title: Sample 20

value: Female

value: classic-NAFLD

value: NAFLD/NASH

value: yes

tag: hdl-cholesterol

tag: ldl-cholesterol


title: st21_dorsal_TAF3_Dam_rep1

status: Public on Oct 23 2024

type: SRA

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

country: United Kingdom

institute: The Gurdon Institute

description: TAF3-phd(H3K4me3)-Dam fusion

library_source: genomic

data_processing:
Analysis was perfomed with damidseq_pipeline script which uses bowtie2 to align reads to given genome, extends the reads until 300bp or the next GATC site, bins the reads into GATC fragments and normalises against Dam-Only control.
Replicates of normalised bedgraphs were quantile normalised to each other, averaged and backtransformed.
Averaged bedgraphs were converted into bigwig format.
Assembly: mm10, dm6, Xla.v9.1
Supplementary files format and content: The processed data are quantile normalised and averaged bigwig files, generated as described.
Library strategy: DamID-Seq

molecule: genomic DNA

organism: Xenopus laevis

source_name: stage 21 embryos (dorsal injection)

extract_protocol:
For Drosophila DamID, 20-50 third instar larval brains were dissected. For mouse samples, in utero electroporation with DamID plasmids was performed on E13.5 embryos. Electroporated cortex was microdissected. For Xenopus samples, mRNA was injected into stage 11 or stage 21 embryos. All tissue collections were followed by genomic DNA extraction with Qiagen DNAeasy blood and tissue kit and processed for DamID according to previous protocols before library prep.
Samples prepared for Illumina sequencing according to a modified TruSeq protocol.

tag: tissue

value: stage 21 embryos (dorsal injection)


title: Sample 19

city: Santander

first: Enrique

last: García Nieto

state: Cantabria

address: C. Cardenal Herrera Oria, s/n

country: Spain

institute: Instituto de Investigación Marqués de Valdecilla

library_source: transcriptomic

data_processing:
Genes were quantified using RSEM (version 1.3.0) with default parameters.
The human gene annotation file was downloaded from gencode release 36 (https://www.gencodegenes.org/).
Mapping and quantification quality checking were performed with GEMTools (https://gemtools.github.io/) and custom python scripts.
A multidimensional scaling plot was performed to inspect sample similarities using the ‘voom’ transformed counts and the top 500 most variable genes.
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: EGN_RNAseq_Normalized_data: Excel file incuding gene normalized expression for each sample.
Supplementary files format and content: EGN_RNAseq_Processed_data: Differential gene expression (IMID-NAFLD vs. Classic-NAFLD) adjusted for BMI, sex, and fibrosis severity.

molecule: total RNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Liver biopsies were obtained percutaneously with a Tru-Cut biopsy needle following a standard procedure in patients with suspected significant liver fibrosis according to liver stiffness measurement (LSM).

extract_protocol:
Freshly frozen biopsies were disrupted using Kimble® Pellet Pestle® Cordless Motor (DWK Life Sciences, Cat. No.: 749540-0000). RNA extraction was performed using the PureLink™ RNA Mini Kit (Invitrogen, Cat. No.: 12183018A) adding an extrapurification process with the PureLink™ DNase Set (Invitrogen, Cat. No.: 12185010).
RNA-seq reads were mapped against the human reference genome (GRCh38) using STAR (version 2.5.3a) with ENCODE parameters.

treatment_protocol: Total RNA was obtained from freshly frozen biopsies

value: Liver

tag: Sex

value: Male

tag: case/control

value: IMID-NAFLD

tag: disease

value: NAFLD & IBD

tag: fibrosis degree

tag: obesity

value: no

value: No

tag: hypertension

tag: fasting glycemia

tag: total cholesterol

tag: tryglicerides


title: st21_ventral_TAF3_Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion

source_name: stage 21 embryos (ventral injection)

value: stage 21 embryos (ventral injection)


title: RPE, 14 days post torpor, Rep3

city: Baltimore

first: Kurt

last: Weir

address: 733 North Broadway

country: USA

institute: Johns Hopkins School of Medicine

data_processing:
de novo transcriptome generation with Trinity v2.13.1
alignment with Bowtie2 v2.4.1
quantification with RSEM v1.2.15
Assembly: de novo transcriptome
Supplementary files format and content: .Robj file containing matrix with RSEM expression values for each gene in each sample

organism: Ictidomys tridecemlineatus

source_name: Retinal pigment epithelium

extract_protocol:
Total RNA was isolated with the miRNeasy micro kit with an optional DNase step, per the manufacturer’s protocol (Qiagen, Hilden, Germany)
The total RNA was used to generate cDNA libraries with the Illumina TruSeq stranded Total RNA kit

value: Retinal pigment epithelium

tag: condition

value: 14 days post torpor


title: RPE, 14 days post torpor, Rep4


title: 0001-0020_Screening

type: RNA

city: London

first: Rose

last: Hodgson

address: 2 Monnery Road

institute: MiNA Therapeutics

hyb_protocol: RNA expression profiling was performed using the nCounter ®PanCancer IO360 Profiling Panel from NanoString (NanoString Technologies, Seattle, USA). The PanCancer IO360 Profiling Panel contains 770 probes. Hybridization was performed according to manufacturer’s instructions. Hybridized probes were then purified and immobilized on a streptavidin-coated cartridge using the nCounter Prep Station (NanoString Technologies).

scan_protocol: Data collection was carried out on the nCounter Digital Analyzer (NanoString Technologies) following the manufacturer’s instructions to count individual fluorescent barcodes and quantify target RNA molecules present in each sample. For each assay, a scan of 490 fields of view was performed.

data_processing: The quality control enable to keep good quality data with a binding density that range between 0.05 to 2.25. The linearity of positive controls was checked using the R2 of regression between the counts and the concentration of positive controls. No samples were removed from analysis based on a threshold of R2 < 0.75. Unwanted variation was determined by specifying the following housekeeping genes as controlGenes within the DESeq2 v1.36.0 estimateSizeFactors function and as negative control genes within RUVSeq v1.30.0 function RUVg: “UBB”, “PUM1”, “TLK2”, “DNAJC14”, “SF3A1”, “POLR2A”, “SDHA”, “STK11IP”, “NRDE2”, “TBP”, “OAZ1”, “TBC1D10B”, “GUSB”, “PSMC4”, “TMUB2”, “MRPL19”, “G6PD”,”ERCC3”. These factors were included in both data normalisation and transformation by Variance Stabilising transformation (VST) for data visualisation.

source_name: Colon

extract_protocol: RNA was extracted from FFPE tissues using QIAGEN RNeasy FFPE extraction kits (QIAGEN GmbH, Hilden, Germany). Annotations from the pathologist performing H&E staining were used to guide removal of normal tissue from the slides by spectrophotometry prior to nucleic acid extraction, which occurred after tissue deparaffinization and lysis. Each extracted RNA was independently quantified using a NanoDrop spectrophotometer (NanoDrop Technologies, Oxfordshire, UK) and quality checked (Agilent Bioanalyzer, Santa Clara, United States). Degradation assessment was quantified as the percentage of RNA fragments smaller than 300 base pairs using RNA 6000 Nano Kit (Agilent Bioanalyzer, Santa Clara, United States). Good sample quality was defined as less than 50% of RNA fragments of 50 to 300 base pairs in size.

tag: outcome

value: PD


title: Sample 18


title: RPE, 14 days post torpor, Rep2


title: st21_ventral_Dam_rep1

description: Dam-Only control


title: 0001-0017_Screening

source_name: ExtrahepaticCholangiocarcinoma


title: Sample 17


title: Sample 21


title: RPE, 14 days post torpor, Rep1


title: st11_TAF3_Dam_rep3

description: TAF3-phd(H3K4me3)-Dam fusion

source_name: stage 11 embryos

value: stage 11 embryos


title: Sample 16


title: 0001-0017_C2D16


title: Sample 15


title: st11_TAF3_Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion


title: 0001-0016_Screening

source_name: Ovarian


title: 0001-0015_C2D16

source_name: Recto-sigmoid


title: st_11_Dam_rep2

description: Dam-Only control


title: Sample 14


title: RPE, 3 days post torpor, Rep6

value: 3 days post torpor


title: st11_TAF3_Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion


title: RPE, 3 days post torpor, Rep4


title: 0001-0015_Screening


title: 0001-0016_C2D16


title: Sample 13

value: Female


title: st_11_Dam_rep1

description: Dam-Only control


title: K18_BA.1

city: La Jolla

first: Lars

last: Pache

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Adapters and Barcodes from the raw reads were trimmed using Porechop tool
Triimed reads were mapped with reference genome using minimap2
Mapped reads were further sortted and indexed using Samtools
Indexed reads in bam files used to generate FPKM values for each genes using FeatureCounts tool
FPKM counts from all smaples were combined together in gene_count_FPKM.csv file
Assembly: GRCm39
Supplementary files format and content: comma sperated value file include FPKM values of each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Bronchoalveolar lavage

extract_protocol:
RNA was isolated using TriZol method, followed by poly-A RNA enrinchmenrt using NEB's NEBNext® Poly(A) mRNA Magnetic Isolation Module
Library was prepared by using Oxford's cDNA-PCR Sequencing Kit (SQK-PCS111) following manufacture's protocol

value: Bronchoalveolar lavage

tag: cell type

tag: genotype

value: WT

tag: treatment

value: BA.1 infection

tag: time

value: Day 30


title: RPE, 3 days post torpor, Rep3


title: Sample 12

value: Liver

value: yes

tag: hdl-cholesterol

tag: ldl-cholesterol


title: 129S1_BA.1

tag: tissue


title: RPE, 3 days post torpor, Rep2


title: 0001-0012_C2D16

source_name: OvarianSerousCarcinoma


title: Sample 10

tag: Sex

value: Male

tag: case/control

value: IMID-NAFLD

value: NAFLD & Psoriasis


title: RPE, 3 days post torpor, Rep1


title: Sample 11

tag: disease

value: NAFLD & Hidradenitis

tag: fibrosis degree

value: No


title: RPE, 3 days post torpor, Rep5

value: Retinal pigment epithelium


title: RPE, Torpor, Rep6

value: Torpor


title: 0001-0012_Screening

value: PD


title: 0001-0011_Screening

source_name: Oesophago-gastricAdenocarcinoma

value: SD


title: RPE, Torpor, Rep5


title: Sample 9

tag: obesity

value: no

tag: hypertension


title: Sample 8

tag: fasting glycemia

tag: total cholesterol


title: 72h IFM expressing Antp Replicate 6

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description: Act88F-Gal4 pupal IFM expressing Antp at 72h APF

data_processing:
Base calling was performed using bcl2fastq
Reads were uniquely mapped to the dm6 genome using subread-align (Subread package) on the command line using default parameters
Reads aligning to dm6 (release r6.42) exons were counted using featureCounts (Subread package) with stranded features turned on using otherwise default paramters
Differentially expressed genes were called using DESeq2 (version 1.34)
Assembly: dm6
Supplementary files format and content: Differentially expressed genes from DESeq2 analyses in tab-delimited plain text format
Supplementary files format and content: Raw stranded exon counts in tab-delimited plain text format

organism: Drosophila melanogaster

source_name: 72h APF pupal dissected IFM

extract_protocol:
Act88F-GAL4 driving expression of UAS-GFP or UAS-Ant  pupa were staged at 25°C and dissected in ice-cold PBS. The dissection was performed according to a published protocol (Weitkunat and Schnorrer, 2014). Hand-isolated IFM from 6 to 8 pupa were directly collected in the kit-provided Lysis buffer supplemented with 2-Mercaptoethanol (#M6250, Sigma), homogenised with a small pestle and RNA was extracted using RNA extraction Microkit (#74004, Qiagen).
RNA-Seq libraries were generated from polyA RNA using the Illumina SMARTer Stranded RNA-seq Kit strictly according to manufacturer's instructionsand 15 PCR cycles for amplification.

