title: LP_aZbtb1_ChIP_rep2

value: anti-Zbtb1 Abs (a mixture of 2.5 ug of S303-242A (Bethyl) and 2.5 ug of ab79456 (Abcam))


title: 25, S-methoprene, rep3

status: Public on Sep 10 2022

type: SRA

city: Providence

first: Corinne

last: Hutfilz

state: Rhode Island

address: 171 Meeting St.

country: USA

institute: Brown University

description: virgin female adult dissected fat body. 25 days old.

library_source: genomic

data_processing:
FastQC data assessment
Adapter trimming via Trimgalore! and Cutadapt
Alignment to dm6 reference genome using Bowtie2 (--no-discordant and a maximum fragment length of 1000 bp)
Mitochondrial read removal via Shell and Samtools
Conversion to .bam via Samtools
Removal of optical duplicates via Picard tools and Samtools
Peaks called using MACS2 (min.FDR cutoff 0.05 and parameters --nomodel, --shift -100, --extsize 200, --keep-dup-all and –call-summits)
Blacklisted regions removed via Bedtools intersect
Differential accessibility analyzed via DiffBind
Assembly: dm6
Supplementary files format and content: comma-separated values (.csv). Data represent the set of loci that become accessible or inaccessible in response to temperature, but not S-methoprene or juvenile hormone status.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: All flies were reared at 25C on agar-based standard diet. Virgins were collected and divided into the appropriate conditions within 8 hours post-eclosion. Flies remained in those conditions for 25 days, at which time flies were sacrificed and dissected for fat body tissue.

extract_protocol:
Fat body was harvested by dissection using 25 flies per replicate, using only those flies whose ovaries displayed the proper response to S-methoprene supplementation or temperature effect. Flies with either S-methoprene or at 25C had large, viable ovaries, whereas flies at 11C with ethanol displayed the regressed ovarian morphology characteristic of diapause.
Nuclear extraction and library preparation protocols were adapted from Cources et al., 2017 and Davie et al., 2015 using the omni-ATAC adaptation. The NEBNext™ Illumina library quantification kit from New England Biosciences was used to measure final library concentration (Ref # E7630S, lot 10013445). The Nextera™ DNA library prep kit from Illumina (Ref # 15028212, lot 20256848) was used to tagment DNA, ligate adapter sequences and amplify fragments. Adapter sequences used are available (Supplemental table X). The quality of ATAC-seq libraries was assessed via Bioanalyzer (Agilent) prior to sequencing.

treatment_protocol: Flies were supplemented with 10 uL of 99% ethanol once every 2 days, or supplemented with 10 uL 39.4 mm S-methoprene diluted in 99% ethanol every 2 days. Treatment was administered via volatilization.

tag: tissue

value: Fat body

tag: genotype

tag: treatment


title: BCOR P0 rep2

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description: Bamcoverage .bigwig file/MACS2 peak calling .bed file

data_processing:
Library strategy: CUT&RUN
RNA-Seq: Fastq reads were pre-processed using “FastQGroomer” and “Trimmomatic” algorithms (Bolger et al. 2014), then mapped against the mm10 genome using “Tophat” (Kim etal. 2013). Gene counts were generated using “htseq-count” followed by “DeSeq2” (Anders et al. 2015 ; Love et al. 2014). R-studio was used to annotate and merge data. Heatmaps were generated using Morpheus program (https://software.broadinstitute.org/morpheus/) with k-means clustering. Gene Ontology (GO) analysis (allowing to detect which terms are under- or over- represented using annotations within a specific genes set) was ran using David 6.8 tool (Huang da et al. 2009).
CUT&RUN: Fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using default parameters. Bamcoverage was used to generate bigwig files.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: Raw ht-seq counts in tabular format and excel spreadsheet results of DESeq2 analysis of RNA-seq data generated from retinal cells with BCOR knockdown
Supplementary_files_format_and_content: Bigwig tracks files and MACS2 peaks bed files for scored peaks in CUT&RUN

organism: Mus musculus

source_name: Retina

growth_protocol: In vivo electroporation of P0 eyes was performed as described previously (de Melo et al. 2011) using plasmid DNA at 1ug/ul (pSilencer-shBcor or empty vector pSilencer-CAG-Venus as control).

extract_protocol:
RNA-seq: RNA extraction was performed as detailed by manufactorer (RNeasy mini kit, Qiagen).
CUT&RUN: Genomic DNA extraction was performed as per manufactorers guidelines (QIAquick Nucleotide Removal Kit).
RNA-seq: Samples quantity (RNA Integrity Number = RIN) and quality were assessed using the Agilent RNA 6000 Pico Kit (Agilent #5067-1513) on the Bioanalyzer 2100. Libraries preparation started with rRNA depletion using the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324). 3.0 ng to 5.1 ng of total RNA were used for rRNA depletion of the total RNA. Speed-vac sublimation was performed on some samples to reduce RNA volume to 17ul in order to start the depletion reaction. rRNA depleted RNA were then purified with AGENCOURT® RNA CLEAN® XP Kit (Beckman Coulter). The samples were eluted in 8.5ul of H2O to continue the library preparation using SMARTer® Stranded RNA-Seq Kit (Takara Bio USA, Inc. #634836 or #634837).
CUT&RUN: Libraries were prepared with the KAPA DNA HyperPrep Kit (Roche 07962363001 - KK8504). This protocol includes an End-Repair/A-tailing step and an adapter ligation step followed by a PCR amplification (enrichment) of ligated fragments.
RNA-seq: The 1st strand synthesis was performed using a modified N6 primer (the SMART Stranded N6 Primer) in order to obtain full length fragments. The full-length, single-stranded (ss) cDNA fragments were purified with Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). PCR Enrichment + indexing step of 15 cycles was then performed using the Illumina Indexing Primer Set provided by the kit. The final enriched product (library, after PCR) was purified using Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). Libraries were eluted in 16 ml of elution buffer. Quality and quantification of the libraries were assessed using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626) on the Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted and pooled equimolar prior to paired-end sequencing performed with 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System.
CUT&RUN: The adapters used for ligation were IDT for Illumina TruSeq UD Indexes (Illumina - 20022371). The final enriched product (library, after PCR) was purified using KAPA purification beads (Roche 07983298001 - KK8002) and a dual-SPRI size selection was performed (with KAPA beads) to select fragments between 180-500 bp. Libraries were then quantified using a Nanodrop microvolume spectrophotometer (ng/l) and quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent -5067-4626) on a Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted, pooled equimolar and sequenced in pair end 50 cycles (PE50) on a S1 flowcell (Illumina - 20012863) of the Illumina NovaSeq 6000 System.

treatment_protocol: The electroporated eyes were collected at post-natal day 21 and processed for dissection, dissociation and FACS sorting. Dissociation was done with StemPro Accutase (Thermo Fisher) for 30 minutes instead of papain and cells were treated with propidium iodide (PI) solution prior to sorting. 10 to 15% of cells were excluded due to cell death. Multiple sorted GFP+ cells samples were combined to obtain 30 000 - 70 000 cells per replicate (n=2)

tag: cell type

value: Retinal cells

tag: mouse line

value: WT

tag: strain

tag: age

tag: condition

value: BCOR


title: BC.50291 PDX P0 passage tumor sample

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

library_source: transcriptomic single cell

data_processing:
Alignment with STARv2.5.3 to GRCh38 or with bowtie2 to Hg19 and mm10 for PDX samples, as indicated below
Gene-level raw counts summarization with STARv2.5.3 quant-mode. In the case of PDX samples, xenomapper tool was to generate counts from reads selectively mapping to human transcriptome and not mouse.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and viper analysis as described in manuscript.
Assembly: GRCh38.v90 or as indicated below.
Supplementary files format and content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for VIPER analysis of differential protein activity for perturbation or pharmacodynamic samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: PDX tumor sample, RNASeq

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500 or NovaSeq 6000 sequencer, as indicated below for each file.

treatment_protocol: Drug perturbations profiles in cell lines were done at 24 hours, and in some cell lines also at 6 hours (short time point) after introducing drug, as indicated by appropriate column names in the sample plate maps and processed data files

value: PDX tumor sample, RNASeq

value: PDX of breast cancer


title: BCOR P0 rep1


title: LP_aZbtb1_ChIP_rep1

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai Univ

data_processing:
ChIP-seq; Sequencing data were mapped to the mouse genome build NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
QuantSeq; Adaptor sequences were trimmed from the raw RNA-seq reads with fastp. Trimmed reads of each sample were mapped to the reference mouse genome mm10 by using STAR and normalized to 1 million reads in the original library. Genes with an average of 10 or more reads in either group were subjected for further analysis.  Differentially Expressed Genes (DEGs) were defined with P < 0.05, |log2FC| > 1, and TPM > 10 based on measurements from three biologically independent replicates for each sample type.
Assembly: mm10
Supplementary files format and content: Processed files include BED-files  All genomic coordinates are relative to mm10 mouse assembly.

source_name: LP cells

growth_protocol: A LP cell line was cultured on OP9 monolayers using OP9 medium (α-MEM, 10% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of SCF (Pepro Tech Inc), 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  Every 2-3 days, cultured cells were disaggregated, filtered through 40-um nylon mesh, and re-cultured on new OP9 monolayers with medium containing cytokines above.

extract_protocol: Ten million of LP cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by an additional 10 min with addition of formaldehyde up to 1 %.  The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with HBSS (Gibco).  Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec. sonication followed by 30 sec. rest, with high power.  Five ug of anti-Zbtb1 Abs (a mixture of 2.5 ug of S303-242A (Bethyl) and 2.5 ug of ab79455 (Abcam)) or anti-Cbfa2t3 (a mixture of 2.5 ug of 17190-1-AP (Proteintech) and 2.5 ug of sc-373691 (Santa Cruz)) were pre-bound to Dynabeads anti-Rabbit Ig or Protein A/G (Invitrogen) and then added to the diluted chromatin complexes.  The samples were incubated overnight at 4 °C, then washed and eluted for 6 h at 65 °C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 50 mM NaCl, 1 % SDS, and 50 ug/ml proteinase K).  Precipitated chromatin fragments were cleaned up using ChIP DNA Clean & Concentrator (Zymo).  ChIP-seq libraries were constructed using NEBNext Ultra II DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB), and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

tag: cell line

value: LP

value: Cultured on OP9

tag: chip (antibody)

tag: sgrna


title: 25, S-methoprene, rep1


title: BC.50291 patient tumor sample

source_name: Patient tumor sample, breast recurrence from breast cancer, RNASeq

value: breast cancer


title: Otx2 E14


title: NF1 OPG

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

library_source: transcriptomic

data_processing:
Single-cell barcoding, cDNA amplification and Gene Expression Library Construction were performed using Chromium Single Cell 3ʹ Reagent Kits v3
10x Genomics® was used for sequencing
sequencing data were analyzed in Partek Flow using CPM normalization and graphbased clustering using the Louvain clustering algorithm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM normalized values for each Sample

molecule: total RNA

source_name: optic nerve

growth_protocol: Nf1OPG mice spontaneously generate LGG in their optic nerves

extract_protocol:
Mice were perfused with PBS and optic nerves were harvested. A single cell suspension was prepared using adult brain dissociation kit (Miltenyi Biotec 130-107-677)
using Chromium Single Cell 3ʹ Reagent Kits v3

treatment_protocol: LGGs are fully formed a 12 weeks of age

value: 12 weeks


title: 25, EtOH, rep1


title: PAC.05647 patient tumor sample

source_name: Patient tumor sample, liver metastasis from pancreatic cancer, RNASeq

value: pancreatic cancer


title: Wild type Pol2Ser5 hair matrix P4.5

status: Public on Sep 09 2022

city: BOSTON

first: Guodong

last: Chen

state: MA

address: 609 Albany Street, ROOM 414

department: Dermatology

institute: Boston University

description: Primary keratinocytes

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed by using trim-galore with default paramaters.
Trimmed eads were aligned to the GRCm38 genome using Bowtie. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using bamCoverage in deeptools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

source_name: Hair matrix keratinocytes

extract_protocol:
Native cells were isolated from mice skin with FACS. Only living cells were used for CUT&Tag following the manual of CUTANA™ CUT&Tag kit.
DNA libraries are amplified for 18-21 cycles with 25 μl of NEBNext® High-Fidelity 2x PCR Master Mix (NEB, #M0541) and 2.5 μl of unique i5 and i7 index primers for Illumina.

