title: VirginM_6

data_processing:
Sequenced samples were quality controlled using FastQC v0.11.5 and aligned using HISAT2 v2.0.4
Gene counts were produced for the same annotations using featureCounts within subread v2.0.0
Analysis of differential expression was performed within R using the DESeq2 package (v1.24.0)
Quality assessments were performed, including PCA and hierarchical clustering, prior to analysis of differential expression using the Wald test with a specified FDR (alpha<0.05)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files containing raw read counts

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (Qiagen). 200 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepard using NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module following manufacturer's protocols.

treatment_protocol: Lactating mice at day 7 lactation, and age-matched virgin females and males were used.

value: Male


title: B1

status: Public on Mar 20 2025

type: SRA

city: San Antonio

first: Nu

last: Zhang

state: Texas

address: 7703 Floyd Curl, Medical Building/ 5.025V

country: USA

institute: UT Health Science Center

description: Old male Treg 1

library_source: transcriptomic

data_processing:
Aligned the reads with refernece genome using Kallisto
Assembly: mm10
Supplementary files format and content: xls file include raw counts for each sample along with ENSEMBL id and gene name

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
RNA was extracted using zymol RNA extraction kit
RNA libraries were prepared using Takara bio's high sensitivity kit SMARTER-seq as per manufactures protocol

tag: tissue

value: spleen

tag: age

value: Old

tag: Sex

value: male

tag: cell type

tag: genotype

value: WT


title: TRIB1 ASO rep1

type: RNA

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

hyb_protocol: Samples were hybridized to a Clariom_D array (Affymetrix) and scanned at the Centre for Applied Genomics (TCAG), Toronto

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Relative expression changes assessed by Expression Console

label: Biotin

organism: Homo sapiens

source_name: HepaRG cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Confluent HepaRGs were maintained in William's E, 10% serum, pen/strep and 2% DMSO for 2 weeks

extract_protocol: High Pure RNA isolation using Trizol and cartridges

treatment_protocol: On days 11-14 after 2%DMSO supplementation, HepaRG in 24 well plates were treated for 72 h with 60 nM final of cognate ASOs.  ASOs targeting TRIBAL /TRIB1AL (TRIBALASO2), TRIB1 (TRIB1ASO2) or a control (NTASO).

tag: cell line

value: HepaRG 2D cell culture


title: MLE12_H2Bub_IP_CTR_Rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

library_source: genomic

data_processing:
Raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
PCR duplicates were removed using MarkDuplicates.jar from picard-tools-1.119
bam files were merged with bamtools merge (default settings).
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Peaks were annotated with annotatePeaks.pl default setting
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: MLE12 cells were fixed and harvested on the plate

extract_protocol:
107 control, Rnf20+/-, and Rnf20+/-HIF1   KD MLE12 cells were fixed with 1% methanol-free formaldehyde for 10 min at room temperature. 125 mM glycine was added to quench the fixation. After three washes with PBS, cells were suspended in cold PBS at a concentration of 5  106/ml. Equal volume of 2   lysis buffer (100 mM Tris-HCl pH8, 300 mM NaCl, 2% Triton X-100, 10 mM CaCl2) was added for 10 min on ice with gentle shaking. The nuclei were washed with cold PBS and centrifuged at 2500 g, 4   C for 5 min. Chromatin was sheared using a Covaris Ultrasonicator (10% duty factor, 200 cycles, 75 A) for 6 min and the samples were clarified at 16 000g for 15 min. Next, the extracts were pre-cleaned with 75   l protein G beads for 2 h at 4  C, then incubated with 0.5   g Pol II antibody (14958S, Cell Signalling), 1   g Pol II p-Ser5 (ab5131, Abcam), 1   g Pol II p-Ser2 (13499s, Cell Signalling), 1   g H2Bub1 (5546S, Cell Signalling) or 1   g H3K4me3 (ab8580, Abcam) antibodies overnight at 4  C, followed by binding to 75   l BSA-coated protein G beads. Immunoprecipitates were washed twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 150 mM NaCl), three times with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 500 mM NaCl), twice with LiCl buffer (10 mM Tris-HCl pH7.5, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and then eluted with Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA pH8.0, 1% SDS). Samples were treated with RNase A for 1 h at 37   C, followed by Protein K digestion for 2 h at 37   C, and cross-linking was reversed by incubation at 65   C overnight. DNA was purified by using the Qiagen mini elute PCR purification kit (Qiagen, 28004).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S/L, E7103S/L) according to the manufacturer's instructions.