value: 72h APF pupal dissected IFM

value: Antp expressing


title: 0001-0009_C2D16

source_name: EccrineAdenocarcinoma


title: 72h IFM expressing Antp Replicate 5


title: RPE, Torpor, Rep4

tag: condition


title: BY-2-CAP: BY4741-CAP-rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: 5'CaPseq for wildtype replicate 2

data_processing:
Library strategy: 5PSeq
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
For HT-5Pseq data, HT-5Pseq reads were trimmed 3’-sequecing adapter using cutadapt V1.16.  The 8-nt random barcodes on the 5’ ends of reads were extracted and added to the header of fastq file as the UMI using UMItools (v0.5.4). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome by star/2.7.0  with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5’ end. Duplicated 5’ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMItools (v0.5.4).
For The distribution of nucleotide position of 5’ends were performed using Fivepseq package (PMID: 33575643), including relative to start, stop codon and codon specific pausing. Specifically, the unique 5’mRNA reads in biological samples were summed up and normalized to reads per million (rpm). Then the relative position of 5’mRNA reads to all codons of all ORF were summed at each position. The metagene plot was showed as the sum value versus the relative distance from respective codon.
Genome_build: Saccharomyces cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Yeast cells were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30ºC. Pre-cultures were grown overnight in 250 mL flasks and agitated at 190 rpm. The next day, pre-cultures were diluted to OD600 = 0.05 and grown until an OD600 of ~0.5 was reached.

extract_protocol:
Total RNA was isolated by the standard phenol: chloroform method, and DNA was removed by DNase I treatment. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
HT-5Pseq libraries were prepared as previously (PMID: 33870233). In brief, 6 μg of DNA-free total RNA were directly ligated with RNA/RNA oligo containing UMI (RNA rP5_RND oligo). Ligated RNA was reverse transcribed and primed with Illumina PE2 compatible oligos containing random hexamers and oligo-dT. RNA in RNA/DNA hybrid was depleted by sodium hydroxide with 20 min at 65 degree incubation. Ribosomal RNAs were depleted using DSN (Duplex-specific nuclease) with the mixture of ribosomal DNA probes. Samples were amplified by PCR and sequence in an Illumina NextSeq 500 instrument using 60 sequencing cycles for read1 and 15 cycles for read 2. For 5’Cap-seq, 5’capped mRNAs were captured as previous described (cite Pelechano et.al 2016). Specifically, 10 µg total RNA were treated with calf intestinal alkaline phosphatase (NEB, CIP) to remove 5′P molecules (fragmented and non-capped). After purification, mRNA 5’cap were removed by Cap-Clip (Biozyme), resulting in 5’P molecules from previously capped molecules. The following steps is the same as the one described for HT-5Pseq (see above) with variations only for skipping removing ribosomal RNA.

treatment_protocol: Yeast cells at OD600 of ~0.5 were recovered by centrifugation and flash-frozen in liquid nitrogen.

tag: parental strain

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)


title: RPE, Torpor, Rep3


title: 72h IFM expressing Antp Replicate 4


title: Sample 6

value: NAFLD & IBD

tag: tryglicerides


title: Sample 7

value: Female


title: K18_mock

value: Bronchoalveolar lavage

tag: cell type

tag: genotype

value: WT

value: Mock Infection

value: Day 30


title: 0001-0020_C2D16

tag: outcome


title: 0001-0009_Screening


title: 72h IFM expressing GFP Replicate 3

description: Act88F-Gal4 pupal IFM expressing GFP (WT) at 72h APF

tag: treatment

value: GFP expressing


title: 0001-0011_C2D16


title: wt_3: BY4741 _rep3

description: HT-5Pseq for wildtype replicate 2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: 129S1_mock

tag: time


title: Sample 5

tag: tissue

value: Liver

value: classic-NAFLD

value: NAFLD/NASH

value: yes

tag: hdl-cholesterol

tag: ldl-cholesterol


title: wt_2: BY4741 _rep2

description: HT-5Pseq for wildtype replicate 2


title: RPE, Torpor, Rep1

value: Retinal pigment epithelium

value: Torpor


title: 72h IFM expressing GFP Replicate 2

value: 72h APF pupal dissected IFM


title: Sample 4

tag: Sex

value: Male

tag: case/control

tag: disease

value: No


title: RPE, Torpor, Rep2


title: 72h IFM expressing GFP Replicate 1


title: RPE, Prehibernation, Rep6

value: Prehibernation


title: Sample 3

tag: fibrosis degree

tag: obesity

tag: hypertension


title: BY-1-CAP: BY4741-CAP-rep1

description: 5'CaPseq for wildtype replicate 1

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)


title: wt_1: BY4741 _rep1

description: HT-5Pseq for wildtype replicate 1


title: Sample 2

tag: fasting glycemia

tag: total cholesterol


title: NLS_3: Xrn1-ΔNLS1_rep3

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking NLS1  replicate 3

value: BY4741, Xrn1-{delta}NLS1

tag: parental strain


title: wrky82-m2, imbibed embryo, biol rep 3

city: St Paul

first: Nathan

last: Springer

state: MN

address: 1479 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota

data_processing:
nf-core RNA-seq pipeline Nextflow v20.10.0 for initial QC and raw read counting
Reads were trimmed using Trim Galore! v0.6.5 and aligned to the W22 reference genome using Hisat2 v2.1.0 with default parameters (hisat2 -x $db $input -p 12 --met-stderr --new-summary). Uniquely aligned reads were counted per feature by featureCounts v2.0.1.
Raw read counts were normalized by library size and corrected for library composition bias using the TMM normalization approach in edgeR v3.28.0 to give CPM (Counts Per Million reads) for each gene in each sample. CPM values were normalized by W22 gene CDS lengths to give FPKM (Fragments Per Kilobase of exon per Million reads) values.
Genes were considered expressed if their CPM was ≥ 1 in at least one sample per tissue
Assembly: Zea mays W22
Supplementary files format and content: Tab-delimited text file includes raw read counts, TMM normalized CPM values, FPKM values for each W22 gene in every sample. The B73v4 gene ID is recorded for W22 genes with one-to-one gene models between W22 and B73v4. The expressed column indicates if the W22 gene was considered expressed in our experiment (TRUE or FALSE). The filtered_DE column indicates if the gene was filtered from the differential expression analysis (TRUE = filtered out, FALSE = included). See Materials and Methods: Identification of TF mutant allele DE genes for further description.

organism: Zea mays

source_name: imbibed embryo

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit
Paired-end libraries were prepared from a minimum of 500 ng of total RNA using the standard Illumina TruSeq Stranded mRNA library protocol. Single-end libraries were prepared from 2 µg of total RNA using the Illumina TruSeq RNA Sample Prep Kit

value: imbibed embryo

tag: developmental stage

value: R6, ~60 days after pollination, harvested and dried seed

tag: age

value: 140 days after sowing

tag: uniformmu id

value: mutant


title: wrky82-m2, imbibed embryo, biol rep 2

tag: genotype

tag: treatment


title: NLS_2: Xrn1-ΔNLS1_rep2

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking NLS1  replicate 2


title: RPE, Prehibernation, Rep5

tag: tissue

tag: condition


title: wrky82-m2, imbibed embryo, biol rep 1


title: Sample 1

tag: hdl-cholesterol

tag: ldl-cholesterol

tag: tryglicerides


title: wrky87-m1, imbibed embryo, biol rep 3


title: LNCap,CSS,6M,rep3

city: Jinan

first: Qianqian

last: Zhou

state: Shandong Province

address: 44 Wenhua Xi Rd.

country: China

institute: Shandong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: prostate

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

tag: cell line

value: LNCaP

tag: cell type

value: prostate cells

value: WT


title: RPE, Prehibernation, Rep3


title: NLS2_1b: Xrn1-ΔNLS2_rep2

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking NLS2  replicate 2

value: BY4741, Xrn1-{delta}NLS2


title: RPE, Prehibernation, Rep2

value: Retinal pigment epithelium


title: NLS_1: Xrn1-ΔNLS1_rep1

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking NLS1  replicate 1


title: LNCap,CSS,6M,rep2


title: wrky87-m1, imbibed embryo, biol rep 2


title: RPE, Euthermia, Rep4

value: Euthermia


title: LNCap,FBS,6M,rep3


title: NLS2_1a: Xrn1-ΔNLS2_rep1

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking NLS2  replicate 1


title: LNCap,CSS,6M,rep1


title: RPE, Prehibernation, Rep1


title: RPE, Prehibernation, Rep4


title: NLS1_NLS2_2: Xrn1-ΔNLS1&NLS2_rep2

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking both NLS sequences  replicate 2

value: BY4741, Xrn1-{delta}NLS1&NLS2


title: wrky82-m1, imbibed embryo, biol rep 3


title: RPE, Euthermia, Rep3


title: NLS1_NLS2_1: Xrn1-ΔNLS1&NLS2_rep1

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking both NLS sequences  replicate 1


title: LNCap,FBS,6M,rep2


title: Liver, 14 days post torpor, Rep3

value: Liver

value: 14 days post torpor


title: wrky82-m1, imbibed embryo, biol rep 1


title: NLS1_NLS2_3: Xrn1-ΔNLS1&NLS2_rep3

description: HT-5Pseq for  xrn1Δ  transformed with a version lacking both NLS sequences  replicate 3


title: x-Y3b: xrn1∆ + YCpLac33_rep3

description: HT-5Pseq for xrn1Δ transformed with empty vector (YCpLac33) replicate 3


title: LNCap,FBS,6M,rep1


title: RPE, Euthermia, Rep2


title: wrky82-m1, imbibed embryo, biol rep 2


title: Retina, 14 days post torpor, Rep6

source_name: Retina

value: Retina


title: HCT116_Cl3_shU1_Baseline_D14_K27me3_R2

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description:
Clone3_NoDox_H3K27me3_shared_peaks_coordinate.bed
Clones_H3K27me3_shared_peaks_coordinates.bed