value: Hair matrix keratinocytes

tag: chip antibody

value: Pol2Ser5 (Abcam, #ab5408)

value: Wild type


title: BCOR E14


title: Wild type Pol2Ser5 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: Wild type Lef1 hair matrix P4.5

description: Primary keratinocytes

value: Lef1 (Cell Signaling, #2230)


title: Wild type Lef1 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: Wild type H3K4me3 hair matrix P4.5

description: Primary keratinocytes


title: Wild type IgG hair matrix P4.5

description: Primary keratinocytes


title: Retina 1 Cut&Run IgG

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Healthy female retina, age 75

data_processing:
library strategy: Cut&Run
Cut&Run datasets have been processed by trimming the adaptors using cutadapt (Martin, 2011)
Read were mapping locally with bowtie2 (Langmead & Salzberg, 2012) allowing dovetail on a chimeric genome (Human hg38, S. cerevisiae S288C; E. coli ASM584v2), no internal normalization has been performed in these datasets since the proportion of read mapping on the yeast or on the bacterial genome was too low.
Read mapping on the human genome have been then extracted, filtered for quality, duplicates, and blacklisted regions (ENCODE dataset ENCFF419RSJ) using samtools (Li et al., 2009).
Quality of the experiment have been visualized on IGV (Robinson et al., 2017) after conversion to bigwig using deepTools (Ramierz et al., 2014).
The chromatin annotation used for this project is an integration of public and lab produced chromatin histone marks (H3K27Ac, H3K4me2, H3K4me3, H3K9me3) and our best dataset of chromatin accessibility.
This integration has been performed by transforming the read coverage to 500bp signal and by computing chromatin states using ChromHMM tool (Ernst & Kellis, 2017).
Models defining between 5 and 20 chromatin states were tested. For each model, we calculated the mean correlation between each chromatin state and the most similar chromatin state in each model with additional states.
After 10 chromatin states, this correlation plateaued indicating that identify additional chromatin states provides minimal information.
For each state of the 10-states model, the average coverage for the chromatin marks and accessibility are computed using HOMER (Heinz et al., 2013; Heinz et al., 2018) and the chromatin signatures for each segment are used to manually infer a biological annotation of each state.
The average distributions of each state around the expressed and non-expressed genes are computed as a quality control using HOMER using our previously published list of expressed genes in human retina (Ratnapriya et al., 2019) and all the other genes from HOMER TSS list as non-expressed genes.
The segments of the chromatin states enriched for active histone marks identified by ChromHMM have been merged to generate a set of regions called here CREs.
This list of CREs has been integrated with the H3K27Ac ChIP-seq coverage and the corresponding input coverage to identify SE using the ROSE algorithm (Whyte et al., 2013; Love et al., 2013).
Assembly: hg38
Supplementary files format and content: Read coverage in bigwig format for each sample
Supplementary files format and content: Consensus super-enhancers called from Cut&Run, ChIP-seq, and ATAC-seq data in bed format

source_name: Adult Retina

extract_protocol:
Peripheral retina samples were dissociated using papain as previously described (Fadl et al., 2020), cryopreserved in HBSS solution containing 10% DMSO and slowly frozen using a Mr. Frosty container (Invitrogen, CA, USA). CUT&RUN was performed as previously described (Skene & Henikoff, 2017) using 200-300,000 cells per experiment. Antibodies against H3K9me3 (Rabbit, cat.no. ab8898, Abcam, Cambridge, UK), H3K4me3 (Rabbit, cat.no. ab8580, Abcam, Cambridge, UK) and control IgG (Rabbit, cat.no. 011-000-002, Jackson ImmunoResearch Laboratories, PA, USA) were used at a concentration of 1:100 in 100ul and pA-MNase conjugated to protein A (generous gift of Dr. Steven Henikoff, Howard Hughes Medical Institute, WA, USA) was used at a concentration of 700 ng/ml. Released DNA fragments were purified using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany).
Libraries were prepared with SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA, Inc, CA, USA) and amplified with 15 PCR cycles (60°C extension). Pair-end sequencing was performed with read length of 50 base pairs using the HiSeq 2500 platform (Illumina, CA, USA).

value: Adult Retina

tag: gender

value: female

tag: subject status

value: healthy


title: Wild type Dlx3 hair matrix P4.5

description: Primary keratinocytes

value: Dlx3 (Abcam, #ab66390)


title: Wild type H3K27ac hair matrix P4.5

description: Primary keratinocytes

value: H3K27ac (Abcam, #ab4729)


title: Wild type H3K4me1 hair matrix P4.5

description: Primary keratinocytes

value: H3K4me1 (Diagenode, #C1541094)


title: Retina 1 Cut&Run H3K9me3

description: Healthy female retina, age 75


title: Wild type H3K27me3 hair matrix P4.5

description: Primary keratinocytes


title: Retina 1 Cut&Run H3K4me3

description: Healthy female retina, age 75


title: Retina 4 ATAC-seq

data_processing:
ATAC-seq from five human retinas have been analyzed by trimming the reads for Nextera transposase sequence and reducing their size to maximum 25bp using cutadapt (Martin, 2011) and FASTX toolkit (FASTX-Toolkit, RRID:SCR_005534).
Trimmed reads have been mapped on hg38 using bowtie2 (Langmead & Salzberg, 2012) and filtered for quality, duplicates and blacklisted regions (ENCODE dataset ENCFF419RSJ) using samtools (Li et al., 2009).
Two sets of aligned read pairs have been produced: TN5-shifted and non-shifted, to use with general tools (TN5-shifted) or specialized tools already including a TN5 shifting step (non-shifted).
Quality controls have been performed on the aligned read pairs by computing the normalized enrichment at TSS using HOMER (Heinz et al., 2013; Heinz et al., 2018), and by computing the fragment size.
Retina NDRI005 has been chosen as the best dataset from this QC and has been used as input for ChromHMM (Ernst & Kellis, 2017) annotation.
Models defining between 5 and 20 chromatin states were tested. For each model, we calculated the mean correlation between each chromatin state and the most similar chromatin state in each model with additional states.
After 10 chromatin states, this correlation plateaued indicating that identify additional chromatin states provides minimal information.
For each state of the 10-states model, the average coverage for the chromatin marks and accessibility are computed using HOMER (Heinz et al., 2013; Heinz et al., 2018) and the chromatin signatures for each segment are used to manually infer a biological annotation of each state.
The average distributions of each state around the expressed and non-expressed genes are computed as a quality control using HOMER using our previously published list of expressed genes in human retina (Ratnapriya et al., 2019) and all the other genes from HOMER TSS list as non-expressed genes.
The segments of the chromatin states enriched for active histone marks identified by ChromHMM have been merged to generate a set of regions called here CREs.
This list of CREs has been integrated with the H3K27Ac ChIP-seq coverage and the corresponding input coverage to identify SE using the ROSE algorithm (Whyte et al., 2013; Love et al., 2013).
Assembly: hg38
Supplementary files format and content: Read coverage with TN5 shift per sample in bigwig format.
Supplementary files format and content: Accessible peaks per sample without TN5 shift in narrowPeak format
Supplementary files format and content: Consensus accessible footprints observed in at least 3 samples in bed format
Supplementary files format and content: Consensus super-enhancers called from Cut&Run, ChIP-seq, and ATAC-seq data in bed format

extract_protocol:
ATAC-seq was performed with fresh dissociated cells from five retinas. Tagmentation and library preparation were carried out as described (Buenrostro, 2015) using Nextera DNA Library Prep kit (FC-121-1030, Illumina, San Diego, CA). Dissociated cells were quantified using a hemocytometer, and 50,000 cells were tagmented in a reaction mix containing 5 µl Tn5, 25 µl TD buffer 2X, 20 µl nuclease-free water in a thermomix with 600rpm agitation. The DNA was purified using the “MinElute PCR Purification” kit (Qiagen, 28004) followed by a two-sided size selection using a 0.5 and 1.5 ratio of SPRIselect reagent (Beckman Coulter B233181).
All the DNA was used to prepare the libraries. Libraries were sequenced pair-end using the HiSeq 2500 platform (Illumina, CA, USA) at a read length of 50 base pairs.

value: male


title: Wild type CTCF hair matrix P4.5

description: Primary keratinocytes

value: CTCF (Diagenode, #C15410210)


title: 11, EtOH, rep1

value: Fat body


title: Retina 2 ATAC-seq


title: Wild type Dlx3 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: Retina 3 ATAC-seq


title: Wild type 5hmC hair matrix P4.5

description: Primary keratinocytes

value: 5hmC (Active Motif, #39769)


title: Retina 1 ATAC-seq


title: Tet2/3 DKO Pol2Ser5 hair matrix P4.5

description: Primary keratinocytes

value: Tet2/3 DKO


title: Tet2/3 DKO Pol2Ser5 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: Tet2/3 DKO Lef1 hair matrix P4.5

description: Primary keratinocytes


title: HCT116 Hi-C

data_processing:
Hi-C analysis was performed with HiCUP (Wingett et al., 2015) using Arima-specific in silico digested hg38 genome for the retina samples and the HCT116.
Filtered bam files produced by HiCUP have been converted to .hic files using Juicer (Durand et al., 2016) and to HOMER (Heinz et al., 2013; Heinz et al., 2018) tag directories.
Retina Hi-C resolution has been estimated at 3.06 kb using HiCRes (Marchal et al., 2022).
Reproducibility between samples as well as correlation with Hi-C from other tissues have been assessed using HiCRep (Yang et al., 2017) by computing the average SCC for chromosomes 1 to 22.
Compartments have been called using HOMER using 100kb sliding windows with a step of 50kb (using options superRes and res, respectively),
Loops have been called using FitHiC (Ay et al., 2014) on the merged Hi-C datasets, using 5 kb resolution and an FDR threshold of 0.01.
TADs calling has been performed on the merged samples using domaincaller (Dixon et al., 2012), using raw contact maps of 10kb bins.
Insulation scores have been computed using the diamond insulation tool from cooltools (DOI 10.5281/zenodo.5214125), using 100 kb windows with 5 kb bins.
Assembly: hg38
Supplementary files format and content: Compartments for each sample in bed format.
Supplementary files format and content: Consensus binary contact maps for use with Juicer in hic format.
Supplementary files format and content: Consensus TAD calls in bed format.
Supplementary files format and content: Consensus loops in bedpe format.