value: control

tag: antibody

value: Ubiquityl-Histone H2B (Lys120) (D11) XP® Cell Signalling


title: sgCtrl_H3K36me3_2

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

data_processing:
3' ends adapter sequences were removed using Trim Galore! (version 0.6.5) and Cutadapt (version 2.8).
The reads were then mapped to the spike-in genome (sacCer3) initially, and the remaining reads were subsequently mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 800 bp (less than 1% of the total) were excluded from subsequent analysis.
To generate the signal landscape, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was multiplied by 1x10-6 divided by a library size. These values were then averaged over a 10 bp resolution and written in bigWig files.
For the bigWig files (v1), the library size is the number of uniquely mapped fragments after deduplication. For the bigWig files (v2) of H3K4me3, the library size is the number of fragments uniquely mapped to the spike-in genome. For the bigWig files (v2) of H3K36me3, the library size is the number of fragments uniquely mapped to the common significant gene bodies . A list of common significant gene bodies in all H3K36me3 samples was determined by comparing against IgG and input samples using a binomial test with FDR ≤ 0.05.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: PC-3M human prostate cancer cells were cultured  in Dulbecco’s modified Eagle’s (DMEM) medium with 10% FBS and 1% penicillin/streptomycin and incubated at 37 °C under 5% CO2.

extract_protocol:
CUT&RUN was carried out using the CUT&RUN Assay Kit (Cell Signaling Technology,86652) as per the manufacturer’s instructions
Sequencing libraries were prepared using the DNA Library Prep Kit (Cell Signaling Technology, 56795) for Illumina Platforms

treatment_protocol: PC-3M Ctrl and ASH1L knockout stable cell lines were generated using CRISPR-Cas9 system and selected by puromycin

value: human prostate cancer cells

value: Ctrl

tag: treatment

value: stable cell line

tag: cut&run antibody

value: H3K36me3 (Abcam, ab9050)


title: VirginM_4

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

molecule: polyA RNA

source_name: Ileum

growth_protocol: Mice were fed a standard diet whilst breeding or in maintenance colonies; RM3 during breeding and RM1 for maintenance and experiment (Special Diets Services)

value: Ileum

tag: mating status

value: Virgin


title: MLE12_Rnf20_Het_RNA_seq_Rep3

data_processing:
Raw reads were Trimmed with trimmomatic-0.36.jar (ILLUMINACLIP:<Truseq_SE.fa>}:2:30:10  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15 CROP:48 HEADCROP:7
The trimmed reads were mapped to the mm10 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
Differential expression was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR.
Excel was used to filter differentially regulated genes (fold change ≥1.5; log2 fold change ≤-0.58, ≥0.58; p-value < 0.05.)
Assembly: mm10
Supplementary files format and content: xls

source_name: Lung Epithelial cells MLE-12

growth_protocol: All the cell lines are cultrured in DMEM F-12 medium with 1%P/S,10%FCS and 1%glutamin.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
BGI_RNA Seq

treatment_protocol: Heter cell line were generated by CRISPR-Cas9 system, check the cell lines by genotyping,q-pcr and WB, cell growth in standered medium, harvest the RNA when cells growth to 70% -80% confluency.

value: Lung Epithelial cells MLE-12

value: Rnf20 +/- heterozygous line


title: TRIBAL ASO rep2


title: sgASH_input_for_H3K4me3

value: ASH1L Knockout


title: MLE12_Rnf20_Het_RNA_seq_Rep2


title: sgASH_input_for_H3K36me3


title: MLE12_H2Bub_IP_hetRnf20_Rep1


title: TRIBAL ASO rep1


title: MLE12_Rnf20_Het_RNA_seq_Rep1


title: VirginM_1

value: Male


title: CTL rep3


title: sgASH_igG_for_H3K4me3

value: IgG control (Cell Signaling Technology, 66362)


title: MLE12_Rnf20_Ctrl_RNA_seq_Rep3

value: Rnf20 +/+ CTR


title: sgASH_igG_for_H3K36me3


title: VirginF_6

value: Female


title: MLE12_Rnf20_Ctrl_RNA_seq_Rep2


title: CTL rep2


title: VirginF_5


title: VirginM_5


title: sgASH_H3K4me3_2

value: H3K4me3 (Cell Signaling Technology, 9751)