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).
ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.5.0) and quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) and were deduplicated using removeDups from samblaster (v.0.1.24) (144). Aligned BAM files were used for quality control analysis with “deeptools” (v3.2.0) ‘plotFingerprint’ and ‘plotPCA’ functions. Aligned SAM files were then processed for pair-end reads with high mapping quality (MAQ >= 20).
Peaks were called with EDD (Enriched Domain Detector) with default parameters for each individual sample. Conserved peaks between biological duplicates were determined by calculating the proximity of replicate 1 peaks to replicate 2 peaks  using the ‘closest’ command from “bedtools” (v2.25.0). Peaks were considered conserved among biological replicates if the peaks overlapped or were within 200 bp of each other.
Assembly: hg38
Supplementary files format and content: *.bed; contains genomic coordinates for all reproducible peaks

growth_protocol: HCT116 colon cancer cell line was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol:
Cells  were fixed in buffer (1% formaldehyde, 50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min at room temp with shaking and then quenched with 125 mM glycine 5 min at room temp. Cells were scraped into cold PBS, washed 2X with cold PBS, flash frozen in liquid N2, and stored at -80°C until use. Thawed pellets were lysed in LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche protease inhibitor cocktail) for 20 min with rotation at 4°C and cleared by centrifugation at 300 x g for 5 min at 4°C. Supernatant with intact nuclei was set aside. Cell pellets were lysed again in 4x LB1 (LB1 with 2% NP-40 and 1% Triton X-100) for 20 min. Intact nuclei from this and the saved supernatant were collected by centrifugation at 1,700 x g for 5 min at 4°C, resuspended and washed in LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 min with rotation at 4°C, and collected again by centrifugation at 1,700 x g for 5 min at 4°C. Nuclei were gently rinsed 2x with LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) without disturbing the pellet. Nuclei were resuspended in 1 mL LB3 and transferred to a 1 ml milliTUBE (Covaris). Chromatin was sheared to a range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 450 µg of chromatin was brought to 500 µL in LB3 and 500 µL of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added. Prepared chromatin was pre-cleared by incubation with 20 µL of pre-washed Dynabeads Protein G magnetic beads (Invitrogen, 10004D) for 3 hours at 4°C with rotation. After bead removal, 10% input (100 µL) of pre-cleared chromatin was removed and set aside. Pre-cleared chromatin was immunoprecipitated with 5 µL of H3K27me3 antibody (Cell Signaling 9733) or 5 ul of H3K9me3 (Active Motif 39161) overnight at 4°C with constant rotation. Protein G magnetic beads (35 µL/IP) were blocked in buffer containing PBS, 0.5% BSA, and 20 µg Herring Sperm DNA (Sigma, D7290) with rotation at 4°C overnight. Blocked beads were washed 3X with PBS and 0.5% BSA and 2X with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours with rotation at 4°C. Bead-immuno-chromatin complexes were then washed 3X for 5 min with rotation at 4°C with WB1, 3X with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2X with WB1, and 1X with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were incubated in 50 µl of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) at 65°C for 15 min in 50 µL volume to elute immuno-chromatin complexes. The elution step was repeated, and eluates combined. Eluents and input were incubated overnight at 65°C with constant shaking to reverse crosslinks, followed by incubation at 37°C for 1 hour with DNase-free RNase A, then at 37°C for 2 hours with 10 µL of Proteinase K (20 mg/mL stock). DNA was isolated with a 1.5x ratio of KAPA Pure Beads (KAPA Biosystems KK8000) to DNA volume.
Immunoprecipitated fragments and saved inputs were quantified with a Qubit dsDNA High Sensitivity Assay kit (Invitrogen Q32851), and 10 ng of purified DNA for each IP and input sample were used for library preparation with the KAPA Hyper Prep Kit (Kapa Biosystems KR0961). TAZ and Combo treatments required two IPs per biological replicate to attain enough material for library preparation, and this doubling has been accounted for in the parameters for siQ-ChIP (88,89) for these samples. Library preparation including fragment end-repair, A-tail extension, and adapter ligation was conducted per the manufacturer’s instructions (KAPA). Adapter-ligated fragments were amplified with 11 cycles following the recommended thermocycler program, and DNA was purified with two rounds of purification using KAPA Pure Beads (KK8000). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 75 bp, paired end sequencing was performed on an Illumina NextSeq 500 sequencer using a 150 bp HO sequencing kit (v2) (Illumina Inc., San Diego, CA, USA) or 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit to a minimum read depth of 50M read pairs per IP library and 100M read pairs per Input library.

treatment_protocol: In all cases, Baseline (or NoDox) samples were grown in culture for 2 weeks in the absence of doxycycline, and serve as the baseline methylome control for Knockdown and Recovery samples. Knockdown samples were treated with doxycycline (10 ng/mL) for two weeks to induce expression of the shRNA. Recovery samples were treated with doxycycline for two weeks (to induce knockdown of the target protein), and then doxycycline was removed for an additional two weeks to measure recovery methylation dynamics with re-expression of the either UHRF1 or DNMT1. Transgenes for WT and mutant UHRF1 and DNMT1 were stably introduced into the clonally expanded Cl9 shUHRF1 and Cl3 shDNMT1 cell lines, respectively. Doxycycline treatment (10 ng/mL) over 2 weeks depleted the endogenous enzyme in the presence of the transgene protein cover.

value: Colorectal Carcinoma epithelial cells

value: Doxycycline-inducible shRNA against UHRF1

value: No Doxycycyline for 14 days

tag: antibody

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)

tag: sequence length

value: 2 x 50 bp


title: wrky8-m2, imbibed embryo, biol rep 2

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: wrky8-m2, imbibed embryo, biol rep 3


title: wrky87-m1, imbibed embryo, biol rep 1


title: Retina, 14 days post torpor, Rep5


title: x-Y1: xrn1∆ + YCpLac33_rep1

description: HT-5Pseq for xrn1Δ transformed with empty vector (YCpLac33) replicate 1


title: HCT116_Cl3_shU1_Baseline_D14_K27me3


title: x-L3: xrn1∆ + pLCM9_rep3

description: HT-5Pseq for  xrn1Δ  transformed with Rat1∆NLS-Xrn1-Cterm-3xFLAG replicate 3

value: xrn1{delta} + pLCM9 (YCpLac33+ Rat1{delta}NLS-Xrn1-Cterm-3xFLAG)

tag: construct


title: Retina, 14 days post torpor, Rep4


title: HCT116_Cl3_shU1_Baseline_D14_K9me3_R2

description:
Clone3_NoDox_H3K9me3_shared_peaks_coordinate.bed
Clones_H3K9me3_shared_peaks_coordinates.bed


title: x-L2: xrn1∆ + pLCM9_rep2

description: HT-5Pseq for  xrn1Δ  transformed with Rat1∆NLS-Xrn1-Cterm-3xFLAG replicate 2


title: wrky8-m1, imbibed embryo, biol rep 3


title: HCT116_Cl3_shU1_Baseline_D14_K9me3_R1


title: Retina, 14 days post torpor, Rep3


title: RPE, Euthermia, Rep1


title: HCT116_Cl3_shU1_Baseline_Input


title: wrky8-m1, imbibed embryo, biol rep 1


title: Retina, 14 days post torpor, Rep2


title: wrky8-m1, imbibed embryo, biol rep 2


title: x-Y3: xrn1∆ + YCpLac33_rep2

description: HT-5Pseq for xrn1Δ transformed with empty vector (YCpLac33) replicate 2


title: x-L1: xrn1∆ + pLCM9_rep1

description: HT-5Pseq for  xrn1Δ  transformed with Rat1∆NLS-Xrn1-Cterm-3xFLAG replicate 1


title: Retina, 14 days post torpor, Rep1


title: HCT116_Cl6_shU1_Baseline_D14_K27me3_R2

description:
Clone6_NoDox_H3K27me3_shared_peaks_coordinate.bed
Clones_H3K27me3_shared_peaks_coordinates.bed


title: x-B3: xrn1∆ + pBBM3_rep3

description: HT-5Pseq for  xrn1Δ  transformed with Rat1-∆NLS version without the FLAG epitopes replicate 3

value: xrn1{delta} + pBBM3(Rat1-{delta}NLS)


title: wrky2-m2, coleoptile tip, biol rep 3

source_name: coleoptile tip

value: coleoptile tip

value: 6 days after sowing


title: Retina, 3 days post torpor, Rep6

value: 3 days post torpor


title: LCS8740_iCTC_ER

city: Galveston

first: Manuel Jr

middle: Sabalo

last: Vidal

state: Texas

address: 301 University Drive

department: Department of Obstetrics and Gynecology

institute: UTMB

description:
Chorionic trophoblast, no treatment
No treatment

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Placenta

extract_protocol:
Total RNA was extracted using Trizol reagent (hermofisher, 15596018) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0. Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA).

value: Placenta

value: iCTC

value: Chorionic trophoblast

value: SV40-T immortalized


title: wrky2-m2, coleoptile tip, biol rep 2


title: x-B1: xrn1∆ + pBBM3_rep1

description: HT-5Pseq for  xrn1Δ  transformed with Rat1-∆NLS version without the FLAG epitopes replicate 1


title: HCT116_Cl6_shU1_Baseline_D14_K27me3_R1

value: Colorectal Carcinoma epithelial cells

value: Doxycycline-inducible shRNA against UHRF1


title: Retina, 3 days post torpor, Rep5

value: Retina


title: wrky2-m2, coleoptile tip, biol rep 1


title: Retina, 3 days post torpor, Rep4


title: wt-Y3b: BY4741 + YCpLac33_rep3

description: HT-5Pseq for wildtype transformed with empty vector (YCpLac33) replicate 3