extract_protocol:
Freshly dissected human retina tissue was crosslinked with 1% formaldehyde in PBS for 10 min, quenched with 125 mM glycine for 5 min and frozen until use for Hi-C experiments. Before processing for Hi-C, samples were crosslinked again in 2% formaldehyde for 10 minutes, then quenched with 125 mM glycine 5 min. For HCT116 cell line (ATCC, VA, USA), 7x106 cells were crosslinked with 2% formaldehyde for 10 min, quenched for 5 min with stop solution I, lysed, and processed for Hi-C using ARIMA-Hi-C kit.
Hi-C was performed on isolated nuclei using Arima-Hi-C kit (Arima Genomics, CA, USA) and Hyper Prep DNA-seq library prep kit (KK8502; Kapa Biosciences, MA, USA), following the manufacturers’ instructions. The libraries were sequenced on HiSeq 2500 platform (Illumina, CA, USA) at a read length of 101 to 126 base pairs and approximately 600 million read pairs per sample.

value: Human colon cancer cell line


title: Tet2/3 DKO Lef1 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: Tet2/3 DKO H3K4me3 hair matrix P4.5

description: Primary keratinocytes


title: Retina 1 Hi-C

description:
Healthy female retina, age 75
All_merged_using_Homer.hic
MergeRetina2_Domain_Call_TADs_10kb.bed
all_merge_loops_5kb_fdr_0.01.bedpe


title: KYSE-30 METTL3KO_rescuewithMETTL3WT_rep3

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling
Assembly: hg19
Supplementary files format and content: bigwig file, CpG information file

growth_protocol: KYSE-30 cells were cultured in DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for m6A-IP and input were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina HiSeqX Ten PE150 platform. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated paired-end reads (2× 125 bp). CUT&Tag sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions.

treatment_protocol: Short hairpin RNA (shRNA) targeting METTL3, TET1, FXR1 or scramble control or plasmids was commercially synthesis and transfected using lipofectamine 3000 (Life Technologies). Stable knockdown cells were generated by lentiviral infection and puromycin selection.

value: sgMETTL3 rescue with wild type METTL3

tag: assay type

value: WGBS


title: Retina 3 Hi-C

description:
Healthy male retina, age 75
All_merged_using_Homer.hic
MergeRetina2_Domain_Call_TADs_10kb.bed
all_merge_loops_5kb_fdr_0.01.bedpe


title: KYSE-30 METTL3KO_rescuewithMETTL3WT_rep2


title: Tet2/3 DKO H3K4me1 hair matrix P4.5

description: Primary keratinocytes

value: Hair matrix keratinocytes


title: Retina 2 Hi-C

description:
Healthy male retina, age 77
All_merged_using_Homer.hic
MergeRetina2_Domain_Call_TADs_10kb.bed
all_merge_loops_5kb_fdr_0.01.bedpe


title: Tet2/3 DKO H3K27me3 hair matrix P4.5

description: Primary keratinocytes


title: Retina 4 Hi-C

description:
Healthy male retina, age 76
All_merged_using_Homer.hic
MergeRetina2_Domain_Call_TADs_10kb.bed
all_merge_loops_5kb_fdr_0.01.bedpe


title: Tet2/3 DKO Dlx3 hair matrix P4.5

description: Primary keratinocytes


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT_rep2

value: sgMETTL3 rescue with mutant METTL3


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT_rep1


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT_rep3


title: Retina 5 ATAC-seq


title: Tet2/3 DKO Dlx3 5-aza treated hair matrix P4.5

description: Primary keratinocytes


title: KYSE-30 METTL3KO_rep2


title: Tet2/3 DKO H3K27ac hair matrix P4.5

description: Primary keratinocytes


title: Tet2/3 DKO CTCF hair matrix P4.5

description: Primary keratinocytes


title: KYSE-30 METTL3KO_rep1


title: KYSE-30 METTL3Control_rep3

value: wild type


title: KYSE-30 METTL3KO_rep3


title: Tet2/3 DKO 5hmC hair matrix P4.5

description: Primary keratinocytes


title: breast milk EVs_obese pre-pregnancy BMI_donor 6

type: RNA

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing: Raw data in RCC format were imported into R and normalized with the RUVg procedure (https://doi.org/10.1093/bib/bbaa163l).  DE analysis was conducted with DESeq2.

source_name: breast milk EVs

label_protocol: If the donor's pre-pregnancy BMI is less than 25, they are labeled the normal pre-pregnancy BMI group, and if the pre-pregnancy BMI is more than 30, they are labeled the obese prepregnancy BMI group.

extract_protocol: Breast milk EVs (bEVs) were isolated using ultracentrifugation. First, frozen breast milk was thawed at 4 °C overnight. Breast milk (15 ml) was centrifuged at 3000 g x 3 to remove bulk fat. The remaining supernatant was then centrifuged at 12,000 g for 40 minutes to remove the remaining fat and cell debris. After filtering with a 0.22-µm syringe filter, samples were centrifuged at 100,000 g for 2 hours to pellet EVs. The EV pellet was resuspended in 300 µl sterile PBS and rotated overnight at 4 °C.

treatment_protocol: No treatment

value: human breast milk

tag: rna population

value: Extracellular Vesicle miRNA

tag: pre-pregnancy bmi

value: obese


title: breast milk EVs_obese pre-pregnancy BMI_donor 62

tag: tissue


title: breast milk EVs_obese pre-pregnancy BMI_donor 69


title: KYSE-30 METTL3Control_rep2

tag: genotype


title: KYSE-30 METTL3Control_rep1


title: KYSE-30 FXR1KO_rescuewithFXR1WT_rep3 WGBS

value: sgFXR1 rescue with wild type FXR1


title: KYSE-30 FXR1KO_rescuewithFXR1WT_rep2 WGBS


title: breast milk EVs_obese pre-pregnancy BMI_donor 74


title: KYSE-30 FXR1KO_rescuewithFXR1MUT_rep3 WGBS

value: sgFXR1 rescue with KHdeleted FXR1


title: breast milk EVs_obese pre-pregnancy BMI_donor 2


title: KYSE-30 FXR1KO_rescuewithFXR1WT_rep1 WGBS


title: breast milk EVs_obese pre-pregnancy BMI_donor 73


title: KYSE-30 METTL3KO_rescuewithMETTL3WT_rep1


title: KYSE-30 FXR1KO_rep3 WGBS


title: KYSE-30 FXR1KO_rep2 WGBS


title: KYSE-30 FXR1KO_rep1 WGBS


title: breast milk EVs_obese pre-pregnancy BMI_donor 18


title: breast milk EVs_obese pre-pregnancy BMI_donor 49


title: breast milk EVs_obese pre-pregnancy BMI_donor 38


title: breast milk EVs_obese pre-pregnancy BMI_donor 67


title: KYSE-30 FXR1Control_rep2 WGBS


title: breast milk EVs_obese pre-pregnancy BMI_donor 91


title: breast milk EVs_obese pre-pregnancy BMI_donor 71


title: breast milk EVs_obese pre-pregnancy BMI_donor 66


title: KYSE-30 FXR1Control_rep1 WGBS


title: breast milk EVs_obese pre-pregnancy BMI_donor 12


title: KYSE-30 shMETTL3 WGBS rep2

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag and PARCLIP reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling, Piranha was used for CLIP peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file, CpG information file

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for m6A-IP and input were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina HiSeqX Ten PE150 platform. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated paired-end reads (2× 125 bp). CUT&Tag sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions. PAR-CLIP seqiencing was performed in NEBNext small RNA library prep kit (E7330S) and sequenced on Illumina. Hiseq4000.


title: KYSE-30 WT WGBS rep2


title: KYSE-30 FXR1KO_rescuewithFXR1MUT_rep2 WGBS


title: breast milk EVs_normal pre-pregnancy BMI_donor 90

value: normal


title: breast milk EVs_obese pre-pregnancy BMI_donor 40


title: breast milk EVs_obese pre-pregnancy BMI_donor 82


title: breast milk EVs_normal pre-pregnancy BMI_donor 89


title: KYSE-30 FXR1KO_rescuewithFXR1MUT_rep1 WGBS


title: KYSE-30 shMETTL3 WGBS rep1


title: KYSE-30 WT WGBS rep1


title: breast milk EVs_obese pre-pregnancy BMI_donor 86


title: serum_2

first: Jinhu

last: Guo

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: hg18
Supplementary_files_format_and_content: excel,expression profiles

source_name: serum

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Serum_1 was collected at standard working schedule and serum_2 was collected at nonstandard working schedule.

value: serum

tag: working schedule

value: nonstandard working schedule


title: serum_1

value: standard working schedule


title: breast milk EVs_normal pre-pregnancy BMI_donor 83


title: breast milk EVs_obese pre-pregnancy BMI_donor 84


title: breast milk EVs_normal pre-pregnancy BMI_donor 78


title: KYSE-30 FXR1Control_rep3 WGBS


title: breast milk EVs_normal pre-pregnancy BMI_donor 75


title: 408, 8 Gy, rep2

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Radiation, single dose of 8 Gy replicate 2

data_processing:
BWA was used for alignment
Picard was used for removing duplicates
MACS2 was used for peak calling
Assembly: GRCh38
Supplementary files format and content: peaks, CountMatrix_ATACseq_IRC_646.txt

growth_protocol: Cells were maintained in growth media containing DMEM:F12 with B27 supplement and Pen-strep containing growth factors EGF and FGF.

extract_protocol:
Nuclei were extracted according to previously published protocol (Buenrostro JD et al., 2015)
Libraries were prepared according to previously published protocol (Buenrostro JD et al., 2015)

treatment_protocol: Cells were pre-treated with C646 and radiated for 2-days prior to nuclei isolation

tag: cell type

value: GBM cells

tag: treatment

value: Radiation, single dose of 8 Gy


title: 408, 8 Gy, rep1

description: Radiation, single dose of 8 Gy replicate 1


title: breast milk EVs_normal pre-pregnancy BMI_donor 70


title: breast milk EVs_normal pre-pregnancy BMI_donor 65


title: CRBN_r1_d0_batch1

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

data_processing:
Raw sequencing reads were converted to fastq format using samtools (v1.10).
Sequencing adapters were removed, and the low-quality reads were filtered using the Trimmomatic tool (v0.39) in SE mode with standard settings.
Short reads were aligned to the expression cassette using aln algorithm from the bwa software package (v0.7.17) with the -n 5 parameter allowing for 5 mismatches, followed by bwa samse command to generate SAM files.
Mutation calling was performed using the AnalyzeSaturationMutagenesis tool from GATK (v4.1.8.1).
Alignment files were sorted using SortSam function from the Picard toolkit (v2.25.1).
Assembly: hg38
Supplementary files format and content: aaCounts files as generated by the AnalyzeSaturationMutagenesis GATK function

source_name: RKO colon carcinoma cell line

growth_protocol: Eight million RKO CRBN-/- or VHL-/- were transduced at a MOI of 0.3 yielding a calculated library representation of 1664 and 1380 cells per variant for VHL and CRBN respectively. For each transduction one million cells were seeded in a 12-well plate with 8 µgml-1 polybrene (SantaCruz, SC-134220), the titrated amount of lentivirus filled to 1 ml with culture media. The plate was centrifuged at 765 x g for 1 h at 37°C and cells were detached after 6 h of incubation at 37°C, pooled and expanded. 48 hrs after transduction, pools were selected by adding 20 µgml-1 blasticidine for 7 days.