title: CTL rep1

value: HepaRG 2D cell culture


title: MLE12_Rnf20_Ctrl_RNA_seq_Rep1


title: VirginF_4


title: sgCtrl_H3K36me3_1


title: sgASH_H3K4me3_1


title: VirginM_3


title: VirginM_2


title: delta pcnB/pil::Tn, 37C, replicate 3

city: Santa Cruz

first: Victoria

last: Auerbuch

address: 1156 High Street

institute: University of California Santa Cruz

description: Library name: 1970-37-3

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3).
Read mapping was performed with HISAT2.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm.
Assembly: see accession numbers CP032566 and CP032567 for Yersinia pseudotuberculosis pIB1 genome
Supplementary files format and content: data delimited text file 26C_mean_masterFile includes TMM values per annotated gene (average of all three replicates) for all 26 degrees C samples
Supplementary files format and content: data delimited text file 37C_mean_masterFile includes TMM values per annotated gene (average of all three replicates) for all 37 degree C samples

organism: Yersinia pseudotuberculosis

source_name: bacterial culture

growth_protocol: Y. pseudotuberculosis IP2666pIB1 strains were grown in 3 mL LB overnight at 26°C and diluted the following morning to an OD600 of 0.2 in 5 mL of fresh LB. Each strain was diluted into two separate cultures (one for each temperature). For 26°C samples, cultures were diluted in plain LB media and grown shaking at 26°C for 3 hrs before extracting RNA. For 37°C samples, cultures were diluted into LB low calcium media (containing 20 mM sodium oxalate and 20 mM MgCl2) and grown shaking at 26°C for 1.5 hours before shifting to 37°C to growing shaking for an additional 1.5 hours. After incubating, 1-2 mL of each culture was collected and pelleted for 5 mins at 4,000 rpm (~200 xg).

extract_protocol:
Supernatants were removed and cell pellets were resuspended in 1mL RNA Protect (Qiagen) and total RNA was isolated using the RNeasy minikit (Qiagen) according to the manufacturer’s protocol. DNA was removed from samples using the TURBO DNA-free kit (Life Technologies/Thermo Fischer) and RNA quality was determined using an Agilent 2000 Bioanalyzer. Samples were DNase treated with Invitrogen DNase.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp IDT for Illumina indices.

treatment_protocol: No treatment

value: bacterial culture

value: strain IP2666pIB1

value: LB media

value: delta pcnB/pil::Tn

value: 1.5 hours at 26 degrees C with agitation, then 1.5 hours at 37 degrees C with agitation

tag: batch


title: sgASH_H3K36me3_2

value: human prostate cancer cells

value: stable cell line

value: H3K36me3 (Abcam, ab9050)


title: delta pcnB/pil::Tn, 37C, replicate 2

description: Library name: 1970-37-2


title: VirginF_3

value: Ileum

value: Virgin


title: MLE12_RNF20_HET_shHif1a_H3K4me3_input_r1

description: Library name: 08MLE12_RNF20_shHif1a_H3K4me3_input_r1

data_processing:
The raw reads' visualization was trimmed using Trimmomatic (Bolger et al. 2014), min a length of 15 bp and Quality score of a minimum of 15.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
PCR duplicates were removed using MarkDuplicates.jar from picard-tools-1.119
bam files were merged with bamtools merge (default settings).
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC
Supplementary files format and content: BigWig files

growth_protocol: MLE-12 (mouse epithelial cells) were grown according to manufacture's recommendation

value: mouse epithelial cells

value: Rnf20_het+ shHIF1a

value: viral transfection with shHIF1A

value: Input


title: VirginF_2

value: Female


title: delta pcnB/pil::Tn, 37C, replicate 1

description: Library name: 1970-37-1


title: MLE12_RNF20_HET_H3K4me3_input_r2

description: Library name: 07MLE12_RNF20_HET_H3K4me3_input_r2

value: viral transfection with Empty Plko Vector


title: MLE12_RNF20_HET_H3K4me3_input_r1

description: Library name: 07MLE12_RNF20_HET_H3K4me3_input_r1


title: VirginF_1


title: Lactating_6

value: Lactating


title: delta pcnB, 37C, replicate 2

description: Library name: 1968-37-2

value: bacterial culture

value: delta pcnB


title: U87 RNase R-1

city: Bedford Park

first: Simon

middle: J

last: Conn

state: SA

address: Flinders Drive

country: Australia

institute: Flinders University

data_processing:
High-throughput sequencing was performed using Illumina NovaSeq
Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files using cutadapt
The FASTQ files were mapped aganist the modified (SynCRS incorported) human refrence genome (hg38) using STAR spliced alignment algorithm  (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR produced chimeric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Assembly: Modified hg38 (SynCRS incorporated)
Supplementary files format and content: Tab-delimited text files include gene counts for each sample
Supplementary files format and content: Tab-delimited text files include CIRCexplorer2 produced number of Junction reads for each sample

source_name: Cell line

growth_protocol: Human glioblastoma cell line (U87) were grown in DMEM with 10% FBS at 37oC

extract_protocol:
RNA was extracted using TriZOL and Direct-zol RNA extration columns (Zymo Research). SynCRS1-6 were spiked-in at known amounts to 2ug of RNA which was then digested with RNase R (2U/ug RNA; Epicentre) for 30mins at 37oC, then purified by Rneasy MinElute Cleanup kit (Qiagen).
Stranded RNA Libraries were constructed with RNase R-treated RNA using the Tecan Universal RNA-Seq Library with Human Probe (for rRNA depletion) protocol M01508 V2.