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)


title: st_11_Dam_rep3

description: Dam-Only control

value: stage 11 embryos


title: W22, tassel stem, biol rep 3

source_name: tassel stem

value: tassel stem

value: 80 days after sowing

value: not applicable

value: control


title: x-B2: xrn1∆ + pBBM3_rep2

description: HT-5Pseq for  xrn1Δ  transformed with Rat1-∆NLS version without the FLAG epitopes replicate 2

value: xrn1{delta} + pBBM3(Rat1-{delta}NLS)


title: Retina, 3 days post torpor, Rep3


title: wt-Y3: BY4741 + YCpLac33_rep2

description: HT-5Pseq for wildtype transformed with empty vector (YCpLac33) replicate 2


title: LCS9483_STB_1

description:
Syncytiotrophoblast, no treatment
No treatment

value: Cytotrophoblast

value: Syncytiotrophoblast


title: wt-B3: BY4741 + pBBM3_rep3

description: HT-5Pseq for wildtype transformed with Rat1-∆NLS version without the FLAG epitopes replicate 3

value: BY4741 + pBBM3 (Rat1-{delta}NLS)


title: Retina, 3 days post torpor, Rep2

value: 3 days post torpor


title: LCS9483_STB_2

value: Placenta


title: W22, tassel stem, biol rep 1


title: wt-Y1: BY4741 + YCpLac33_rep1

description: HT-5Pseq for wildtype transformed with empty vector (YCpLac33) replicate 1


title: W22, seedling leaf, biol rep 2

source_name: seedling leaf

value: seedling leaf

value: 10 days after sowing


title: W22, seedling leaf, biol rep 4


title: wt-B2: BY4741 + pBBM3_rep2

description: HT-5Pseq for wildtype transformed with Rat1-∆NLS version without the FLAG epitopes replicate 2


title: W22, seedling leaf, biol rep 3


title: Retina, 3 days post torpor, Rep1


title: LCS8791_ER_C_FORS

description:
Cytotrophoblast, forskolin treatment
Cells were treated with 50 uM forskolin

value: hPTC-CTB

value: SV40-T immortalized

value: Forskolin


title: LCS8791_ER_B_FORS

description:
BeWo, forskolin treatment
Cells were treated with 50 uM forskolin

source_name: Choriocarcinoma

value: Choriocarcinoma

value: BeWo

value: Wild type


title: wt-B1: BY4741 + pBBM3_rep1

description: HT-5Pseq for wildtype transformed with Rat1-∆NLS version without the FLAG epitopes replicate 1

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)


title: xrn1_2: xrn1∆ _rep2

description: HT-5Pseq for xrn1Δ replicate 2


title: Retina, Torpor, Rep5

value: Retina

value: Torpor


title: LCS9483_CTB_com

description:
Commercial cytotrophoblast, no treatment
No treatment

value: Commercial trophoblast


title: LCS9483_STB_3

value: Cytotrophoblast


title: W22, tassel stem, biol rep 2

value: tassel stem

value: 80 days after sowing

value: not applicable

value: control


title: Retina, Torpor, Rep3


title: W22, seedling leaf, biol rep 1

value: seedling leaf


title: LCS9483_CTB_3

description:
Cytotrophoblast, no treatment
No treatment

value: Placenta


title: LCS9483_pPTC

description:
Placental trophoblast, no treatment
No treatment


title: xrn1Rat1_2: xrn1Δ + Rat1-∆NLS-3xFlag_rep2

description: HT-5Pseq for xrn1Δ transformed with Rat1-∆NLS-3xFlag replicate 2


title: Retina, Torpor, Rep6


title: W22, imbibed embryo, biol rep 4

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing


title: LCS9483_EVT_1

description:
EVT, no treatment
No treatment

value: hPTC-EVT

value: Extravillous trophoblast

value: SV40-T immortalized


title: Retina, Torpor, Rep2


title: Retina, Torpor, Rep1


title: LCS9483_CTB_2

value: hPTC-CTB


title: LCS9483_CTB_1


title: W22, imbibed embryo, biol rep 1


title: Retina, Prehibernation, Rep5

value: Retina

value: Prehibernation


title: W22, imbibed embryo, biol rep 2


title: W22, coleoptile tip, biol rep 4

value: coleoptile tip

value: 6 days after sowing


title: C_LPS_2

description:
Cytotrophoblast, LPS treatment
Cells were treated with 100 ng/mL of LPS

value: Cytotrophoblast

value: LPS


title: xrn1_1: xrn1∆ _rep1

description: HT-5Pseq for xrn1Δ replicate 1

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)


title: wtRat1_2: BY4741 + Rat1-∆NLS-3xFlag_rep2

description: HT-5Pseq for strain of wildtype transformed with Rat1-∆NLS-3xFlag replicate 2

value: BY4741 + pLCM5 (Rat1-{delta}NLS-3xFlag)


title: Retina, Prehibernation, Rep4


title: W22, coleoptile tip, biol rep 3

value: not applicable

value: control


title: wtRat1_1: BY4741 + Rat1-∆NLS-3xFlag_rep1

description: HT-5Pseq for strain of wildtype transformed with Rat1-∆NLS-3xFlag replicate 1


title: Retina, Prehibernation, Rep3


title: W22, imbibed embryo, biol rep 3

value: imbibed embryo


title: W22, coleoptile tip, biol rep 2


title: Retina, Torpor, Rep4

value: Torpor


title: Retina, Prehibernation, Rep2


title: C_Ctrl_3

value: Placenta


title: Mut OFF 2, modified without SAM ligand

city: Chapel Hill

first: Patrick

middle: Stephen

last: Irving

state: NC

address: 250 Bell Tower Dr.

department: Chemistry

institute: The University of North Carolina at Chapel Hill

description:
Sequences aligned to SAMIII_MutOFF2 (see supplementary file)
All files with prefix "SAMIII_MutOFF2_noSAM" in included supplementary files

library_source: other

data_processing:
ShapeMapper v2.1.5
RingMapper
PairMapper
DanceMapper (--fit option)
DanceMapper (--pairmap --rings options)
Assembly: Reference sequences are provided as supplementary data files and are noted in SAMPLE description field.
Supplementary files format and content: shapemap_profiles.tar.gz contains files of the format _profile.txt from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: ringmap_correlations.tar.gz contains files from RingMapper. Each row in these tables describes a correlated mutation event between two nucleotides. Files with -0- or -1- are computed from the corresponding DanceMap population.
Supplementary files format and content: pairmap_files.tar.gz contains _pairmap.txt files from PairMapper. Each row in these tables describes a correlated mutation even between two 3-nucleotide, complimentary windows. Files with -0- or -1- are computed from the corresponding DanceMap population.
Supplementary files format and content: dancemap_reactivities.tar.gz contains _reactivities.txt files from DanceMapper. Each row in these tables describes the modelled per-nucleotide reactivity for each population in an ensemble.

molecule: other

organism: Enterococcus faecalis

extract_protocol:
RNA was generated by in vitro transcription with T7 polymerase
MaP-RT was performed using targeted primers. Two rounds of PCR were performed to add Illumina adapter sequences and barcodes.

value: Mut OFF 2

value: DMS, no ligand


title: xrn1Rat1_1: xrn1Δ + Rat1-∆NLS-3xFlag_rep1

description: HT-5Pseq for xrn1Δ transformed with Rat1-∆NLS-3xFlag replicate 1


title: C_LPS_1

value: SV40-T immortalized


title: W22, coleoptile tip, biol rep 1


title: Mut OFF 2, modified with SAM ligand

description:
Sequences aligned to SAMIII_MutOFF2 (see supplementary file)
All files with prefix "SAMIII_MutOFF2_SAM" in included supplementary files

value: DMS, with ligand


title: C_Ctrl_2

value: hPTC-CTB


title: wt_2: BY4741_rep2

description: HT-5Pseq for wildtype replicate 2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 DCP2-GFP

value: GFP


title: Retina, Prehibernation, Rep1

value: Retina

value: Prehibernation


title: Retina, Prehibernation, Rep6


title: sbp20-m3, imbibed embryo, biol rep 3

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: Retina, Euthermia, Rep6

value: Euthermia


title: Mut OFF 2, unmodified

description:
Sequences aligned to SAMIII_MutOFF2 (see supplementary file)
Quantification included in MutOFF2_modified_SAM and MutOFF2_modified

value: control


title: C_Ctrl_1

value: Cytotrophoblast


title: sbp20-m3, imbibed embryo, biol rep 1

value: imbibed embryo


title: C_CSE_3

description:
Cytotrophoblast, no treatment
Cells were treated with 1:50 CSE

value: Placenta


title: Retina, Euthermia, Rep5


title: Mut OFF 1, modified with SAM ligand

description:
Sequences aligned to SAMIII_MutOFF1 (see supplementary file)
All files with prefix "SAMIII_MutOFF1_SAM" in included supplementary files

value: Mut OFF 1


title: sbp20-m3, imbibed embryo, biol rep 2


title: Mut OFF 1, modified without SAM ligand

description:
Sequences aligned to SAMIII_MutOFF1 (see supplementary file)
All files with prefix "SAMIII_MutOFF1_noSAM" in included supplementary files

value: DMS, no ligand


title: Retina, Euthermia, Rep4


title: Mut OFF 1, unmodified

description:
Sequences aligned to SAMIII_MutOFF1 (see supplementary file)
Quantification included in MutOFF1_modified_SAM and MutOFF1_modified


title: sbp20-m2, imbibed embryo, biol rep 3


title: B_LPS_3

description:
BeWo, LPS treatment
Cells were treated with 100 ng/mL of LPS

value: Choriocarcinoma

value: BeWo

value: Wild type

value: LPS


title: sbp20-m2, imbibed embryo, biol rep 1


title: C_CSE_2

value: hPTC-CTB

value: SV40-T immortalized


title: Retina, Euthermia, Rep2

value: Retina


title: Retina, Euthermia, Rep3


title: C_CSE_1


title: Mut ON 2, modified without SAM ligand

description:
Sequences aligned to SAMIII_MutON2 (see supplementary file)
All files with prefix "SAMIII_MutON2_noSAM" in included supplementary files

value: Mut ON 2


title: sbp20-m2, imbibed embryo, biol rep 2

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing


title: Retina, Euthermia, Rep1

value: Euthermia


title: Mut ON 2, unmodified

description:
Sequences aligned to SAMIII_MutON2 (see supplementary file)
Quantification included in MutON2_modified_SAM and MutON2_modified

value: control


title: mybr32-m1, seedling leaf, biol rep 3

value: seedling leaf

value: 10 days after sowing

value: mutant


title: Mut ON 2, modified with SAM ligand

description:
Sequences aligned to SAMIII_MutON2 (see supplementary file)
All files with prefix "SAMIII_MutON2_SAM" in included supplementary files

value: DMS, with ligand


title: B_LPS_2


title: Mut ON 1, modified without SAM ligand

description:
Sequences aligned to SAMIII_MutON1 (see supplementary file)
All files with prefix "SAMIII_MutON1_noSAM" in included supplementary files

value: Mut ON 1

value: DMS, no ligand


title: Hypothalamus, 14 days post torpor, Rep3

source_name: Hypothalamus

value: Hypothalamus

value: 14 days post torpor


title: LCS8791_ER_B_LPS

value: Choriocarcinoma

value: BeWo

value: Wild type

value: LPS


title: Hypothalamus, 14 days post torpor, Rep2


title: mybr32-m1, seedling leaf, biol rep 1


title: B_Ctrl_3

description:
BeWo, no treatment
No treatment


title: Mut ON 1, modified with SAM ligand

description:
Sequences aligned to SAMIII_MutON1 (see supplementary file)
All files with prefix "SAMIII_MutON1_SAM" in included supplementary files