extract_protocol:
Genomic DNA (gDNA) was extracted from frozen cell pellets following the QIAamp DNA Mini Kit (Qiagen, 51304).
VHL and CRBN were amplified via PCR from gDNA with primers CRBN_GA_fwd & rev and VHL_GA_fwd & rev for CRBN and VHL, respectively. Primer sequences are available in Supplementary Table 5 of the linked publication. The total isolated gDNA was processed in batches of 5 µg per PCR reaction with Q5 polymerase (NEB, M0491L). One PCR reaction contained 10 µl 5x reaction buffer, 10 µl 5x GC enhancer, 2.5 µl primer mix containing 10 μM forward and reverse primer each, 1 µl dNTP mix (10 μM each), 1 µl Q5 polymerase and nuclease-free water to bring the reaction volume to 50 µl. Target amplification was achieved by performing: 30 s initial denaturation at 95°C; next for 20 to 28 cycles: 15 s at 95°C, 30 s at 57°C and 2 min at 72°C; followed by a final extension for 5 min at 72°C. The cycle number for specific amplification of the 700 base-pair (VHL) and 1.4 kilo-base-pair (CRBN) targets was confirmed by agarose gel electrophoresis. PCR reactions for each treatment were pooled and purified using AMPure XP beads (Beckman Coulter, 10136224) according to standard protocol for double-sided clean up in a 0.3:1 and 1:1 ratio. The purity and integrity of the PCR products were analysed on an Agilent 2100 Bioanalyzer following manufacturer recommendations for high sensitivity DNA chips (Agilent, 5067-4626). Sequencing libraries were prepared using Nextera DNA Library Prep Kit (Illumina, FC-131-1024) following standard manufacturer instructions for amplicon libraries. After purification of the tagmented and PCR amplified DNA libraries quality control was performed by analysis on an Agilent 2100 Bioanalyzer following manufacturer recommendations for high sensitivity DNA chips (Agilent, 5067-4626). Final sequencing libraries were pooled in equimolar amounts and sequenced running 50-bp single-end reads on a HiSeq4000.

treatment_protocol: Independent mutational scanning resistance screens were performed in replicates by treating 2.5 million cells, splitting and retreating after 4 days and harvesting 2.5 million cell pellets after a total of 7 day treatment with the indicated drug and dose.

value: colon carcinoma cells

tag: gene

value: CRBN

value: untreated

tag: dosage

tag: time

tag: batch

tag: replicate

value: RKO

value: Cancer Cell Line


title: breast milk EVs_normal pre-pregnancy BMI_donor 87


title: 408, 0 Gy C646, rep2

description: Untreated 0Gy C646 replicate 2

tag: pre-treatment

value: Untreated

tag: cell line


title: 408, 0 Gy, rep2

description: Untreated 0Gy replicate 2


title: 408, 8 Gy, Day2-3

description: Radiation, single dose of 8 Gy replicate 3

data_processing:
BWA was used for alignment
Picard was used for removing duplicates
MACS2 was used for peak calling
Assembly: GRCh38
Supplementary files format and content: peaks

treatment_protocol: Cells were radiated for 2-days prior to nuclei isolation


title: 408, 8 Gy, Day2-2


title: 408, 8 Gy, Day2-1


title: 408, 8 Gy C646, rep1

description: Radiation, single dose of 8 Gy C646 replicate 1


title: breast milk EVs_normal pre-pregnancy BMI_donor 76

value: human breast milk


title: breast milk EVs_normal pre-pregnancy BMI_donor 77

value: Extracellular Vesicle miRNA


title: 408, 8 Gy C646, rep2

description: Radiation, single dose of 8 Gy C646 replicate 2


title: breast milk EVs_normal pre-pregnancy BMI_donor 56


title: 408, 0 Gy, rep1

description: Untreated 0Gy replicate 1


title: 408, 0 Gy-3

description: 408 untreated replicate 3


title: breast milk EVs_normal pre-pregnancy BMI_donor 53


title: breast milk EVs_normal pre-pregnancy BMI_donor 52


title: breast milk EVs_normal pre-pregnancy BMI_donor 61


title: breast milk EVs_normal pre-pregnancy BMI_donor 60


title: breast milk EVs_normal pre-pregnancy BMI_donor 63


title: breast milk EVs_normal pre-pregnancy BMI_donor 47


title: breast milk EVs_normal pre-pregnancy BMI_donor 51


title: 408, 0 Gy-1

description: 408 untreated replicate 1


title: 408, 0 Gy-2

description: 408 untreated replicate 2


title: breast milk EVs_normal pre-pregnancy BMI_donor 45


title: breast milk EVs_normal pre-pregnancy BMI_donor 50


title: breast milk EVs_normal pre-pregnancy BMI_donor 48


title: 408, 0 Gy C646, rep1

description: Untreated 0Gy C646 replicate 1


title: 408, 8Gy, HATi, D7, 2

description:
8 GY + C646
Radiation, single dose of 8 Gy, C646 Day 7 replicate 2

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to GRCh38 using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

extract_protocol:
RNA extraction was performed using Qiagen RNEasy Microkit
cDNA libraries were prepared using TruSeq Stranded RNA (100ng) + Ribozero Gold

treatment_protocol: Cells were first radiated for 7 day time point and then radiated for 2-day time point to collect all samples on the same day.


title: 408, 8Gy, HATi, D7, 1

description:
8 GY + C646
Radiation, single dose of 8 Gy, C646 Day 7 replicate 1


title: 408, 8Gy, HATi, D7, 3

description:
8 GY + C646
Radiation, single dose of 8 Gy, C646 Day 7 replicate 3


title: 408, 8Gy, D7, 3

description:
8 Gy
Radiation, single dose of 8 Gy, Day 7 replicate 3


title: breast milk EVs_normal pre-pregnancy BMI_donor 44


title: breast milk EVs_normal pre-pregnancy BMI_donor 43


title: breast milk EVs_normal pre-pregnancy BMI_donor 41


title: breast milk EVs_normal pre-pregnancy BMI_donor 42


title: 408, 8Gy, D7, 1

description:
8 Gy
Radiation, single dose of 8 Gy, Day 7 replicate 1


title: breast milk EVs_normal pre-pregnancy BMI_donor 36


title: 408, 8Gy, 3

description:
8 Gy
Radiation, single dose of 8 Gy replicate 3


title: 408, 0Gy, HATi, D7, 3

description:
C646
Untreated, 0 Gy C646 relicate 3


title: 408, 8Gy, 2

description:
8 Gy
Radiation, single dose of 8 Gy replicate 2


title: 408, 8Gy, 1

description:
8 Gy
Radiation, single dose of 8 Gy replicate 1


title: breast milk EVs_normal pre-pregnancy BMI_donor 35


title: 408, 0Gy, HATi, D7, 2

description:
C646
Untreated, 0 Gy C646 relicate 2


title: 408, 0Gy, HATi, D7, 1

description:
C646
Untreated, 0 Gy C646 relicate 1


title: breast milk EVs_normal pre-pregnancy BMI_donor 34


title: breast milk EVs_normal pre-pregnancy BMI_donor 29


title: breast milk EVs_normal pre-pregnancy BMI_donor 28


title: 408, 0Gy, 3

description:
0 Gy
Untreated, 0 Gy replicate 3


title: 408, 0Gy, 2

description:
0 Gy
Untreated, 0 Gy replicate 2


title: 408, 8Gy, D7, 2

description:
8 Gy
Radiation, single dose of 8 Gy, Day 7 replicate 2


title: breast milk EVs_normal pre-pregnancy BMI_donor 27


title: breast milk EVs_normal pre-pregnancy BMI_donor 26


title: dBET6_25X_50X_pool

data_processing:
Raw sequencing reads were converted to fastq files using the bamtools convert (v2.5.1).
Sequencing adapters and low-quality reads were trimmed using the Trimmomatic tool (v0.39) in SE mode with standard settings.
Reads were aligned to the hg38/GRCh38 assembly of the human reference genome using aln and samse algorithms from the bwa package (v0.7.17).
Unmapped reads were removed using the CleanSam function from the Picard toolkit (v2.25.1).
Reads were sorted and duplicate reads filtered using the SortSam and MarkDuplicates Picard tools (v2.25.1).
Read groups were added by the Picard AddOrReplaceReadGroups tool.
The Mutect2 function from the GATK (v4.1.8.1) was used to call variants. The variants were annotated using the Ensembl Variant Effect Predictor tool (v103.1)
Assembly: hg38 (GRCh38)
Supplementary files format and content: vcf file with output from MuTect2 annotated by VEP

source_name: chronic myelogenous leukemia (CML) cell line

growth_protocol: One hundred million KBM7 cells were treated with DMSO or 10X (100 nM), 25X (250 nM), 50X (500 nM) EC50 of dBET6 or ARV in 50 ml medium. After 25 d, Ficoll-gradient centrifugation with Lymphocyte Separation Media (Corning, COR25-072-CV) was performed according to manufacturer’s protocols. Cells were recovered for one day, counted and PBS washed pellets were stored at -80 °C.

extract_protocol:
gDNA extraction was performed (QIAamp DNA Mini, QIAGEN 51304) and DNA content was determined with Qubit dsDNA HS Kit (Thermo Fisher, Q32854).
500 ng of the gDNA was subjected to DNA library preparation using the NEBNext Ultra II FS DNA Library Prep kit for Illumina (New England Biolabs, E7805S) following manufacturer’s instructions (protocol for inputs >100 ng). Fragments were size-selected using AMPure XP beads (Beckman Coulter, 10136224) for fragments of 150-350 bp. Adaptor-ligated DNA was amplified in five cycles by PCR using NEBnext Multiplex Oligos for Illumina (Set1 E7335 and Set2 E75000). For hybrid capture, xGen Gene Capture Pools for the 29 genes of interest were purchased from IDT (see Supplementary Table 1) and 500 ng of DNA was used as input. Hybridization was performed for 16h following the supplier’s protocols, including the xGen Universal Blocker-TS Mix (IDT, 1075475) blocking oligos. Post-capture PCR was performed with the NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541S) for 14-20 cycles. Sequencing libraries were quantified using the Qubit dsDNA HS Kit (Thermo Fisher Q32854) and analyzed on an Agilent 2100 Bioanalyzer before sequencing on a HiSeq 4000 (50 bp single-end).