treatment_protocol: No treatment was applied to these cells

value: Cell line

value: glioblastoma

value: RNase R digestion


title: Lactating_5


title: U87 RNase R-2


title: XGIC67_C_P6

type: genomic

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

description:
Xenograft derived GICs; PDX seeded with primary GICs; patient 67
Illumina Infinium MethylationEPIC v1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC v2 Beadchip using standard Illumina protocol

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

data_processing: EPIC microarray data were analysed using a cross-package Bioconductor workflow in R, employing the methylation specific packages minfi, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, missMethyl and DMRcate as well as limma as described in PMID:27347385

label: Cy3, Cy5

label_protocol: not provided

growth_protocol: GIC were maintained in NeuroCult NS-A Proliferation kit medium, 1% Pen/Strep, 2µg/ml Heparin, 20ng/ml murine EGF and 10ng/ml human FGF. iNSC were cultured in 0.5X Advanced DMEM/F-12 , 0.5X Neurobasal medium, 1X Neurobasal Induction supplement and 1X pen/strep

extract_protocol: DNA and RNA were extracted from tissue samples using the FFPE RNA/DNA Purification Plus Kit (Norgen, 54300) as per manufacturer protocol. For cells (GICs/GICRs/XGICs/XGICRs/IRGICs) both DNA and RNA were extracted from pellets containing one well of a 6-well plate (confluency 80%) using the RNA/DNA/Protein Purification Plus Kit (Norgen, 47700) following the instructions provided by the manufacturer. The extracted DNA was further purified following the protocol of the Genomic DNA Clean & Concentrator-25 kit (Zymo research, D4011).


title: sgCtrl_igG_for_H3K36me3

value: human prostate cancer cells

value: Ctrl

value: IgG control (Cell Signaling Technology, 66362)


title: MLE12_RNF20_HET_shHif1a_H3K4me3_ChIP_r2

description: Library name: 06MLE12_RNF20_shHif1a_H3K4me3_ChIP_r2


title: XGIC67_C_P5

source_name: Xenograft derived GICs; PDX seeded with primary GICs; patient 67


title: pil::Tn, 37C, replicate 3

description: Library name: 1276-37-3

value: strain IP2666pIB1

value: LB media

value: 1.5 hours at 26 degrees C with agitation, then 1.5 hours at 37 degrees C with agitation


title: delta pcnB, 37C, replicate 1

description: Library name: 1968-37-1


title: MLE12_RNF20_HET_shHif1a_H3K4me3_input_r2

description: Library name: 08MLE12_RNF20_shHif1a_H3K4me3_input_r2

value: mouse epithelial cells

value: Rnf20_het+ shHIF1a


title: Lactating_3

value: Ileum


title: MLE12_RNF20_HET_H3K4me3_ChIP_r2

description: Library name: 05MLE12_RNF20_HET_H3K4me3_ChIP_r2


title: MLE12_RNF20_HET_shHif1a_H3K4me3_ChIP_r1

description: Library name: 05MLE12_RNF20_shHif1a_H3K4me3_ChIP_r1

value: viral transfection with shHIF1A


title: 2573-Brain_vehicle

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: 2573-Brain

data_processing:
Reads were mapped to the mouse reference genome (UCSC, GRCm39) using the alignment tool STAR (v2.7.10b). Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0). HTSeq (v.0.2.0) and python (v.2.7) was used for counting mapped sequencing reads. RSeQC (v5.0.1) was used to further quality control mapped sequenced reads.
Quantified read counts were normalized and analyzed using DESeq2 (v1.12.3) to determine differential expression between groups, within the R statistical computing environment (v4.2.2)
Pairwise differential expression analysis were performed with DESeq2. Identical read filtering parameters were used for different organs, and genes with read counts < 5 in at least half of the samples per treatment group were removed.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Brain

extract_protocol:
Total RNA from tissue was isolated using the PureLink RNA mini kit using manufacturer’s instructions (Invitrogen). Genomic DNA was removed using RapidOut DNA Removal Kit (ThermoFisher).
Sequencing libraries were constructed using a 3’ Tag-based approach (TagSeq), targeting the 3’ end of mRNA fragments.
3’ TagSeq was performed by the University of Texas Genomic Sequencing and Analysis Facility (RRID#: SCR_021713) . Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550bp on a 2% gel using the Blue Pippin (Sage Science).  The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were then sequenced on the NovaSeq 6000 (Illumina) instrument with single-end, 100-bp reads.