title: B_Ctrl_2

description:
BeWo, no treatment
No treatment


title: Hypothalamus, 14 days post torpor, Rep1


title: mybr21-m1, imbibed embryo, biol rep 3

value: imbibed embryo


title: Mut ON 1, unmodified

description:
Sequences aligned to SAMIII_MutON1 (see supplementary file)
Quantification included in MutON1_modified_SAM and MutON1_modified


title: Hypothalamus, 3 days post torpor, Rep3

value: 3 days post torpor


title: wt_1: BY4741_rep1

description: HT-5Pseq for wildtype replicate 1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 DCP2-GFP

value: BY4741(MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0)

value: GFP


title: Native, modified without SAM ligand

description:
Sequences aligned to SAMIII_native (see supplementary file)
All files with prefix "SAMIII_native_noSAM" in included supplementary files

value: native


title: B_Ctrl_1

description:
BeWo, no treatment
No treatment


title: B_CSE_3

description:
BeWo, CSE treatment
Cells were treated with 1:50 CSE

value: CSE


title: Hypothalamus, 3 days post torpor, Rep2


title: mybr21-m1, imbibed embryo, biol rep 1

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: mybr21-m1, imbibed embryo, biol rep 2


title: Hypothalamus, 3 days post torpor, Rep1


title: B_CSE_2


title: Native, modified with SAM ligand

description:
Sequences aligned to SAMIII_native (see supplementary file)
All files with prefix "SAMIII_native_SAM" in included supplementary files

value: DMS, with ligand


title: Hypothalamus, Torpor, Rep3

value: Hypothalamus

value: Torpor


title: myb40-m2, coleoptile tip, biol rep 3

value: coleoptile tip

value: 6 days after sowing


title: B_CSE_1

value: Choriocarcinoma

value: BeWo

value: Wild type


title: wor_TAF3_Dam_rep3

description: TAF3-phd(H3K4me3)-Dam fusion

source_name: 3rd instar larval brain

value: 3rd instar larval brain

value: NSCs


title: myb40-m2, coleoptile tip, biol rep 2


title: Hypothalamus, Torpor, Rep2


title: C_LPS_3

description:
Cytotrophoblast, LPS treatment
Cells were treated with 100 ng/mL of LPS

value: Placenta

value: hPTC-CTB

value: Cytotrophoblast

value: SV40-T immortalized

value: LPS


title: myb40-m2, coleoptile tip, biol rep 1


title: wor_TAF3_Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion


title: Hypothalamus, Torpor, Rep1


title: myb40-m1, coleoptile tip, biol rep 3


title: GATA6_36h_CUT&Tag rep1

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The CUT&Tag datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Assembly: hg38
Library strategy: CUT&Tag

source_name: human embryonic stem cell H9

growth_protocol: hESCs were routinely cultured in mTeSRTM1 medium (STEMCELL Technologies, 85850) and  were cultured in DE induction medium  during differentiation

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The CUT&Tag DNA library for sequencing was constructed with Hyperactive Universal CUT&TAG Assay Kit for Illumina (Vazyme, TD903) according to manufacturer’s instructions

treatment_protocol: hESCs were routinely cultured without special treatment.

value: differentiating, female embryonic stem cells

value: wild type

value: CST no 5851

value: no treatment


title: wor_TAF3_Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion


title: Hypothalamus, Prehibernation, Rep3

value: Hypothalamus

value: Prehibernation


title: wrky8-m2, imbibed embryo, biol rep 1

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: A5KO.Input

description: total mRNA

data_processing:
library strategy: meRIP-seq
bcl2fastq conversion software v2.17 used for basecalling.
The MeRIP-seq datasets were aligned to the human Genome hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using exomePeak2 software with the default parameters and annotated by ChIPseeker software
Assembly: hg38

extract_protocol:
The collected samples are extracted by RL solution, according to the manufacturers instructions of FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112)
The MeRIP library for sequencing was constructed by Novogene Co, Ltd.

treatment_protocol: Wild-type hESCs were routinely cultured without special treatment, while the manipulated hESCs underwent a gene editing of ALKBH5 knockout knockout

value: DE induction


title: mybr32-m1, seedling leaf, biol rep 2

value: seedling leaf

value: 10 days after sowing


title: Native, unmodified

description:
Sequences aligned to SAMIII_native (see supplementary file)
Quantification included in Native_modified_SAM and Native_modified

value: native

value: control


title: myb40-m1, coleoptile tip, biol rep 1

value: coleoptile tip

value: 6 days after sowing


title: Hypothalamus, Prehibernation, Rep2


title: wor_Cbx7_Dam_rep1

description: Cbx7(H3K27me3)-Dam fusion

value: 3rd instar larval brain

value: NSCs


title: A5KO.IP

description: mRNA with m6A

value: differentiating, female embryonic stem cells

value: CST no 56593


title: wor_Cbx7_Dam_rep2

description: Cbx7(H3K27me3)-Dam fusion


title: Hypothalamus, Prehibernation, Rep1

value: Hypothalamus


title: myb40-m1, coleoptile tip, biol rep 2


title: jmj13-m4, tassel stem, biol rep 3

value: tassel stem

value: 80 days after sowing


title: Hypothalamus, Euthermia, Rep3

value: Euthermia


title: wt.Input

description: total mRNA

value: wild type


title: wor_H3K9ac_Dam_rep2

description: H3K9ac-mintbody-Dam fusion


title: wt.IP

description: mRNA with m6A


title: GATA6_36h_CUT&Tag rep2

value: CST no 5851

value: no treatment


title: jmj13-m4, tassel stem, biol rep 2

value: mutant


title: wor_H3K9ac_Dam_rep1

description: H3K9ac-mintbody-Dam fusion


title: Hypothalamus, Euthermia, Rep2


title: DKK4_KO2_A_D3_RNA_seq rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (hg38) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1)
Assembly: hg38
Supplementary files format and content: Comma-separated value file containing  RNA-seq data(TPM)

extract_protocol:
The collected samples are extracted by RL solution, according to the manufacturers instructions of FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112)
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: Wild-type hESCs were routinely cultured without special treatment, while the manipulated hESCs underwent a gene editing of ALKBH5 knockout or DKK4 knockout

value: Gene Knockout of DKK4

tag: passage


title: wor_H4K20me1_Dam_rep2

description: H4K20me1-mintobody-Dam fusion


title: jmj13-m4, tassel stem, biol rep 1


title: LCS8791_ER_C_LPS

value: Placenta

value: hPTC-CTB

value: Cytotrophoblast

value: SV40-T immortalized

value: LPS


title: Hypothalamus, Euthermia, Rep1


title: wor_H4K20me1_Dam_rep1

description: H4K20me1-mintobody-Dam fusion

value: 3rd instar larval brain

value: NSCs


title: DKK4_KO2_A_D3_RNA_seq rep1

value: differentiating, female embryonic stem cells


title: Cortex, 14 days post torpor, Rep3

source_name: Cortex

value: Cortex

value: 14 days post torpor


title: hsf6-m2, imbibed embryo, biol rep 2

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing


title: wor_Dam_rep3

description: Dam-Only control


title: Cortex, 14 days post torpor, Rep2


title: DKK4_KO2_A_D1_RNA_seq rep1


title: wor_Dam_rep2

description: Dam-Only control


title: Cortex, 14 days post torpor, Rep1


title: wor_Dam_rep1

description: Dam-Only control


title: Cortex, 3 days post torpor, Rep3

value: 3 days post torpor


title: DKK4_KO2_A_D0_RNA_seq rep1

value: undifferentiated, female embryonic stem cells


title: hsf6-m1, imbibed embryo, biol rep 3

value: mutant


title: DKK4_KO2_A_D0_RNA_seq rep2

value: Gene Knockout of DKK4


title: hsf6-m1, imbibed embryo, biol rep 1


title: DKK4_KO1_A_D3_RNA_seq rep2


title: Cortex, 3 days post torpor, Rep2


title: VPNS2_1

city: Hohhot

first: qiudi

last: shen

address: 235 University Street West

institute: Inner Mongolia University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then 1 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. F
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Escherichia coli

extract_protocol:
Total RNA was isolated using RNAprep Pure Cell/Bacteria Kit DP430 of QIAGEN according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: strain

tag: agent

value: violet phosphorene nanosheets

tag: time


title: Cortex, 3 days post torpor, Rep1


title: hsf6-m2, imbibed embryo, biol rep 3

tag: developmental stage

tag: age

tag: uniformmu id


title: hsf29-m2, imbibed embryo, biol rep 3

tag: tissue

tag: genotype

tag: treatment


title: DKK4_KO1_A_D1_RNA_seq rep2


title: DKK4_KO2_A_D1_RNA_seq rep2


title: Cortex, Torpor, Rep2

tag: condition

value: Torpor


title: hsf6-m2, imbibed embryo, biol rep 1


title: VPNS1_1


title: hsf29-m2, imbibed embryo, biol rep 2


title: Cortex, Torpor, Rep3


title: C3_1

value: control


title: hsf29-m2, imbibed embryo, biol rep 1


title: Cortex, Torpor, Rep1


title: C2_1


title: hsf6-m1, imbibed embryo, biol rep 2


title: VPNS3_1


title: DKK4_KO1_A_D0_RNA_seq rep2


title: Cortex, Prehibernation, Rep3

value: Prehibernation


title: C1_1


title: hsf29-m1, imbibed embryo, biol rep 3


title: DKK4_KO1_A_D0_RNA_seq rep1


title: Cortex, Prehibernation, Rep2


title: hsf29-m1, imbibed embryo, biol rep 2


title: Cortex, Prehibernation, Rep1


title: hsf29-m1, imbibed embryo, biol rep 1


title: DKK4_KO1_A_D3_RNA_seq rep1


title: hsf20-m1, imbibed embryo, biol rep 3


title: hsf20-m1, imbibed embryo, biol rep 2


title: KO_IgG [Cut&Tag]

city: Shanghai

first: Shuai

last: Zhang

address: 220 Handan Rd., Shanghai

institute: fudan university

data_processing:
library strategy: cut&tag
cut&tag raw reads were obtained from an Illumina X-10 sequence analyzer.
We utilized Fastqc (v0.1.0) for raw data quality summary. Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than75 bp.
Paired-end reads were aligned using Bowtie2 version 2.2.5 with options: --local --very-sensitive --local-no-unal --no-mixed -–no-discordant –phred33 -I 10 -X 700.
we used macs2 callpeak with parameters –p 1e-5 –keep-dup all For peak calling.
Mapping results were normalized to CPM (counts per million mapped reads) and converted to bigwig files for visualization by bamCoverage.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: primary OPC

extract_protocol:
DNA were prepared using a commercial kit (Vazyme, Nanjing, China, TD901)  following manufacturer's protocols.
cut&tag libraries were prepared using a commercial kit (Vazyme, Nanjing, China, TD901)  following manufacturer's protocols.