tag: disease

value: chronic myelogenous leukemia (CML)

value: 25-50 times EC50


title: 408, 0Gy, 1

description:
0 Gy
Untreated, 0 Gy replicate 1


title: wt

value: wild-type


title: breast milk EVs_normal pre-pregnancy BMI_donor 25

value: normal


title: dBET6_25X

value: 25 times EC50


title: ARV_25X_50X_pool


title: breast milk EVs_normal pre-pregnancy BMI_donor 20


title: breast milk EVs_normal pre-pregnancy BMI_donor 24


title: breast milk EVs_normal pre-pregnancy BMI_donor 14


title: breast milk EVs_normal pre-pregnancy BMI_donor 21


title: breast milk EVs_normal pre-pregnancy BMI_donor 13


title: dBET6_50X

value: 50 times EC50


title: breast milk EVs_normal pre-pregnancy BMI_donor 9


title: breast milk EVs_normal pre-pregnancy BMI_donor 19


title: ARV_50X


title: breast milk EVs_normal pre-pregnancy BMI_donor 33


title: breast milk EVs_normal pre-pregnancy BMI_donor 16


title: CRBN_dBET6_r3_batch3

value: colon carcinoma cell line


title: CRBN_DMSO_r2_batch3

value: DMSO


title: ARV_25X


title: CRBN_dBET6_r2_batch3


title: B220+CD19+ B cells from mLNs [mLN_DEX_3]

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The libraries were sequenced on NextSeq 500 (Illumina) by paired-end run (38x38 or 42x42 bp). Three nucleotides from 5′ end of read 2 were trimmed by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Reads were mapped to mouse cDNA/ncRNA transcriptomes (GRCm38 ensembl v89) and quantified in transcripts per million (TPM) with kallisto (v0.46.2, k-mer index 25, bootstrap 60).
Differential gene expression analysis was conducted in RStudio (v4.1.0) with biomaRt, tximport, edgeR, Glimma, and limma packages with generalized linear model (GLM) likelihood ratio test and robust genewise dispersion parameter estimates.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Mesenteric lymph nodes

growth_protocol: Purified splenic CD19+ B cells were cultured in complete media containing 1 µg/mL anti-mouse CD40 monoclonal antibody and 10 ng/mL IL-4.

extract_protocol:
Total RNA was isolated by RNeasy Micro Kit (QIAGEN, 74004).
RNA-seq libraries were prepped by SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara, 634413).

treatment_protocol: Cells were incubated with either 0.1% DMSO or 100 ng/mL dexamethasone for 12 hours from 48 to 54 and 72 to 78 hours. Outside of the two 6 hour incubations up through the 96 hour time point, washed cells were resuspended in complete media with 0.5 µg/mL anti-CD40 and 5 ng/mL IL-4.

value: Mesenteric lymph nodes

value: Primary cell

value: in vivo B cells (CD45+, c-Kit-, B220+)

value: WT B6 mice

value: DEX


title: CRBN_dBET6_r1_batch3

value: colon carcinoma cells

value: CRBN

value: RKO


title: CRBN_DMSO_r3_batch3


title: breast milk EVs_normal pre-pregnancy BMI_donor 11

value: human breast milk

value: Extracellular Vesicle miRNA


title: B220+CD19+ B cells from mLNs [mLN_DEX_1]


title: CRBN_dBET57_r3_batch3


title: B220+CD19+ B cells from mLNs [mLN_DEX_2]


title: B220+CD19+ B cells from mLNs [mLN_Cont_1]

value: Vehicle


title: breast milk EVs_normal pre-pregnancy BMI_donor 5


title: B220+CD19+ B cells from mLNs [mLN_Cont_2]


title: breast milk EVs_normal pre-pregnancy BMI_donor 7


title: CRBN_dBET57_r2_batch3


title: breast milk EVs_normal pre-pregnancy BMI_donor 3


title: Sorted IgE+ B cells cultured ex vivo 96 hours [IgE_DEX_2]

source_name: Spleen

value: Spleen

value: ex vivo B cells


title: B220+CD19+ B cells from mLNs [mLN_Cont_3]


title: CRBN_dBET57_r1_batch3


title: CRBN_DMSO_r1_batch3


title: CRBN_CC90009_r2_batch3


title: CRBN_CC90009_r3_batch3


title: breast milk EVs_normal pre-pregnancy BMI_donor 1

value: normal


title: CRBN_CC885_r3_batch3


title: Sorted IgE+ B cells cultured ex vivo 96 hours [IgE_Cont_2]


title: Sorted IgE+ B cells cultured ex vivo 96 hours [IgE_DEX_1]


title: CRBN_CC90009_r1_batch3


title: CRBN_CC885_r2_batch3


title: Sorted IgE+ B cells cultured ex vivo 96 hours [IgE_Cont_1]


title: CRBN_CC885_r1_batch3


title: Bulk B cells cultured ex vivo 96 hours [DEX_1]


title: VHL_r2_ACBI1_2_7d_batch2

value: VHL

value: 2 uM


title: Bulk B cells cultured ex vivo 96 hours [DEX_2]


title: VHL_r1_ACBI1_2_7d_batch2

value: colon carcinoma cell line


title: VHL_r2_DAT551_2_7d_batch2


title: Bulk B cells cultured ex vivo 96 hours [Cont_1]


title: Bulk B cells cultured ex vivo 96 hours [Cont_2]


title: Control (CD45 positive cells)

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Raw reads were demultiplexed by Chromium Barcodes and used as input for Starsolo (2.7.3a) with parameters (--soloType CB_UMI_Simple --soloBarcodeReadLength 0) to match cell barcodes to whitelist('--soloType CB_UMI_Simple --soloBarcodeReadLength 0').
As reference ensembl mouse genome mm10 (release 99) was used.
Secondary analysis was performed in Scanpy (1.6).
Genome_build: mm10
Supplementary_files_format_and_content: anndata object

source_name: CD45 positive cells

extract_protocol:
Bone marrow derived cell were isolated from C57BL/6 mice tibia and femur using an aseptic technique. The bone marrow was flushed out of the bone marrow cavity by using a 26-gauge needle with 10ml PBS. Subsequently cell suspension was passed through a 70µm nylon mesh. After a 10 min centrifugation step at 500 x g, cells were incubated in 2ml red cell lysis buffer for red blood cell removal. After 4 min incubation time, lysis was stopped by adding 23 ml PBS.. Cells were resuspended in PBS and FACS sorted for CD45 cells using an AriaIII-sorter and 7-AAD as indicator for dead cells. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample.
Single cell libraries were generated on 10x Chromium Controler (10x Genomics)  with 16000 cells as input following standard protocol.

tag: strain


title: VHL_r2_DAT548_500_7d_batch2


title: VHL_r1_DAT551_2_7d_batch2


title: VHL_r2_DMSO_7d_batch2

value: DMSO


title: VHL_r1_DAT548_500_7d_batch2


title: CRBN_r1_DMSO_batch1


title: VHL_Library_r2_batch2

value: Library


title: VHL_r1_DMSO_7d_batch2


title: VHL_Library_r1_batch2


title: VHL_r1_MZ1_500_batch1


title: VHL_r2_MZ1_500_batch1


title: VHL_r2_ARV771_5_batch1

value: 5 nM


title: VHL_r2_ARV771_50_batch1

value: 50 nM


title: VHL_r1_ARV771_50_batch1


title: CRBN_r1_dBET6_500_batch1


title: VHL_r2_ARV771_500_batch1


title: VHL_r2_DMSO_batch1


title: VHL_r1_DMSO_batch1


title: KYSE-30 WT FXR1 PARCLIP-seq rep3

description: library strategy: PARCLIP-seq

value: wild type


title: Lung, BLM, 7117, 6

city: Yokohama-shi Aoba-ku

first: Shinji

last: Kojima

address: Kamoshida-cho 1000

institute: Mitsubishi Tanabe Pharma Corporation

description: MT-7117 treated group

hyb_protocol: Labeled cRNA samples were fragmented, and then hybridized with the Agilent SurePrint G3 Mouse GE v2 8 × 60 K Microarray (Agilent Technologies) using a Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: The microarray was washed with the Gene Expression Wash Buffers Pack (Agilent Technologies).  Slides were scanned on the Agilent Sure Scan Microarray Scanner(Agilent Technologies) .

data_processing: Signal intensities were evaluated with Agilent Feature Extraction software 12.0. Signal intensities were imported to GeneSpring14.9(Agilent) and were applied 75% percentile shift normalization.

source_name: Bleomycin, MT-7117 treated

label_protocol: The RNA was then Cy3-labeled using a Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies)

extract_protocol: Total RNA of mouse lung tissue samples were isolated using RNeasy 96 Universal Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The purity, concentration, and quality of the RNA samples were confirmed with NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) and Agilent 2100 bioanalyser (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Ten-week-old female C3H/HeNCrlCrlj mice were used. The backs of mice were shaved, and the middle of the backs were marked with oil-based red ink. Phosphate-buffered saline (PBS) or BLM (Nippon Kayaku, Tokyo, Japan) (0.15 mg/0.1 mL per animal) was subcutaneously injected at the marked site once daily from day 0 to day 25 (since repeated BLM injections reduced the body weights of the mice remarkably, BLM injection was suspended several times for all groups). MT-7117 solutions at 0.1 mL/10 g of body weight were orally administered once daily (approximately 2 hours before the BLM injection) for 29 consecutive days from day 0 until the day before the end of evaluation (day 28). On day 29, mice were euthanized by inhalation anesthesia with isoflurane, and the lung was dissected.

value: Lung

tag: age

tag: gender

value: Female

tag: disease state

value: bleomycin-induced systemic sclerosis model


title: Lung, BLM, 7117, 1

description: MT-7117 treated group

tag: tissue


title: Lung, BLM, 7117, 8

description: MT-7117 treated group


title: VHL_r1_ARV771_5_batch1

value: colon carcinoma cells

value: RKO


title: Lung, BLM, 7117, 5

description: MT-7117 treated group


title: Lung, BLM, 7117, 9

description: MT-7117 treated group


title: Lung, BLM, 7117, 10

description: MT-7117 treated group


title: Lung, BLM, 7117, 4

description: MT-7117 treated group


title: Lung, BLM, 7117, 2

description: MT-7117 treated group


title: KYSE-30 WT FXR1 PARCLIP-seq rep1

description: library strategy: PARCLIP-seq

tag: genotype


title: VHL_r1_ARV771_500_batch1


title: Lung, BLM, 8

description: control group with disease

source_name: Bleomycin, vehicle

value: vehicle


title: Lung, BLM, 7

description: control group with disease


title: Lung, BLM, 2

description: control group with disease


title: Lung, BLM, 7117, 3

description: MT-7117 treated group


title: Lung, BLM, 7117, 7

description: MT-7117 treated group


title: KYSE-30 WT FXR1 PARCLIP-seq rep2

description: library strategy: PARCLIP-seq


title: Lung, BLM, 10

description: control group with disease


title: Lung, BLM, 6

description: control group with disease


title: Lung, BLM, 9

description: control group with disease


title: Lung, BLM, 4

description: control group with disease


title: Lung, BLM, 5

description: control group with disease


title: Lung, BLM, 3

description: control group with disease


title: KYSE-30 FXR1KO m6A-INPUT rep3

tag: assay type

value: RIP-seq


title: KYSE-30 FXR1KO m6A-INPUT rep2


title: Tet2/3 DKO 5-aza treated RNA replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore.
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR.
Read count was extracted with HTseq, and differential expressed genes were calculated with DESeq2 under R language.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample groups

source_name: hair matrix keratinocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
For untreated mice, skin is harvested at P4.5 directly.
For 5-aza treated mice, 50 µg 5-aza (Sigma) is given through subcutaneous injection at P2.5, and skin is harvested at P4.5.