value: Brain

value: total homogenate

tag: strain

value: vehicle

value: Male


title: sgASH_H3K36me3_1

value: ASH1L Knockout

value: stable cell line

value: H3K36me3 (Abcam, ab9050)


title: Lactating_4

value: Lactating

value: Female


title: XGIC67_B_P6

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 67


title: XGIC67_B_P5


title: pil::Tn, 37C, replicate 2

description: Library name: 1276-37-2

value: bacterial culture

value: strain IP2666pIB1


title: Lactating_2


title: TRIBAL ASO rep3

value: HepaRG 2D cell culture


title: MLE12_RNF20_HET_H3K4me3_ChIP_r1

description: Library name: 04MLE12_RNF20_HET_H3K4me3_ChIP_r1

value: mouse epithelial cells

value: viral transfection with Empty Plko Vector


title: delta pcnB, 37C, replicate 3

description: Library name: 1968-37-3

value: LB media

value: delta pcnB

value: 1.5 hours at 26 degrees C with agitation, then 1.5 hours at 37 degrees C with agitation


title: pil::Tn, 37C, replicate 1

description: Library name: 1276-37-1


title: early HCC cells  from DEN-induced mice, knockdown Mef2d, input

city: chongqing

first: li

last: ni

state: State...

address: chongqing univeristy

department: Oncology laboratory

country: China

institute: chongqing univeristy

data_processing:
nf-core/cutandrun pipline
Assembly: mm10
Supplementary files format and content: bigWig (bw) file
Library strategy: CUT&Tag

source_name: eHCC

extract_protocol:
the cells of Mef2dΔHep or Mef2dfl/fl primary early HCC cells isolated from single DEN-treated mouse were collected and then subjected to total RNA extraction using CUT&RUN Kit  according to the manufacturer’s instructions protocols.
Chromatin immunoprecipitation using antibodies to enrich DNA fragments The library was constructed with CUT&Tag-IT™ Assay Kit according to the manufacturer’s instructions;

value: eHCC

value: early HCC cells

value: KO


title: XGIC67_A_P6


title: Lactating_1

value: Ileum


title: wildtype, 37C, replicate 3

description: Library name: 983-37-3

value: wildtype


title: early HCC cells  from DEN-induced mice, knockdown Mef2d, H3K4me3


title: Daidzein treated FGSCs rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by QCutadapt (V1.9.1) to be high quality clean data.
Mapping:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis:Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And top GO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: mm9
Supplementary files format and content: all.fpkm.txt

source_name: ovary

growth_protocol: FGSCs were cultured in Minimum Essential Medium-alpha (MEM-alpha; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 1 mM non-essential amino acids (Invitrogen Life Sciences,C A, USA), 6 mg/mL penicillin (Amresco , Lardner, PA, USA), 30 μg/mL pyruvate (Amresco), 2 mM L-glutamine (Amresco), 100 μM β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA), 10 ng/mL mouse leukemia inhibitory factor (Santa Cruz Biotechnology), 40 ng/mL mouse glial cell line-derived neurotrophic factor (R&D Systems, Minneapolis, MN, USA), 10 ng/mL mouse basic fibroblast growth factor (BD Biosciences, Franklin Lakes, NJ, USA), and 20 ng/mL mouse epidermal growth factor (PeproTech, NJ, USA).

extract_protocol:
Total RNA of FGSCs was extracted using Trizol reagent (Life Technologies, CA, USA), in accordance with the manufacturer’s instructions. The quality of total RNA was analyzed using Nanodrop Lite (Thermo Fisher Scientific ). A total of 1 mg of RNA was reverse-transcribed into cDNA using a reverse-transcription kit (Takara, Tokyo, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: FGSC was treated with DMSO and daidzein at different concentrations

value: Female germline stem cells (FGSCs)