value: primary OPC

value: KO


title: ALKBH5_KO2_C_D1_RNA_seq rep2

value: Gene Knockout of ALKBH5


title: WT_IgG [Cut&Tag]

value: WT


title: DKK4_KO1_A_D1_RNA_seq rep1

value: differentiating, female embryonic stem cells


title: ALKBH5_KO2_C_D3_RNA_seq rep2


title: Cortex, Euthermia, Rep3

value: Cortex

value: Euthermia


title: ALKBH5_KO2_C_D3_RNA_seq rep1


title: iOL,KO,SP1,rep1 [Cut&Tag]


title: iOL,WT,SP1,rep2 [Cut&Tag]


title: Cortex, Euthermia, Rep2


title: ALKBH5_KO2_A_D3_RNA_seq rep2


title: iOL,KO,SP1,rep2 [Cut&Tag]


title: ALKBH5_KO2_A_D3_RNA_seq rep1


title: ALKBH5_KO2_A_36h_RNA_seq rep2


title: iOL,KO,P300,rep2 [Cut&Tag]


title: iOL,WT,SP1,rep1 [Cut&Tag]


title: IF_3

city: Graz

first: Jelena

last: Krstic

address: Neue Stiftingtalstrasse 6

department: Department of Cell Biology, Histology and Embryology

country: Austria

institute: Medical University of Graz

data_processing:
sequenced data were aligned to the UCSC mm39 genome, Data were analyzed by Dr. Tom
DEseq2 was used for differential expression detection, Genes with an adjusted p-value < 0.05 and log2FC > 0.585 were considered differentially expressed.
Assembly: UCSC mm39
Supplementary files format and content: .xlsx file with TPM values of all genes was extracted

source_name: liver

extract_protocol:
Rna was isolated with PeqGOLD total RNA kit (Peqlab); quality was checked with Tape-Station (RNA screen tape, avg RIN:9)
BGI Strand-Specific mRNA Library Preparation (DNBSEQ); Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS)

value: liver

value: wt

value: IF


title: IF_1


title: IF_2


title: hsf13-m1, seedling leaf, biol rep 3

value: seedling leaf

value: 10 days after sowing


title: hsf18-m1, imbibed embryo, biol rep 1

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: hsf13-m1, seedling leaf, biol rep 2


title: hsf18-m1, imbibed embryo, biol rep 2


title: ALKBH5_KO2_C_D1_RNA_seq rep1


title: Cortex, Euthermia, Rep1


title: hsf20-m1, imbibed embryo, biol rep 1


title: iOL,WT,P300,rep2 [Cut&Tag]


title: hsf13-m1, seedling leaf, biol rep 1


title: ALKBH5_KO2_D0_RNA_seq rep2

value: undifferentiated, female embryonic stem cells


title: hsf18-m1, imbibed embryo, biol rep 3


title: FED_1

value: Fed


title: ALKBH5_KO2_A_36h_RNA_seq rep1


title: FED_2


title: iOL,KO,rep4 [KO_3]

data_processing:
RNA-seq raw reads were obtained from an Illumina X-10 sequence analyzer.
Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than 75 bp .
the filtered clean reads were mapped to the mouse reference genome mm10 with tophat2, and gene quantification and differential expression analysis were performed by cuffdiff with parameters -b -u.
Mapping results were converted to bigwig files for visualization.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: brain

growth_protocol: Primary OPCs were purified by immunopanning as the protocol, and they  were maintained in Sato growth medium supplemented with mitogens 10 ng/ml PDGF-AA and 1 ng/ml NT-3 and antibiotics in humidified atmosphere with 10% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries.
We used a commercial RNA library kit (NEB 7760) to prepare the RNA-seq library with the manufacturer’s specifications.

treatment_protocol: OPC differentiation was induced by treatment of 1-day post confluent cells (designated day 0, D0) with 15 nM T3 (Sigma) and 10 ng/ml ciliary neurotrophic factor.

value: brain

value: primary OPC

value: T3 differentiation, 1day


title: iOL,WT,P300,rep1 [Cut&Tag]

value: WT


title: ALKBH5_KO2_A_D1_RNA_seq rep1

value: differentiating, female embryonic stem cells

value: Gene Knockout of ALKBH5


title: FMD_4

value: liver

value: FMD-diet


title: iOL,KO,rep3 [KO_2]


title: gras75-m1, imbibed embryo, biol rep 3


title: iOL,KO,P300,rep1 [Cut&Tag]

value: KO


title: gras75-m1, imbibed embryo, biol rep 2


title: ALKBH5_KO2_D0_RNA_seq rep1


title: iOL,KO,rep2 [KO_1]


title: FMD_2

value: wt


title: ALKBH5_KO1_C_D3_RNA_seq rep2


title: ALKBH5_KO2_A_D1_RNA_seq rep2


title: iOL,KO,rep1 [KO_0]


title: FMD_1


title: gras75-m1, imbibed embryo, biol rep 1


title: ALKBH5_KO1_C_D3_RNA_seq rep1


title: ALKBH5_KO1_C_D1_RNA_seq rep2


title: gras52-m1, imbibed embryo, biol rep 1


title: iOL,WT,rep3 [WT_2]


title: e2f19-m2, seedling leaf, biol rep 3

value: seedling leaf

value: 10 days after sowing


title: ALKBH5_KO1_C_D1_RNA_seq rep1


title: g_MG_3

city: Jinzhong

first: Jian

last: Wang

address: mingxiannanlu 1

institute: shanxi agricultural university

description: liver from c_MG_3

data_processing:
Sequencing data were called raw reads, and quality control was then performed on the raw reads to obtain clean reads. After quality control, the filtered clean reads were aligned to the reference sequence. Then, gene expression quantification, gene difference analysis, and enrichment analysis were performed. Data quality control was completed using SOAPnuke (v1.5.2). Genome alignment was completed using HISAT2 (2.0.4). Transcript quantification and differential comparison were completed via Bowtie2 (v2.2.5) and DESeq2 (v1.2.8), respectively. Genes were considered to be significantly different if they had a q value (adjusted p value) less than 0.05
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002315.6/
Supplementary files format and content: gene expression FPKM file, excel

organism: Gallus gallus

extract_protocol:
Total RNA was extracted using TRIzol reagent (ET101-01-V2, Beijing TransGen Biotech Co., Ltd, Beijing, China). The RNA concentration and integrity were detected using a Fragment Analyzer (Agilent, California, USA). RNA samples that complied with the criteria of having a concentration of more than 40 ng/μL, an integrity value greater than 7.0, and a total content of 1 μg or more were chosen for further experimentation.
Oligo dT beads were employed to enrich mRNA carrying a poly(A) tail. Subsequently, the RNA was fragmented, and first-strand cDNA production was initiated through random N6-primed reverse transcription. This was followed by the synthesis of second-strand cDNA, where dUTP was utilized instead of dTTP. The resulting cDNA then underwent end-repair and subsequent 3’ adenylation. Afterward, adaptors were attached to the termini of these 3’ adenylated cDNA segments. Before initiating PCR amplification, the strand marked with dUTP was selectively degraded using Uracil-DNA-Glycosylase (UDG). The remaining strand was then amplified to create a cDNA library suitable for sequencing. To enrich the purified cDNA template, multiple rounds of PCR amplification were carried out using PCR primers. Heat was used to denature the PCR product, and subsequently, the single-stranded DNA was circularized with the aid of a splint oligo and DNA ligase. Ultimately, DNA nanoball synthesis and sequencing were executed on the DNBSEQ platform in paired-end 150 sequencing mode.

tag: group

value: MG

tag: breed

value: AA broiler

tag: Sex

value: male


title: g_MG_1

description: liver from c_MG_1


title: g_MG_2

description: liver from c_MG_2


title: gras52-m1, imbibed embryo, biol rep 2

value: imbibed embryo

value: R6, ~60 days after pollination, harvested and dried seed

value: 140 days after sowing

value: mutant


title: ALKBH5_KO1_A_D3_RNA_seq rep2

tag: cell type

tag: cell line


title: e2f19-m2, seedling leaf, biol rep 1


title: iOL,WT,rep2 [WT_1]

value: brain

value: primary OPC

value: T3 differentiation, 1day


title: g_c_3

description: liver from c_c_3

value: c


title: e2f19-m2, seedling leaf, biol rep 2


title: ALKBH5_KO1_A_D3_RNA_seq rep1

value: differentiating, female embryonic stem cells

value: Gene Knockout of ALKBH5


title: FED_3

value: liver

value: Fed


title: iOL,WT,rep4 [WT_3]

value: WT


title: g_c_2

description: liver from c_c_2


title: e2f19-m1, seedling leaf, biol rep 3

value: seedling leaf

value: 10 days after sowing


title: iOL KO input

data_processing:
ChIP-seq raw reads were obtained from an Illumina X-10 sequence analyzer.
We utilized Fastqc (v0.1.0) for raw data quality summary. Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than75 bp.
Clean reads were aligned to the mouse reference genome mm10, and the mapping results were normalized to CPM (counts per million mapped reads) and converted to bigwig files for visualization by bamCoverage.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Briefly, cells were crosslinked with 0.9% formaldehyde for 9 min at room temperature, and formaldehyde was quenched by glycine at a final concentration of 125 μM for 5 minutes. Cells were washed twice with ice-cold PBS and collected by a cell scraper. Cell pellets were lysed and sonicated in lysis buffer (1% SDS, 50 mM Tris-HCl (pH 7.4), 10 mM EDTA), and the chromatin was fragmented into 200-500 bp fragments using a COVARIS S220 sonicator.
ChIP-seq libraries were prepared using a commercial kit (Vazyme, Nanjing, China, ND607)  following manufacturer's protocols.