tag: cell type

value: hair matrix keratinocytes

value: Tet2/Tet3 DKO, Krt14-Cre


title: KYSE-30 FXR1KO m6A-IP rep3


title: KYSE-30 FXR1KO m6A-INPUT rep1


title: KYSE-30 FXR1KO m6A-IP rep2


title: KYSE-30 TET1KO m6A-INPUT rep3


title: Tet2/3 DKO 5-aza treated RNA replicate 1

tag: treatment


title: KYSE-30 FXR1KO m6A-IP rep1


title: KYSE-30 TET1KO m6A-INPUT rep2


title: Lung, BLM, 1

description: control group with disease


title: Lung, PBS, 9

description: control group without disease

source_name: PBS, vehicle

value: control


title: Lung, PBS, 4

description: control group without disease


title: scRNA_TIL_NYESO1_MED12

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: single cell RNA

data_processing:
150 bp paired end sequencing was obtained using the Illumina NovaSeq6000 platform
FASTQ files were trimmed, filtered, and aligned using the cellranger count pipeline from 10X genomics.
Filtered counts matrices containing transcript counts for each single cell were imported into Seurat for downstream processing.
Cells were clustered and visualized using Seurat.
Gene expression values  were normalized and marker genes were identified using Seurat.
Assembly: hg38
Supplementary files format and content: Filtered cell by gene counts matrix generated by 10X cellranger count pipeline.

source_name: tumor infiltrating T cells

extract_protocol:
Single-cell capture was performed using the 10X platform.
10X Chromium Next GEM Single Cell 3’ v 3.1 kit (10X Genomics)

treatment_protocol: Live, NY-ESO-1+ T cells were isolated from tumors by mechanical and enzymatic dissociation followed by FACS.

value: tumor infiltrating T cells

value: sorted from dissociated tumor


title: Wild type 5-aza treated RNA replicate 2

value: WT


title: Lung, PBS, 2

description: control group without disease


title: Lung, PBS, 10

description: control group without disease


title: Lung, PBS, 1

description: control group without disease


title: Lung, PBS, 3

description: control group without disease


title: Lung, PBS, 8

description: control group without disease


title: Lung, PBS, 7

description: control group without disease


title: Lung, PBS, 5

description: control group without disease


title: KYSE-30 TET1KO m6A-INPUT rep1


title: scRNA_TIL_NYESO1_AAVS1

description: single cell RNA


title: KYSE-30 TET1KO m6A-IP rep2


title: Tet2/3 DKO RNA replicate 2


title: KYSE-30 TET1KO m6A-IP rep1


title: Lung, PBS, 6

description: control group without disease


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-INPUT rep3

value: sgMETTL3 rescue with mutant METTL3


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-INPUT rep2


title: Wild type RNA replicate 2


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-INPUT rep3

value: sgMETTL3 rescue with wild type METTL3


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-INPUT rep1


title: Wild type 5-aza treated RNA replicate 1


title: KYSE-30 TET1KO m6A-IP rep3


title: Tet2/3 DKO RNA replicate 1


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-INPUT rep2


title: Epidermis, Experimental biol rep 1

city: Philadelphia

first: Russ

middle: P

last: Carstens

state: PA

address: 412 Curie Blvd

department: Medicine

institute: University of Pennsylvania

description:
epidermis_protein-coding_deseq.tsv
Majiq_junctions.tsv
rMATS_CON_EXP.xlsx
TPMlog_ESRP_epidermis_nobatchcorr.tsv

data_processing:
adapters were trimmed from RNA-Seq samples using BBDuk
aligned to the mouse GRCm38 genome assembly using STAR v.2.5.1B and sorted and indexed using samtools v.1.9
salmon v.0.14.0 was used in mapping-based mode with selective alignment on trimmed fastq files using GENCODE vM23 annotation to create the index
Assembly: mm10
Supplementary files format and content: Alternative splicing analysis from rMATS (Shen et al., NAR. 2012; Shen et al., PNAS. 2014) - rMATS_CON_EXP.xlsx; Sample 1 (Controls); Sample 2 (Experimental)
Supplementary files format and content: Reported splice junctions quantitifed using Majiq (Vaquero-Garcia et al., eLife. 2016) - Majiq_junctions.tsv
Supplementary files format and content: Differential Expressed protein coding genes between control and experimental samples - epidermis_protein-coding_deseq.tsv

source_name: Epidermis

extract_protocol:
Epidermis was harvested from backskin of pups at PND5. RNA was harvested using Rneasy mini plus kit (Qiagen).  At least 1 ug of total RNA was submitted to Genewiz for use in the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep following manufacturer's protocols.

treatment_protocol: Esrp1flox/flox; Esrp2-/- female mice was time crossed to K5rTA tetOCre Esrp1flox/flox; Esrp2-/- male. After pregnancy, female mice fed high dox chow from embryonic day E17 throught weaning to PND 5

value: Epidermis

value: Epithelial

value: K5rTA tetOCre Esrp1flox/flox; Esrp2-/-

value: Dam fed with high dox chow E17 - PND5


title: Epidermis, Experimental biol rep 3


title: Epidermis, Experimental biol rep 4


title: Epidermis, Control biol rep 4

value: Esrp1flox/flox; Esrp2-/-


title: Epidermis, Experimental biol rep 2


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-INPUT rep1


title: KYSE-30 METTL3KO m6A-INPUT rep3


title: Epidermis, Control biol rep 3


title: Epidermis, Control biol rep 2


title: KYSE-30 METTL3KO m6A-INPUT rep1


title: Wild type RNA replicate 1


title: KYSE-30 METTL3KO m6A-INPUT rep2


title: Epidermis, Control biol rep 1


title: KYSE-30 Control m6A-INPUT rep3

value: wild type


title: human gingival fibroblasts, replicate 2, vitamin D3

city: Xiamen

first: Churen

last: Zhang

state: Fujian

address: 55 Zhenhai Avenue, Siming District.

institute: The First Affiliated Hospital of Xiamen University

data_processing:
processing of raw data and filtering of low quality sequences using Fastp (an ultra-fast all-in-one fastq preprocessor, PMID: 30423086)
The HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts, PMID: 25751142) software aligns transcriptome sequencing Reads to the reference genome (GrCM38/mm10).
Reads Count calculation was performed by HTSeq (a python framework to work with high-throughput sequencing data, PMID: 25260700)
Difference analysis by DESeq2 (PMID: 25516281)
Functional enrichment analysis included GO, KEGG
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: gingiva

growth_protocol: human gingival fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol (Thermo Fisher Scientific). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  AMPure XP beads  following manufacturer's protocols.

treatment_protocol: Treat the post confluent cells with 1000nM vitamin D3 (Sigma) and 0.1%  ethanol

value: gingiva

value: primary cell

value: fibroblasts

value: vitamin D3


title: human gingival fibroblasts, replicate 3, vitamin D3


title: human gingival fibroblasts, replicate 1, vitamin D3


title: human gingival fibroblasts, replicate 2, ethanol control

value: ethanol


title: KYSE-30 Control m6A-INPUT rep2

value: RIP-seq


title: epidermis, biol rep 6 - CLIP Sample

description:
ESRP1-CLIP-FLAG-R5P1-R6P1.sites.ucsc.bed
3UTR Sites Unique with Scores_PureCLIP.xlsx
three_prime_utr_peaks.CLIP-FLAG-all.piranha.peak.call.bin.size.10.1.0.covariates2.withHeader.annotated - Copy.xlsx

data_processing:
eCLIP sequencing reads from each of the replicate from CLIP sample group were pooled together, then trimmed to remove adaptor sequences using Cutadapt (v1.16), the 6 individual Input controls from Esrp1 FLAG/FLAG were not pooled.
The trimmed reads were mapped to the grcm38_snp_tran mouse reference genome using Hisat2 aligner (v2.1.0).
Piranha (v.1.2.1),was used for ESRP1 peak calling - mapped reads from the pooled CLIP sample in BED format were input into Piranha for identifying regions of statistically significant read enrichment using the mapped reads from Input sample as covariate for running Piranha.
Processed read counts from 6 replicate for both CLIP and Input were used to call peaks and crosslink sites using PureCLIP, the 6 biological replicates were pooled into 3 replicate pairs and PureCLIP analysis was performed as previously described using default parameters described Krakau et al. 2017. The HOMER software package was used to identify the motifs four to seven nucleotides in length, enriched on the transcript strand within 10 nucleotides of the cross-link sites and calculate the cross-link densities relative to the identified consensus motif.
Assembly: mm10
Supplementary files format and content: Bedfiles from PureCLIP output for paired replicate with matched input: ESRP1-CLIP-FLAG-R1P1-R2P1.sites.ucsc.bed, ESRP1-CLIP-FLAG-R3P1-R4P1.sites.ucsc.bed, ESRP1-CLIP-FLAG-R5P1-R6P1.sites.ucsc.bed
Supplementary files format and content: Annotated output for PureCLIP showing genes with peaks of ESRP1 in 3'UTR - 3UTR Sites Unique with Scores_PureCLIP.xlsx
Supplementary files format and content: Annotated output for Piranha Peak Caller showing genes with peaks of ESRP1 in the 3'UTR - three_prime_utr_peaks.CLIP-FLAG-all.piranha.peak.call.bin.size.10.1.0.covariates2.withHeader.annotated - Copy.xlsx

extract_protocol:
Immunoprecipitants or input samples were run on 4-12% Bis-Tris protien gels and transferred to nitrocellulose membrane. RBP:RNP complexes were excised from membrane by cutting at region of membrane between 75kDA to 140kDa in the appropriate lanes. RNA was released from membrane by treatment of the membrane with urea/proteinase K treatment at 37C, and purified using acid phenol/chloroform/isoamyl alcohol
Libraries were constructed as described Van Nostrand et al Nature Methods 2016. RNA adapters ligated to the RNA were A01 and B01, following reverse transcription DNA adapter ligated to the cDNA was rand3Tr3. Libraries were amplified by PCR using NEB Q5 High Fidelity Mastermix with primers containning Illumina P5 and P7 indices. Libraries (175-350bp) were purified from 3% low melt agarose gel using Qiagen minelute gel extraction kit
eCLIP-Seq

treatment_protocol: Epidermis was harvested from backskin of pups at PND1 using 2.5% trypsin diluted in 1X HBSS. The sheet of epithelial cellswere crosslinked at 400J/cm2 once, twice at 200J/cm2 on ice

tag: clip antibody

value: FLAG (Sigma F1804)


title: epidermis, biol rep 6 - Input


title: human gingival fibroblasts, replicate 1, ethanol control


title: KYSE-30 Control m6A-INPUT rep1

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling
Assembly: hg19
Supplementary files format and content: bigwig file, CpG information file


title: 408, GBM, TX, 0Gy

description: Untreated

data_processing:
Cell Ranger from 10x Genomics was used for alignment and quantification
Assembly: GRCh38
Supplementary files format and content: There are 3 files for each sample: barcodes, features, and count matrix, in the forms of tab-separated values and market exchange format, respectively

source_name: 408, GBM, TX, 0 Gy

extract_protocol: cDNA libaries were constructed according to 10x Genomics chromium reagent kit v3

value: GBM cells

value: patient-derived xenograft

value: Untreated


title: 408, GBM, TX, 8Gy

description: Radiation, single dose of 8 Gy

source_name: 408, GBM, TX , 8 Gy

value: Radiation, single dose of 8 Gy


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-IP rep3

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for m6A-IP and input were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina HiSeqX Ten PE150 platform. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated paired-end reads (2× 125 bp). CUT&Tag sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions.