value: ovary

tag: condition

value: normal

value: daidzein


title: XGIC67_A_P5

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 67


title: wildtype, 37C, replicate 2

description: Library name: 983-37-2

value: bacterial culture

value: strain IP2666pIB1


title: Daidzein treated FGSCs rep1


title: early HCC cells  from DEN-induced mice, knockdown Mef2d, H3K27ac


title: XGIC67R_C_P6

description:
Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67
Illumina Infinium MethylationEPIC v1


title: wildtype, 37C, replicate 1

description: Library name: 983-37-1


title: XGIC67R_C_P5

source_name: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: Control FGSCs rep2

value: DMSO


title: early HCC cells  from DEN-induced mice, Control, input

value: WT


title: delta pcnB/pil::Tn, 26C, replicate 3

description: Library name: 1970-26-3

value: LB media

value: delta pcnB/pil::Tn

value: 3 hours at 26 degrees C with agitation


title: early HCC cells from DEN-induced mice, knockdown Mef2d, ATACSeq

data_processing:
databio/pepatac pipline
Assembly: mm10
Supplementary files format and content: bigWig (bw) file

extract_protocol:
As cell number limitation of primary early HCC cells isolated from single DEN-treated mouse, the cells from Mef2dΔHep or Mef2dfl/fl mice (n > 5 per group) were mixed for ATAC-seq. ATAC-seq libraries were generated from 1 × 10 5purified cells, according to standard protocol.
Assay of transposase accessible chromatin-sequencing to identify the accecible regions on the genome The library was constructed with Nextera DNA library Prep Kit according to the manufacturer’s instructions

value: eHCC


title: delta pcnB/pil::Tn, 26C, replicate 2

description: Library name: 1970-26-2


title: XGIC67R_B_P6

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: early HCC cells from DEN-induced mice, Control, ATACSeq

value: early HCC cells


title: Control FGSCs rep1


title: XGIC67R_B_P5


title: early HCC cells  from DEN-induced mice, Control, H3K4me3


title: delta pcnB, 26C, replicate 3

description: Library name: 1968-26-3

value: delta pcnB


title: XGIC67R_A_P5


title: XGIC67R_A_P6


title: delta pcnB, 26C, replicate 2

description: Library name: 1968-26-2


title: early HCC cells  from DEN-induced mice, Control, H3K27ac


title: delta pcnB, 26C, replicate 1

description: Library name: 1968-26-1


title: MEF2D_WT_TME

library_source: transcriptomic single cell

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0).FASTQ files were aligned to GRCh38 using Cellranger count.
Assembly: mm10
Supplementary files format and content: cellrange format

source_name: eHCC tissue from mice

extract_protocol:
Premalignant liver or early HCC tissues for scRNA-seq were washed with PBS, cut into small pieces (< 1 mm3) on ice, and digested using a Dissociation Kit (Miltenyi Biotec; Cat#130-095-929) according to the manufacturer’s instructions
Libraries were created using 10X Genomics 5' GEX  as per the manufacturer's instructions.

value: eHCC tissue from mice


title: CAKI1_noBCAA_1

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 1824 6th Avenue South

department: Urology

institute: UAB

description:
Library name: CAKI1_noBCAA_1
CAKI-1 cells treated without BCAA for 16 hrs

data_processing:
The RNA-sequencing of BCAA treated and untreated 769-P and CAKI-1 cells were done in replicates. Adapter sequences and low quality reads were trimmed from fastq files using trim_galore.
With TopHat v2.1.0, trimmed raw read sequences were mapped to Homo sapiens reference genome (hg38)
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis was carried out using DESeq2 considering “blind” method for estimating dispersion and “fit-only” sharing mode.  Genes with absolute fold change of 2 or more and p-value <0.05 were considered as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab delimited text file include normalized read counts for each sample from DESeq.

growth_protocol: RCC cell lines were obtained from ATCC. 769-P cells were cultured in RPMI 1640 medium (Corning Life Science) supplemented with 10% FBS (R&D systems) with 100 U/mL penicillin-streptomycin. CAKI-1 cells were maintained in MEM medium supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA from these cultured cells was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RCC cells (769-P and CAKI-1) were treated without or with BCAA (0.38 mM isoleucine, 0.38 mM leucine, and 0.17 mM valine) for 16 hours.