value: primary mouse OPC

value: KO


title: ALKBH5_KO1_A_36h_RNA_seq rep2


title: iOL WT input


title: ALKBH5_KO1_A_36h_RNA_seq rep1


title: g_c_1

description: liver from c_c_1

value: AA broiler

value: male


title: iOL KO H3K27ac-2


title: iOL,WT,rep1 [WT_0]


title: e2f19-m1, seedling leaf, biol rep 2


title: g_MGKC_3

description: liver from c_MGKC_3

value: MGKC


title: ALKBH5_KO1_A_D1_RNA_seq rep2


title: g_MGKC_2

description: liver from c_MGKC_2


title: e2f13-m1, coleoptile tip, biol rep 3

value: coleoptile tip

value: 6 days after sowing

value: mutant


title: iOL KO H3K27ac-1

value: brain

value: T3 differentiation, 1day


title: ALKBH5_KO1_A_D1_RNA_seq rep1

value: differentiating, female embryonic stem cells


title: e2f19-m1, seedling leaf, biol rep 1


title: iOL WT H3K27ac-2


title: g_KC_3

description: liver from c_KC_3

value: KC


title: iOL WT H3K27ac-1


title: g_MGKC_1

description: liver from c_MGKC_1

value: liver


title: ALKBH5_KO1_D0_RNA_seq rep2

value: undifferentiated, female embryonic stem cells

value: Gene Knockout of ALKBH5


title: e2f13-m1, coleoptile tip, biol rep 1


title: e2f13-m1, coleoptile tip, biol rep 2


title: ALKBH5_KO1_D0_RNA_seq rep1


title: wt_C_D3_RNA_seq rep2

value: wild type

value: No Treatment


title: c3h42-m1, tassel stem, biol rep 3

value: tassel stem

value: 80 days after sowing


title: wt_C_D3_RNA_seq rep1


title: WT pituitary, 14week, scRNAseq

city: Guangzhou

first: Yafang

last: Hu

state: Guangdong

address: No.1838, Guangzhou Avenue North

department: Dept. of Neurology

institute: Nanfang Hospital, Southern Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v 3.0.2 (10x Genomics) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pituitary

extract_protocol:
10x chromium scRNA-seq was performed with the pituitaries from two genotypes in two independent runs. The single cell suspension was obtained by incubating the samples with 0.1 mg/ml papain (Sigma) at 37℃ for 5min. After destroyed the red blood cells with eBioscience™ RBC buffer (Invitrogen, Carlsbad, CA ), the single-cell suspension was loaded onto the 10x Genomics single-cell-A chip to capture 5000-8000 cells.
The cDNA library was prepared with 10x Genomics Single Cell 3’ v2 Reagent Kit

value: WT

value: pituitary

value: C57BL/6- B6;CBA-BiTg mice

value: 14 weeks old


title: p25OE pituitary, 14 week, scRNAseq

description: 10x Genomics


title: g_KC_1

description: liver from c_KC_1

value: AA broiler

value: male


title: c3h42-m1, tassel stem, biol rep 2

value: mutant


title: wt_C_D1_RNA_seq rep2


title: p25OE pituitary, 40 week, scRNAseq

description: 10x Genomics

value: 40 weeks old


title: c3h42-m1, tassel stem, biol rep 1


title: f_MG_3

description: lung from c_MG_3

source_name: lung

value: lung

value: MG


title: wt_C_D1_RNA_seq rep1

value: differentiating, female embryonic stem cells


title: f_MG_2

description: lung from c_MG_2


title: bzip76-m3, seedling leaf, biol rep 3

value: seedling leaf

value: 10 days after sowing


title: f_MG_1

description: lung from c_MG_1


title: wt_A_D3_RNA_seq rep2

value: wild type


title: Genomic DNA from spinal ependymoma 88

type: genomic

first: Lara

last: Engertsberger

address: Auenbruggerplatz 34/2

department: Division of Pediatric Hemato-Oncology

description: Relation GSM5600034

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.43.1 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy3 and Cy92

source_name: spinal ependymomas

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega, Madison, WI) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research, Irvine, CA). The DNA Clean & Concentrator-5 (Zymo Research, Irvine, CA) and the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA) were employed to clean and restore the converted DNA.

value: M

tag: extent of resection

value: GTR

tag: who tumor grade

value: myxopapillary WHO grade non-myxopapillary WHO grade 2

tag: classification result v12.5

value: MPE

tag: classification score

tag: OS status

tag: os [days]

tag: pfs status

tag: pfs [days]

tag: material

value: FFPE

tag: reanalysis of

value: spinal ependymomas


title: bzip76-m3, seedling leaf, biol rep 2

tag: tissue

tag: developmental stage

tag: age

tag: uniformmu id

tag: genotype

tag: treatment


title: g_KC_2

description: liver from c_KC_2

value: liver

tag: group

value: KC

tag: breed

tag: Sex


title: Genomic DNA from spinal ependymoma 17

description: Relation GSM5600090, GSM6630056

label: Cy3 and Cy21

value: F

tag: localization

value: lumbosacral

tag: extent of resection

tag: who tumor grade

tag: classification result v12.5


title: Genomic DNA from spinal ependymoma 87

description: Relation GSM2941021, GSM6629585

label: Cy3 and Cy91

value: non-myxopapillary WHO grade 2

tag: classification score

tag: OS status

tag: os [days]

tag: pfs status


title: bzip76-m3, seedling leaf, biol rep 1

tag: tissue

value: mutant


title: f_c_2

description: lung from c_c_2

value: lung

value: c

value: AA broiler

value: male


title: Genomic DNA from spinal ependymoma 8

description: Relation GSM6630209

label: Cy3 and Cy12

value: cervical

value: <GTR

value: SP-EPN

tag: pfs [days]

tag: material

tag: reanalysis of


title: f_MGKC_3

description: lung from c_MGKC_3

value: MGKC


title: bzip76-m2, seedling leaf, biol rep 3

value: seedling leaf

tag: developmental stage

tag: age

value: 10 days after sowing

tag: uniformmu id

tag: genotype


title: wt_A_D1_RNA_seq rep2

tag: cell type

value: differentiating, female embryonic stem cells

tag: cell line

value: wild type

tag: treatment

value: No Treatment

tag: passage


title: bzip76-m2, seedling leaf, biol rep 1


title: bzip76-m2, seedling leaf, biol rep 2


title: f_MGKC_2

description: lung from c_MGKC_2

tag: group

tag: breed

tag: Sex


title: f_c_3

description: lung from c_c_3


title: baf60.21-m2, tassel stem, biol rep 3

value: tassel stem

value: 80 days after sowing


title: f_MGKC_1

description: lung from c_MGKC_1


title: wt_A_D1_RNA_seq rep1


title: baf60.21-m2, tassel stem, biol rep 2


title: wt_A_D3_RNA_seq rep1


title: wt_A_36h_RNA_seq rep2


title: wt_D0_RNA_seq rep2

value: undifferentiated, female embryonic stem cells


title: WT pituitary, 40 week, scRNAseq

description: 10x Genomics

value: WT

value: pituitary

tag: strain

value: C57BL/6- B6;CBA-BiTg mice

value: 40 weeks old


title: pTα1-TAF3_Dam_rep2

city: Cambridge

first: Andrea

last: Brand

address: Tennis Court Rd

institute: The Gurdon Institute

description: TAF3-phd(H3K4me3)-Dam fusion

data_processing:
Analysis was perfomed with damidseq_pipeline script which uses bowtie2 to align reads to given genome, extends the reads until 300bp or the next GATC site, bins the reads into GATC fragments and normalises against Dam-Only control.
Replicates of normalised bedgraphs were quantile normalised to each other, averaged and backtransformed.
Averaged bedgraphs were converted into bigwig format.
Assembly: mm10, dm6, Xla.v9.1
Supplementary files format and content: The processed data are quantile normalised and averaged bigwig files, generated as described.
Library strategy: DamID-Seq

source_name: E13-14 forebrain

extract_protocol:
For Drosophila DamID, 20-50 third instar larval brains were dissected. For mouse samples, in utero electroporation with DamID plasmids was performed on E13.5 embryos. Electroporated cortex was microdissected. For Xenopus samples, mRNA was injected into stage 11 or stage 21 embryos. All tissue collections were followed by genomic DNA extraction with Qiagen DNAeasy blood and tissue kit and processed for DamID according to previous protocols before library prep.
Samples prepared for Illumina sequencing according to a modified TruSeq protocol.

value: E13-14 forebrain

value: IPC


title: Genomic DNA from spinal ependymoma 11

description: Relation GSM7776600, GSM7781281

label: Cy3 and Cy15

value: M

tag: localization

value: cervicothoracic

tag: extent of resection

value: <GTR

tag: who tumor grade

value: non-myxopapillary WHO grade 2

tag: classification result v12.5

tag: classification score

tag: OS status

tag: os [days]

tag: pfs status

value: FFPE

value: spinal ependymomas


title: f_KC_3

description: lung from c_KC_3

tag: tissue

value: lung

value: KC

value: AA broiler

value: male


title: f_c_1

description: lung from c_c_1

value: c


title: wt_D0_RNA_seq rep1

tag: cell type

value: undifferentiated, female embryonic stem cells

tag: genotype

value: wild type

value: No Treatment


title: pcMSC-E2-CM

city: Taipei

first: Le

middle: Duy

last: Cuong

state: Xinyi

address: 6th Floor, No 3-6 Wuxing street, Xinyi, Taipei

department: IPCTRM

country: Taiwan

institute: Taipei Medical University

description: Illumina instrument(75-cycle single-end read, 75SE). Sequencing data was processed using the Illumina softwareBCL2fastq.gz v2.20.

data_processing:
We utilized Trimmomatic to isolate high-quality reads, discarding those shorter than 18 nucleotides
The processed data was then examined using miRDeep2
aligning the reads to the GRCh38 reference genome obtained from UCSC (University of California Santa Cruz)
We employed reads per million mapped reads to measure normalized miRNA expression. This approach was derived by dividing the signal values of each miRNA by the total mapped reads
MirTarget V4 from miRDB version 6 was used to predict miRNA targets. Here, we only included functional human miRNAs from the FuncMir collection (http://www.mirdb.org/FuncMir.html).
Assembly: GRCh38
Supplementary files format and content: Meanwhile, when searching multiple miRNAs or genes for target mining, we excluded gene targets with less than 60 target prediction scores and miRNAs with more than 2000 predicted targets in the genome.

growth_protocol: The cells were cultured in ITS (1%) and 10 mg/mL EGF in MCDB201 (serum free) at 37°C and 5% CO2

extract_protocol:
Total RNA from exosomes (CM and E2-CM) was extracted using the TRIzol LS reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA quality was evaluated using the LabChip RNA 6000 kit (Agilent Technologies, USA) on a Bioanalyzer 2100 (Agilent Technology)
Sample libraries were prepared using the QIAseq miRNA Library Kit (Qiagen, Germany) according to the manufacturer’s guidelines and were then sequenced on an Illumina instrument (75-cycle single-end read, 75SE).

treatment_protocol: At approximately 50% confluence, the medium was replaced with fresh medium containing E2 (100 nM) for 48 h. Next, the culture dishes were washed three times with PBS, the serum-free medium was added, and the cells were cultured for another 48 h to obtain E2-CM.