value: sgMETTL3 rescue with mutant METTL3


title: 408, GBM, 8Gy, Day 2

description: Radiation, single dose of 8 Gy


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-IP rep2


title: epidermis, biol rep 5 - Input

value: Epidermis

value: Epithelial


title: epidermis, biol rep 4 - CLIP Sample

description:
ESRP1-CLIP-FLAG-R3P1-R4P1.sites.ucsc.bed
3UTR Sites Unique with Scores_PureCLIP.xlsx
three_prime_utr_peaks.CLIP-FLAG-all.piranha.peak.call.bin.size.10.1.0.covariates2.withHeader.annotated - Copy.xlsx


title: KYSE-30 FXR1KO_rescuewithKHdeletedFXR1  rep2

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then qualified reads were mapped to hg19 Bowtie2.
MACS2 was used for 5hmC peak calling
Assembly: hg19
Supplementary files format and content: bigwig file
Library strategy: 5hmC Seal-seq

extract_protocol:
Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries were sequenced on Novaseq6000 sequencers.

treatment_protocol: Short hairpin RNA (shRNA) targeting METTL3, FXR1 or scramble control or plasmids was commercially synthesis and transfected using lipofectamine 3000 (Life Technologies). Stable knockdown cells were generated by lentiviral infection and puromycin selection.

value: sgFXR1 rescue with KH deleted FXR1


title: 408, GBM, 8Gy, Day 7

description: Radiation, single dose of 8 Gy

value: Day 7


title: 408, GBM, 0Gy

description: Untreated


title: KYSE-30 FXR1KO_rescuewithKHdeletedFXR1  rep1


title: epidermis, biol rep 5 - CLIP Sample


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT m6A-IP rep1


title: KYSE-30 FXR1KO_rescuewithFXR1WT 5hmC rep3

value: sgFXR1 rescue with wild type FXR1


title: epidermis, biol rep 4 - Input


title: KYSE-30 FXR1KO_rescuewithFXR1WT 5hmC rep2


title: KYSE-30 FXR1KO_rescuewithFXR1WT 5hmC rep1


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-IP rep2

value: sgMETTL3 rescue with wild type METTL3


title: KYSE-30 FXR1KO 5hmC rep3


title: epidermis, biol rep 3 - Input


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-IP rep1


title: KYSE-30 FXR1KO 5hmC rep2


title: epidermis, biol rep 3 - CLIP Sample


title: KYSE-30 FXR1 Control 5hmC rep3

value: wild type


title: KYSE-30 FXR1KO 5hmC rep1


title: KYSE-30 FXR1 Control 5hmC rep2


title: epidermis, biol rep 2 - CLIP Sample

description:
ESRP1-CLIP-FLAG-R1P1-R2P1.sites.ucsc.bed
3UTR Sites Unique with Scores_PureCLIP.xlsx
three_prime_utr_peaks.CLIP-FLAG-all.piranha.peak.call.bin.size.10.1.0.covariates2.withHeader.annotated - Copy.xlsx


title: KYSE-30 METTL3KO m6A-IP rep3


title: epidermis, biol rep 2 - Input


title: KYSE-30 FXR1KO_rescuewithKHdeletedFXR1  rep3


title: KYSE-30 METTL3KO m6A-IP rep2


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT 5hmC rep3


title: KYSE-30 METTL3KO_rescuewithMETTL3WT m6A-IP rep3


title: epidermis, biol rep 1 - CLIP Sample


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT 5hmC rep2


title: KYSE-30 Control m6A-IP rep3


title: KYSE-30 METTL3KO m6A-IP rep1


title: epidermis, biol rep 1 - Input


title: KYSE-30 METTL3KO_rescuewithMETTL3WT 5hmC rep3


title: KYSE-30 METTL3KO_rescuewithMETTL3WT 5hmC rep2


title: KYSE-30 METTL3KO_rescuewithMETTL3MUT 5hmC rep1


title: KYSE-30 METTL3KO_rescuewithMETTL3WT 5hmC rep1


title: KYSE-30 Control m6A-IP rep2


title: KYSE-30 METTL3KO 5hmC rep2


title: KYSE-30 Control m6A-IP rep1


title: KYSE-30 METTL3KO 5hmC rep3


title: KYSE-30 METTL3KO 5hmC rep1


title: KYSE-30 METTL3 Control 5hmC rep3


title: Usp21 KO Treg Biol Sample 2

city: Chicago

first: Deyu

last: Fang

address: 303 E Chicago Avenue

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10

extract_protocol:
nTreg cells were sorted from each of the mice using the Foxp3 YFP reporter.RNA was extracted using the RNeasy Micro Kit (Qiagen, Cat# 74004) from sorted Foxp3+ (YFP+) Treg cells from mouse spleens
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: T Regulatory Cells

value: Usp21 Treg KO


title: Usp21 KO Treg Biol Sample 3


title: KYSE-30 FXR1 Control 5hmC rep1


title: KYSE-30 METTL3 Control 5hmC rep2


title: KYSE-30 METTL3 Control 5hmC rep1


title: KYSE-30 shMETTL3 m6A-INPUT rep2

data_processing:
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag and PARCLIP reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling, Piranha was used for CLIP peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file, CpG information file

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). Genomic DNA was isolated with QIAmp DNA Mini kits (Qiagen).
Sequencing libraries for m6A-IP and input were prepared following the manufacturer’s instructions and sequencing was conducted using Illumina HiSeqX Ten PE150 platform. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated paired-end reads (2× 125 bp). CUT&Tag sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions. PAR-CLIP seqiencing was performed in NEBNext small RNA library prep kit (E7330S) and sequenced on Illumina. Hiseq4000.


title: KYSE-30 shMETTL3 m6A-INPUT rep3


title: Usp22/Usp21 dKO Treg Biol Sample 3

value: Usp21/Usp22 Treg KO


title: KYSE-30 TET1KO_TET1_CUTtag

data_processing:
Library strategy: CUT&Tag
Basecalls performed using CASAVA
Sequenced reads were cleaned for adaptor and low-quality sequence, then RIP-seq reads were mapped to hg19 using STAR, CUT&Tag reads using Bowtie2, WGBS was processed by Bismark.
MACS2 was used for m6A and CUT&Tag peak calling
Assembly: hg19
Supplementary files format and content: bigwig file, CpG information file

value: CUT&Tag-seq


title: Usp22/Usp21 dKO Treg Biol Sample 2


title: KYSE-30 TET1Control_TET1_CUTtag


title: KYSE-30 shMETTL3 m6A-INPUT rep1


title: KYSE-30 METTL3KO_METTL3_CUTtag


title: Usp22/Usp21 dKO Treg Biol Sample 1


title: KYSE-30 METTL3Control_METTL3_CUTtag


title: KYSE-30 WT m6A-INPUT rep3


title: KYSE-30 FXR1KO_FXR1_CUTtag


title: WT Treg Biol Sample 3

value: WT


title: KYSE-30 WT m6A-INPUT rep2


title: KYSE-30 FXR1Control_FXR1_CUTtag


title: WT Treg Biol Sample 2


title: KYSE-30 METTL3KO_TET1_CUTtag_rep1


title: Usp21 KO Treg Biol Sample 1


title: KYSE-30 WT m6A-INPUT rep1


title: KYSE-30 METTL3KO_TET1_CUTtag_rep2


title: MS3

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

institute: Jishou University

data_processing:
Reads were filtered to get rid of DNA contamination and low-quality bases using SOAPnuke v1.4.0 software with a setting of “-l 15 -q 0.2 -n 0.1” . Clean reads were mapped to a draft genome (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/310/875/GCA_020310875.1_C.richardii_v2/) using HISAT v2.1.0 with “--dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2”, during which novel transcripts or even genes were identified. Clean reads were also mapped to genes using Bowtie2 v2.2.5 with “-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200” , and then gene expression level was calculated using Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) and the program RSEM. Differential expression was determined from read counts of genes with DEseq2.
Assembly: GCA_020310875.1_C.richardii_v2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ceratopteris richardii

source_name: callus

extract_protocol:
Total RNA was isolated with CTAB method
mRNA was purified using beads linked with polyA tails. Ion cation was used to fragment mRNA and random the N6 primer was used to perform the retro transcription. Double-strand cDNA was ligated to an adapter on both ends and thus amplified. Single-strand DNA was denatured by heating and then undergo circle replication initiated by a splint oligo so that generated tandem repetitive sequences. The single “ball” of DNA was loaded into individual sequencing holes, and two sequencing reactions were performed from different ends via sequencing-by-synthesis to produce 150 bp reads. The DNBSEQ sequencing platform was employed, and it was run by the manufacture BGI (Shenzhen, China).

value: callus

tag: condition

value: differentiating

value: biol rep 3


title: WT Treg Biol Sample 1


title: MS2

value: biol rep 2


title: KYSE-30 METTL3KO_rescuewithWTMETTL3_TET1_CUTtag_rep2


title: KYSE-30 shMETTL3 m6A-IP rep3


title: BA3

value: proliferating


title: MS1

value: biol rep 1


title: KYSE-30 shMETTL3 m6A-IP rep2


title: ht-lib1_14: mc903_bone_marrow_mc

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files  mapped to mm10 using STAR (annotations based on GENCODE M22)
Gene counts were obtained using featureCounts on GENCODE M22 annotations
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts

source_name: mast cells

extract_protocol:
Up to 100 cells of resident mast cells and integrinβ7+ MCs from both ears of NT mice and MC903-treated mice were collected into CDS sorting solution (Takara Bio Inc, Shiga, Japan) using 96 well plate. Then cDNA was synthesized using SMART-Seq HT (Takara Bio Inc) protocol, and purified using Agencourt AMPure XP (Beckman Coulter).
RNA-seq libraries were prepared using Illumina Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA)

value: bone marrow mast cells


title: KYSE-30 METTL3KO_rescuewithmutMETTL3_TET1_CUTtag_rep3

value: sgMETTL3 rescue with mutant METTL3


title: ht-lib1_15: mc903_bone_marrow_mc


title: KYSE-30 shMETTL3 m6A-IP rep1


title: KYSE-30 WT m6A-IP rep3


title: KYSE-30 METTL3KO_rescuewithWTMETTL3_TET1_CUTtag_rep1


title: ht-lib1_11: mc903_bone_marrow_mc


title: KYSE-30 METTL3KO_rescuewithmutMETTL3_TET1_CUTtag_rep2


title: KYSE-30 METTL3KO_rescuewithmutMETTL3_TET1_CUTtag_rep1


title: BA1


title: KYSE-30 METTL3Control_TET1_CUTtag_rep2


title: ht-lib1_10: mc903_resident_mc

value: resident mast cells


title: KYSE-30 WT m6A-IP rep2


title: KYSE-30 WT m6A-IP rep1


title: ht-lib1_09: mc903_resident_mc


title: ht-lib1_08: mc903_resident_mc


title: AR2

city: Beijing

first: baoli

last: lin

address: No.7 Beinong Road

institute: Beijing Agricultural College

description: AR is a healthy red leaf sample from a bud mutation branches of Acer pictum subsp. mono.