value: clear cell renal cell carcinoma cells

value: no BCAA


title: XGIC67_D_P5


title: XGIC67_D_P6


title: CAKI1_wBCAA_2

description:
Library name: CAKI1_wBCAA_2
CAKI-1 cells treated with BCAA for 16 hrs

value: BCAA


title: CAKI1_noBCAA_2

description:
Library name: CAKI1_noBCAA_2
CAKI-1 cells treated without BCAA for 16 hrs


title: CAKI1_wBCAA_1

description:
Library name: CAKI1_wBCAA_1
CAKI-1 cells treated with BCAA for 16 hrs


title: MEF2D_KO_TME

value: KO


title: 769P_noBCAA_1

description:
Library name: 769P_noBCAA_1
769-P cells treated without BCAA for 16 hrs


title: 769P_noBCAA_2

description:
Library name: 769P_noBCAA_2
769-P cells treated without BCAA for 16 hrs


title: delta pcnB/pil::Tn, 26C, replicate 1

description: Library name: 1970-26-1


title: MEF2D_WT_PME

source_name: Premalignant liver tissue from mice

value: Premalignant liver tissue from mice

value: Premalignant liver cells


title: pil::Tn, 26C, replicate 2

description: Library name: 1276-26-2

value: bacterial culture

value: strain IP2666pIB1


title: MEF2D_KO_PME


title: KC2_4

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to mm10 reference genome using HISAT program with default parameters, Read counts were calculated using RSEM program
Assembly: mm10
Supplementary files format and content: Tab-delimited gene-by-sample text file with raw gene counts  for each sample

source_name: Kupffer cells from DEN-induced murine PME

extract_protocol:
Total RNA was extracted from hepatocytes, early HCC cells, KC1s, and KC2s using TRIzol reagent (Invitrogen; Cat#15596018CN),according to the manufacturer’s instructions
Automated stranded RNA-seq library prep, polyA selection, following manufacturer's protocol

value: Kupffer cells


title: 769P_wBCAA_1

description:
Library name: 769P_wBCAA_1
769-P cells treated with BCAA for 16 hrs


title: 769P_wBCAA_2

description:
Library name: 769P_wBCAA_2
769-P cells treated with BCAA for 16 hrs


title: XGIC39_B_P6

description:
Xenograft derived GICs; PDX seeded with primary GICs; patient 39
Illumina Infinium MethylationEPIC v1


title: pil::Tn, 26C, replicate 1

description: Library name: 1276-26-1

value: LB media


title: wildtype, 26C, replicate 3

description: Library name: 983-26-3

value: wildtype


title: XGIC39_B_P5

source_name: Xenograft derived GICs; PDX seeded with primary GICs; patient 39


title: KC2_3

value: Kupffer cells from DEN-induced murine PME


title: XGIC39_C_P5

value: Xenograft derived GICs; PDX seeded with primary GICs; patient 39


title: wildtype, 26C, replicate 1

description: Library name: 983-26-1

value: 3 hours at 26 degrees C with agitation


title: wildtype, 26C, replicate 2

description: Library name: 983-26-2


title: KC2_2


title: C2 Day23

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: organoids developed from hESCs under under standard conditions

data_processing:
After filtering out cells with less than 500 genes and more than 25% mitochondrial content resulted in 2945 total cell transcriptomes derived from the glutamine-deprived organoids and 2913 transcriptomes are generated from the organoids grown under standard condition. Unsupervised clustering was performed and a t-distributed stochastic neighbor embedding (t-SNE) plot for two-dimensional visualization was generated for each experimental group and clusters were identified and labeled according to well-known differentially expressed marker genes. Combined analysis of cells from organoids derived from glutamine-deprived and standard condition was performed using canonical co-relation analysis function in Seurat R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix files in tab delimited format