value: Placenta

tag: cell line

value: Primary cells

value: Mesenchymal stem cells

tag: treatment

value: Estradiol (100 nM)


title: pTα1-TAF3_Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion

value: E13-14 forebrain

value: IPC


title: Genomic DNA from spinal ependymoma 12

description: Relation GSM7781262

label: Cy3 and Cy16

value: M

tag: age

value: thoracic

value: <GTR

value: WHO grade 3

value: SP-EPN-MYCN

tag: pfs [days]

tag: reanalysis of


title: wt_A_36h_RNA_seq rep1

value: differentiating, female embryonic stem cells

tag: passage


title: baf60.21-m1, tassel stem, biol rep 3

data_processing:
nf-core RNA-seq pipeline Nextflow v20.10.0 for initial QC and raw read counting
Reads were trimmed using Trim Galore! v0.6.5 and aligned to the W22 reference genome using Hisat2 v2.1.0 with default parameters (hisat2 -x $db $input -p 12 --met-stderr --new-summary). Uniquely aligned reads were counted per feature by featureCounts v2.0.1.
Raw read counts were normalized by library size and corrected for library composition bias using the TMM normalization approach in edgeR v3.28.0 to give CPM (Counts Per Million reads) for each gene in each sample. CPM values were normalized by W22 gene CDS lengths to give FPKM (Fragments Per Kilobase of exon per Million reads) values.
Genes were considered expressed if their CPM was ≥ 1 in at least one sample per tissue
Assembly: Zea mays W22
Supplementary files format and content: Tab-delimited text file includes raw read counts, TMM normalized CPM values, FPKM values for each W22 gene in every sample. The B73v4 gene ID is recorded for W22 genes with one-to-one gene models between W22 and B73v4. The expressed column indicates if the W22 gene was considered expressed in our experiment (TRUE or FALSE). The filtered_DE column indicates if the gene was filtered from the differential expression analysis (TRUE = filtered out, FALSE = included). See Materials and Methods: Identification of TF mutant allele DE genes for further description.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit
Paired-end libraries were prepared from a minimum of 500 ng of total RNA using the standard Illumina TruSeq Stranded mRNA library protocol. Single-end libraries were prepared from 2 µg of total RNA using the Illumina TruSeq RNA Sample Prep Kit

value: tassel stem

tag: developmental stage

value: 80 days after sowing

tag: uniformmu id

value: mutant


title: baf60.21-m2, tassel stem, biol rep 1


title: f_KC_2

description: lung from c_KC_2

value: lung

tag: group

value: KC

tag: breed

value: AA broiler

tag: Sex

value: male


title: pTα1-Dam_rep3

description: Dam-Only control


title: c_MG_3

description: ileum from c_MG_3

source_name: ileum

value: ileum

value: MG


title: baf60.21-m1, tassel stem, biol rep 2


title: pTα1-Dam_rep1

description: Dam-Only control

value: E13-14 forebrain


title: Genomic DNA from spinal ependymoma 4

description: Relation GSM5600089, GSM6629213

label: Cy3 and Cy8

tag: localization

value: lumbosacral

tag: extent of resection

tag: who tumor grade

value: myxopapillary WHO grade non-myxopapillary WHO grade 2

tag: classification result v12.5

value: MPE

tag: classification score

tag: OS status

tag: material

value: FFPE

value: spinal ependymomas


title: baf60.21-m1, tassel stem, biol rep 1

tag: tissue

tag: genotype

tag: treatment


title: GC_5_Win

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Bos Taurus reference genome (ARS-UCD1.2) using Bowtie2 (2.2.2)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as transcripts per million (TPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: ARS-UCD1.2
Supplementary files format and content: xlsx file include TPM values for each sample

organism: Bos taurus

source_name: Granulosa Cells

extract_protocol:
Total RNA was isolated from GCs using an RNeasy Plus Micro Kit, according to the manufacturer’s protocol. To remove genomic DNA contaminants, on-column DNA digestion was performed using RNase-free Dnase.
RNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

tag: cell type

value: Granulosa Cells

value: Winter


title: pcMSC-CM

source_name: Placenta

value: Placenta

tag: cell line

value: Primary cells

value: Mesenchymal stem cells

value: No


title: human_875-h2

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description: 10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus , GRCh38-2020-A for homo sapiens
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/. Gene expression and TCR V(D)J data were overlaid by R scRepertoire package.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA). Pathway analyses were performed using DAVID Bioinformatics platform.
Assembly: mm10-2020-A for mus musculus, GRCh38-2020-A for homo sapines
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: brain tumor

extract_protocol:
De-identified human PA samples (4 female sporadic PAs and 1 female NF1-PA; clinical information in Supplemental Table 3) were obtained under an approved Human Studies Protocol as dissociated frozen tumor single cells from the St. Louis Children’s Hospital Pediatric Tumor Bank. The frozen dissociated tumor single cells were thawed and resuspended in DMEM.The cells were then stained with 7-Aminoactinomycin D (7-AAD) (Fisher Scientific, A1310) for sorting using the MoFlo (Siteman Flow Cytometry Core at the Washington University in St Louis). Live cells were collected and submitted for single cell RNA sequencing (scRNA-seq).  Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: brain tumor

tag: age

value: 11 years

value: Female

value: Sporadic


title: c_MG_1

description: ileum from c_MG_1

value: ileum

value: MG

value: AA broiler

value: male


title: human_440h1

description: 10x Genomics

value: 3 years


title: pND1-Cre_floxTAF3-Dam_rep3

description: TAF3-phd(H3K4me3)-Dam fusion

value: E13-14 forebrain

value: Neurons


title: GC_3_Win

value: Granulosa Cells


title: GC_4_Win

value: Winter


title: pND1-Cre_floxTAF3-Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion


title: human_H966

description: 10x Genomics

value: 10 years


title: c_c_3

description: ileum from c_c_3

value: c


title: c_MG_2

description: ileum from c_MG_2


title: pND1-Cre_floxTAF3-Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion


title: GC_1_Win


title: pND1-Cre_floxDam_rep2

description: Dam-Only control


title: human_H590

description: 10x Genomics


title: c_c_1

description: ileum from c_c_1


title: COMB -3

city: Xia Men

first: Yu

last: Luo

address: zhenhai Road

institute: the fiirst affiliated hospital of Xiamen University

description:
FPKM_allsamples
Raw_gene_counts_matrix

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: 786-O renal cancer cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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: 786-O cells were treated with 10uM Everolimus, 1.5uM SGI-1027, 5uM Everolimus combined with1.5uM SGI-1027, or vehicle (DMSO) for 24 hours. Each processing group contains three replicates.

value: Human renal cancer cell line

value: WT


title: f_KC_1

description: lung from c_KC_1

value: lung

value: KC


title: human_S-PA-1

description: 10x Genomics

value: brain tumor

value: Female


title: pND1-Cre_floxDam_rep1

description: Dam-Only control


title: GC_5_Sum

value: Summer


title: COMB -2

description:
FPKM_allsamples
Raw_gene_counts_matrix

value: 5uM Everolimus combined with1.5uM SGI-1027


title: COMB -1

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: c_MGKC_2

description: ileum from c_MGKC_2

value: ileum

value: MGKC

value: AA broiler


title: c_MGKC_3

description: ileum from c_MGKC_3

value: male


title: pHes5_Dam_rep3

description: Dam-Only control

value: E13-14 forebrain

value: RGC


title: c_MGKC_1

description: ileum from c_MGKC_1


title: SGI-1027  -3

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: c_KC_3

description: ileum from c_KC_3


title: E_Win

source_name: Oocyte

extract_protocol:
Total RNA was isolated from oocytes using an RNeasy Plus Micro Kit, according to the manufacturer’s protocol. To remove genomic DNA contaminants, on-column DNA digestion was performed using RNase-free Dnase.
RNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

value: Oocyte

value: Winter


title: c_c_2

description: ileum from c_c_2

value: c


title: c_KC_2

description: ileum from c_KC_2


title: pHes5_Dam_rep1

description: Dam-Only control


title: SGI-1027  -2

description:
FPKM_allsamples
Raw_gene_counts_matrix

value: Human renal cancer cell line


title: D_Win


title: pHes5_H3K9ac_Dam_rep2

description: H3K9ac-mintbody-Dam fusion


title: Everolimmuys -3

description:
FPKM_allsamples
Raw_gene_counts_matrix

value: WT

value: 5uM Everolimus


title: pHes5_H3K9ac_Dam_rep1

description: H3K9ac-mintbody-Dam fusion


title: pHes5_Dam_rep2

description: Dam-Only control


title: pHes5_Dam_rep4

description: Dam-Only control


title: Everolimmuys -2

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: GC_3_Sum

value: Granulosa Cells


title: A_Win


title: c_KC_1

description: ileum from c_KC_1

value: KC


title: 30mM lactate - Rep 3

city: Philadelphia

first: Francisco

last: Albicoro

state: PA

address: 3440 N Broad St

institute: Temple University

data_processing:
Raw reads were subjected to quality control using FastQC.
Trimming of low-quality bases was performed using Sickle.
Reads were aligned to the Salmonella Typhimurium LT2 genome (NC_003197) using EDGE-pro which then calculated the RPKM values.
The raw counts were then normalized using the DESeq2 package in R.
Differential expression analysis was performed using the DESeq2 package in R with a false discovery rate (FDR) of 0.05 and P value of less than 0.05 used to determine significance.
Assembly: Salmonella Typhimurium LT2 genome (NC_003197)
Supplementary files format and content: Table S1 is an excel file containing differential gene expresion analysis of untreated vs treated samples

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: bacteria cell pellet

extract_protocol:
Total RNA was extracted using the hot phenol. RNA quality and quantity were assessed using a nanodrop (Thermo Scientific, USA).
All library construction were prepared according to the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA).

value: bacteria cell pellet

value: 30mM lactate


title: GC_2_Sum

value: Summer


title: pHes5_H4K20me1_Dam_rep3

description: H4K20me1-mintobody-Dam fusion


title: 30mM lactate - Rep 2


title: pHes5_H4K20me1_Dam_rep2

description: H4K20me1-mintobody-Dam fusion


title: Everolimmuys -1

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: 30mM lactate - Rep 1


title: GC_1_Sum


title: C_Sum


title: E_Sum


title: pHes5_H4K20me1_Dam_rep1

description: H4K20me1-mintobody-Dam fusion


title: Untreated - Rep 2

value: untreated


title: B_Sum


title: pHes5_H3K4me3_Dam_rep2

description: TAF3-phd(H3K4me3)-Dam fusion


title: Vehicle(DMSO) -1

description:
FPKM_allsamples
Raw_gene_counts_matrix

value: DMSO


title: SGI-1027  -1

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: pHes5_H3K4me3_Dam_rep1

description: TAF3-phd(H3K4me3)-Dam fusion


title: Vehicle(DMSO) -2

description:
FPKM_allsamples
Raw_gene_counts_matrix


title: Untreated - Rep 3


title: B_Win


title: pTα1-Dam_rep2

description: Dam-Only control

value: IPC