data_processing:
The rawdata data measured by small RNA will be evaluated firstly, mainly for spurious filtering and preliminary judgment of the data.
Sequence reads were 1)Removelow quality tags  2)Removetagswith5'primer contaminants  3)Removetagswithout3'primer  4)Removetagswithoutinsertion  5)RemovetagswithpolyA  6)Removetagsshorterthan18nt  7)Summarizethelengthdistributionofthecleantags
We used the alignment software AASRA to align clean reads to the reference base and other small RNA databases, except  except for Rfam which was matched using cmsearch.
Assembly: FASTA file for novel small RNAs included on series record.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Acer pictum subsp. mono

source_name: leaf cells

growth_protocol: Both wild-type branch leaves and mutant branch leaves of Acer pictum subsp. mono grow in the wild under natural conditions.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The Small RNA Sample Pre Kit was used to construct the library, using the special structure of the 3' and 5' ends of Small RNA (complete phosphate group at the 5' end and hydroxyl group at the 3' end), and using total RNA as the starting sample. After PCR amplification, the target DNA fragments were separated by PAGE gel electrophoresis, and the cDNA library was obtained by cutting and recycling.

treatment_protocol: Two leaves grown in the wild in their natural state were collected and stored in an ultra-low temperature refrigerator at -80 degrees Celsius without any treatment.

value: leaf cells

tag: leaf color

value: red

value: Day 0


title: AR1


title: ht-lib1_07: mc903_resident_mc


title: KYSE-30 METTL3KO_rescuewithWTMETTL3_FXR1_CUTtag_rep3

value: sgMETTL3 rescue with wild type METTL3


title: ht-lib1_13: mc903_bone_marrow_mc


title: PART1 R3

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

data_processing:
Basecalls performed using CASAVA version 1.4
aligned to the hg19 genome assembly using Bowtie2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Exel files include RPKM values for each Sample ...

source_name: MGC-803 cells

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The MGC-803 cells were transfected by lncRNA PART1 and blank vector as control.

tag: passages

tag: shRNA


title: ht-lib1_06: mc903_resident_mc


title: PART1 R2


title: BA2

tag: replicate


title: KYSE-30 METTL3KO_rescuewithWTMETTL3_FXR1_CUTtag_rep2

treatment_protocol: Short hairpin RNA (shRNA) targeting METTL3, TET1, FXR1 or scramble control or plasmids was commercially synthesis and transfected using lipofectamine 3000 (Life Technologies). Stable knockdown cells were generated by lentiviral infection and puromycin selection.

tag: cell line


title: Control

value: control


title: KYSE-30 METTL3KO_rescuewithWTMETTL3_FXR1_CUTtag_rep1


title: ht-lib1_05: nt_resident_mc

value: nt


title: AG1

description: AG is a healthy green leaf sample from a bud mutation branches of Acer pictum subsp. mono (15-20 days ahead of color change) we found.

value: green


title: AR3


title: KYSE-30 METTL3KO_rescuewithmutMETTL3_FXR1_CUTtag_rep2

value: CUT&Tag-seq


title: 07 H23_OPN

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lung

value: cancer cell

value: Cocultured with 10ng/mL of SPP1/osteopontin for 24 hours.


title: ht-lib1_03: nt_resident_mc


title: 06 H23_Mac CM

value: Cocultured with 30% of conditioned medium of macrophages for 24 hours.


title: KYSE-30 METTL3KO_rescuewithmutMETTL3_FXR1_CUTtag_rep1

first: shuang

last: deng

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center


title: KYSE-30 METTL3Control_TET1_CUTtag_rep1

value: wild type


title: KYSE-30 METTL3KO_FXR1_CUTtag_rep3


title: LVS ∆rpsU2 pF-rpsU2-V B

city: Kingston

first: Kathryn

middle: M

last: Ramsey

state: RI

address: 7 Greenhouse Road

department: CMB / BPS

institute: University of Rhode Island

data_processing:
mapping: bowtie2 version 2.2.4 (bowtie2 -N 1 -L 20 -i S,1,0.50 -D 20 --non-deterministic --no-mixed --no-discordant --no-unal )
read counting: HTSeq version 0.11.2 (htseq-count -s reverse -a 1 -t gene -m intersection-nonempty --nonunique all -i locus_tag )
Differential gene expression analysis: DESeq2 version 1.32.0
Assembly: NC_007880
Supplementary files format and content: tab-delimited text files include read count for each feature

organism: Francisella tularensis subsp. holarctica LVS

source_name: bacterial cell

growth_protocol: Cells were collected from mid-log cultures (OD600 0.3-0.4).

extract_protocol:
Nucleic acids were isolated using the Direct-Zol RNA purification kit (Zymo Research) according to the manufacturer’s protocol. Purified nucleic acids were treated with RQ1 Dnase (Promega) for 1 hour at 37°C and RNA was purified with the Direct-Zol RNA purification kit.
Approximately 1.5 μg of RNA isolated as above was sent to the Microbial Genome Sequencing Center (MiGS). After using RiboZero Plus rRNA depletion, libraries were made using Illumina Stranded RNA library preparation and sequenced for a minimum of 12 million paired end reads.

value: bacterial cell

tag: growth phase

value: mid-log

value: {delta}rpsU2 pF-rpsU2-V


title: LVS ∆rpsU2 pF-rpsU2-V C


title: AG3


title: LVS ∆rpsU2 pF C

value: {delta}rpsU2 pF


title: PART1 R1


title: AG2

value: leaf cells


title: 04 HepG2+Mac

source_name: Liver

value: Liver

value: Cocultured with macrophages


title: ht-lib1_01: nt_resident_mc

value: resident mast cells


title: KYSE-30 METTL3KO_FXR1_CUTtag_rep2

city: Guangzhou


title: LVS ∆rpsU2 pF A


title: 02 Huh6+Mac


title: KYSE-30 METTL3KO_FXR1_CUTtag_rep1


title: 03 HepG2

value: Control


title: ht-lib1_04: nt_resident_mc

value: nt


title: LVS pF C

value: WT pF


title: LVS pF A


title: KYSE-30 METTL3Control_FXR1_CUTtag_rep1

value: CUT&Tag-seq


title: 408, 8 Gy, DMC, Day 7, rep2

description:
16_408_8Gy_Dmc_2
iGPC
Radiation, single dose of 8 Gy DMC Day 7 replicate 2

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to GRCh38 using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

source_name: 408, 8 Gy, DMC, Day 7

growth_protocol: Cells were maintained in growth media containing DMEM:F12 with B27 supplement and Pen-strep containing growth factors EGF and FGF, and sorted GEC and GPC were maintained in endothelial media and pericyte media respectively.

extract_protocol:
RNA extraction was performed using Qiagen RNEasy Microkit
cDNA libraries were prepared using TruSeq Stranded RNA (100ng) + Ribozero Gold

treatment_protocol: Cells infected with CDH5-mCherry and DES-mCherry were radiated and FACS sorted using mCherry at 7 days.

value: GBM cells

tag: cell type (sorted)

value: GPC

tag: time

value: Day 7

value: Radiation, single dose of 8


title: KYSE-30 FXR1KO_TET1_CUTtag_rep2


title: 05 H23_CT

value: Lung

value: cancer cell


title: ht-lib1_02: nt_resident_mc


title: 408, 8 Gy, DMC, Day 7, rep1

description:
15_408_8Gy_Dmc_1
iGPC
Radiation, single dose of 8 Gy DMC Day 7 replicate 1


title: A11_N_3

city: Kunming

first: Xuemei

state: Yunnan

address: wuhuaqu

institute: majorbio

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample
Supplementary files format and content: Expression analysis table include TPM values for each WT and Atg11 sample
Supplementary files format and content: Total difference statistics between WT and Atg11 mutants

organism: Orbilia oligospora

source_name: Fungal hyphae cells

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Fungal hyphae cells

value: deltaAoatg11 mutant strain

value: Nitrogen deficiency induction


title: KYSE-30 FXR1KO_TET1_CUTtag_rep1


title: A11_N_2


title: KYSE-30 FXR1KO_rescuewithKHdeletedFXR1_TET1_CUTtag_rep2

value: sgFXR1 rescue with KHdeleted FXR1


title: 408, 8 Gy, VMC, Day 7, rep1

city: Los Angeles

first: Riki

address: 760 Westwood Plaza, Room 37-420

institute: University of California, Los Angeles

description:
11_408_8Gy_Vmc_1
iGEC
Radiation, single dose of 8 Gy VMC Day 7 replicate 1

source_name: 408, 8 Gy, VMC, Day 7

value: GEC


title: 408, 8 Gy, VMC, Day 7, rep2

description:
12_408_8Gy_Vmc_2
iGEC
Radiation, single dose of 8 Gy VMC Day 7 replicate 2


title: 408, 8 Gy, Day 7, rep2

description:
4_408_8Gy_2
8 Gy
Radiation, single dose of 8 Gy Day 7 replicate 2


title: KYSE-30 METTL3Control_FXR1_CUTtag_rep2

value: wild type


title: KYSE-30 FXR1KO_rescuewithFXR1WT_TET1_CUTtag_rep2

value: sgFXR1 rescue with wild type FXR1


title: 408, 0 Gy, DMC, Day 7, rep2

description:
14_408_0Gy_Dmc_2
nGPC
Untreated DMC Day 7 replicate 2

source_name: 408, 0 Gy, DMC, Day 7

value: Untreated


title: WT_N_2


title: KYSE-30 FXR1KO_rescuewithFXR1WT_TET1_CUTtag_rep1


title: 01 Huh6

value: Liver

value: Control


title: KYSE-30 FXR1Control_TET1_CUTtag_rep2

value: CUT&Tag-seq


title: LVS pF B

value: bacterial cell

value: mid-log

value: WT pF


title: 408, 8 Gy, Day 7, rep1

description:
3_408_8Gy_1
8 Gy
Radiation, single dose of 8 Gy Day 7 replicate 1

value: GBM cells

value: Day 7

value: Radiation, single dose of 8


title: KYSE-30 FXR1Control_TET1_CUTtag_rep1


title: KYSE-30 FXR1KO_rescuewithKHdeletedFXR1_TET1_CUTtag_rep1


title: A11_0_3

value: Fungal hyphae cells

value: no treatment


title: A11_0_2

value: deltaAoatg11 mutant strain


title: 408, 0 Gy, DMC, Day 7, rep1

description:
13_408_0Gy_Dmc_1
nGPC
Untreated DMC Day 7 replicate 1

value: GPC


title: WT_N_1

value: Nitrogen deficiency induction


title: 408, 0 Gy, VMC, Day 7, rep2

description:
10_408_0Gy_Vmc_2
nGEC
Untreated VMC Day 7 replicate 2

source_name: 408, 0 Gy, VMC, Day 7

value: GEC