP


title: 520DD_mESC_24_Input_100_2

value: 0 % Mettl3 KO, 100% WT


title: P27_metaplastic tumor

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

data_processing:
We verified the quality of sequence reads using FastQC.
We aligned the reads to the human transcriptome using the hg19 assembly and a GTF of RefSeq genes.
We estimated the transcripts per million using RSEM with the STAR aligner.
Estimated expression values were used for post-analysis and visualization using custom software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of gene expression transcripts per million for RefSeq protein coding transcriptome

source_name: treatment-naïve metaplastic tumor

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from tumors, treated with Dnase I, and depleted of cytoplasmic and mitochondrial ribosomal RNA using Ribo-Zero Gold.
TruSeq Stranded Total RNA

tag: subject status

value: triple-negative breast cancer patient

value: treatment-naive triple negative breast cancer tumor

tag: is metaplastic

value: Y

tag: subtype

value: IM

tag: response

value: RCB - II


title: Tech_m6A_Rep4_Input


title: 5A: vax010_012_d42_L7

tag: subject

tag: time point

tag: experiment

tag: lane

value: monocytes and dendritic cells


title: P28_non-metaplastic tumor

source_name: treatment-naïve non-metaplastic tumor

tag: tissue

value: N

value: RCB - III


title: 520DD_mESC_24_Input_100_1


title: P26_non-metaplastic tumor

value: LAR


title: Tech_m6A_Rep3_IP


title: 520DD_mESC_24_Input_0_3


title: Tech_m6A_Rep3_Input


title: P25_metaplastic tumor

value: MSL


title: 520DD_mESC_24_Input_0_2


title: Tech_m6A_Rep2_IP


title: 5A: vax010_012_d42_L4

source_name: monocytes and dendritic cells


title: 520DD_mESC_24_Input_0_1


title: Tech_m6A_Rep5_Input


title: Tech_m6A_Rep2_Input


title: P24_non-metaplastic tumor

value: RCB - I


title: 520DD_mESC_24_Input_100_3


title: 519MEF_m6Aseq_techRepl_5_IP

value: WT


title: P22_metaplastic tumor

value: M


title: 519MEF_m6Aseq_techRepl_5_Input

growth_protocol: MEFs cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Biological industries, 01-052-1A) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For mEF cells, total RNA was extracted using Nucleozol (Macherey-Nagel, 740404.200).
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)


title: 5A: vax010_012_d42_L2


title: Tech_m6A_Rep1_Input


title: 5A: vax010_012_d42_L1


title: P21_non-metaplastic tumor


title: 5A: vax010_012_d42_L3


title: Tech_m6A_Rep1_IP


title: 4A: vax010_061_d42_L7


title: P20_non-metaplastic tumor


title: 10A: vax010_063_d21_L8


title: 5A: vax010_012_d42_L5


title: 519MEF_m6Aseq_techRepl_4_input


title: SingleRepC_m6A_Input

data_processing:
Library strategy: m6Aseq
alignment using STAR (V. 2.5.3a)
bam2ReadEnds.R (Garcia-Campos et al. 2019) paired-end alignment to the transcriptome (SK1, mm9 gene annotation)
Genome_build: SK1, NCBI37/mm9

extract_protocol:
Yeast total RNA samples were prepared by MasterPure Yeast RNA extraction kit (Lucigen, MPY03100).
m6A-seq: Fragmentation, 3' adapter ligation, m6A-IP, cDNA synthesis, second adapter ligation and enrichment


title: 519MEF_m6Aseq_techRepl_4_IP


title: BMSC_T7L

value: bone marrow-derived mesenchymal stem cell [Late passage (10~13)]


title: 10A: vax010_063_d21_L6


title: 10A: vax010_063_d21_L7


title: 519MEF_m6Aseq_techRepl_3_IP

value: Synaptic Systems (Cat# 202003; RRID:AB_2279214)


title: 5A: vax010_012_d42_L6


title: SingleRepB_m6A_IP


title: P18_metaplastic tumor


title: SingleRepB_m6A_Input


title: 519MEF_m6Aseq_techRepl_3_Input


title: P19_non-metaplastic tumor