source_name: embryonic stem cell

growth_protocol: The H9 human ESC cell-line was purchased from WiCell. H9 cells (passage 35–55) and were maintained in mTeSR1 (Stem Cell Technologies, #05850) according to the manufacturer’s protocol. For differentiation, cells were changed to ReproFF2 media (ReproCELL, #RCHEMD006) supplemented with FGF2 (10 ng/mL) (Life Technologies, #PHG0021) in 10 cm dishes or 6 well plates coated with 1% vol/vol LDEV-Free hESC-qualified Geltrex (Life Technologies, #A1413302) in a 37°C incubator with 5% CO2 for 12-24 hours. hPSCs were passaged using Accutase (STEMCELL Technologies, #07920) or ReLeSR™) every 5-7 days. Cells were incubated in 10 µM ROCK Inhibitor (Y-27632 dihydrochloride, TOCRIS, #1254) for 1 day after passaging. Routine cytogenetics and mycoplasma testing were performed.Differentiation toward nephron progenitor cells was performed following a modified version of a published protocol by Morizane et al (Morizane and Bonventre, 2017a). After a brief wash with PBS, pluripotent stem cells were dissociated with Accutase (STEMCELL Technologies, #07920) or ReLeSR™ (STEMCELL Technologies, #05872). Cells were then plated at a density of 40-50 percent coated with 1% Geltrex (Life Technologies, #A1413202) in stem cell media supplemented with the ROCK inhibitor Y27632 (10 µM) (TOCRIS, #1254). Then, approximately 24 hours after seeding, cells were treated overnight with ReproFF2 supplemented with FGF2 (10 ng/mL). Cells were washed with PBS and then cultured in basic differentiation medium consisting of Advanced RPMI1640 (Life Technologies, #12633-020) and 1X L-GlutaMAX (Life Technologies, #35050-061) supplemented with CHIR99021 (8 µM) (TOCRIS, #4423) for 4 days to induce late primitive streak cells. To induce posterior intermediate mesoderm, cells were then cultured in Advanced RPMI + 1X L-GlutaMAX + activin A (10 ng/mL) (R&D, #338-AC-050) for 3 days. For induction of nephron progenitor cells, the media was then changed to Advanced RPMI + 1X L-GlutaMAX + FGF9 (10 ng/mL) (R&D, #273-F9–025/CF) for 7 days. CHIR99021 (3 µM) was added to the media from day 9 to 11 of differentiation to induce renal vesicles. On day 14, cells were switched to the basic differentiation medium and cultured for an additional 7 to 14 days (total of 21-23 days). The medium was replaced every 2 or 3 days.

extract_protocol:
Organoids were collected by scraping cells from a petri dish (10 cm diameter) and dissociated using cold active protease (Bacillus licheniformis) as described by Adam et al., 2017 (Adam et al., 2017). About 20 organoids generated in 3D culture under each condition were dissociated with 5 mg of cold active protease (Sigma, #P5380) in 1 mL DPBS for 15 min on a slow moving shaker with repeated trituration at 4°C to avoid high temperature artifacts. Cells were passed through a 30 µm cell strainer, washed once in DPBS supplemented with 0.04% BSA, centrifuged at 300 x g for 10 min and adjusted to a concentration of 200,000 cells/mL in 0.04% BSA in DPBS. We followed the DropSeq protocol described by Macosko et al. with some modifications described in detail by Menon et al (Macosko et al., 2015; Menon et al., 2018). Consistent with our previous findings, in the NPC stage (Figure 8A) ~ 500,000 cells were isolated from the standard condition while only ~200,000 cells were detected under the glutamine-deprived condition. Approximately 100,000 cells of each group were loaded onto a DropSeq device for single cell transcriptomic analysis.
DropSeq protocol described by Macosko et al.
Next generation sequencing of generated scRNA-Seq libraries was performed on an Illumina HiSeq2500 platform (paired end 26x115 bp). R1 is the barcode and R2 is the mRNA sequence

tag: time

value: Day 23

value: organoids developed from hESCs

value: standard conditions


title: XGIC39_A_P6


title: pil::Tn, 26C, replicate 3

description: Library name: 1276-26-3


title: XGIC39_A_P5


title: C2 replicate 2 Day9

value: Day 9


title: KC1_4


title: XGIC67R_D_P6

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 67


title: MLE12_Rnf20_Het_PLKO_Pol2_chipseq_INPUT

data_processing:
Raw reads using Trimmomatic (Bolger et al. 2014), min length of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
PCR duplicates were removed using MarkDuplicates.jar from picard-tools-1.119
bam files were merged with bamtools merge (default settings).
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Pausing index was calculated according to the enrichtment of the Pol2 at the TSS (-50 to 300) divided by the enrichment of Pol2 to the gene body plus 3kb from the end ot the transctiptional termination site (TTS) according to (https://github.com/MiMiroot/PIC)
Peaks were annotated with annotatePeaks.pl default setting
Assembly: mm10

value: Rnf20+/- PLKO


title: KC1_3


title: CIH group replicate3

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

description:
Library name: T10
G

library_source: other

data_processing:
1.We used GO enrichment analysis and the KEGG pathway to analyze the advanced functions of differentially expressed miRNA (DEmiR)-targeted genes.These analyses were based on information from the GO resource (http://www.geneontology. org) and the KEGG database (http://www.genome.jp/kegg/), using Cytoscape 3.10. 1 software. P < 0.05 was considered statistically significant enrichment. 2.We selected U6 small nucleolar RNA as the internal control. Subsequently, RT-qPCR was performed three times. The expression of tissue miRNAs was revealed after CIH treatment by RT-qPCR. 3.Data were expressed as mean ± standard deviation (SD) from independent experiments and statistical analysis performed using SPSS (version 19.0) and Prism 7.0 (GraphPad). We compared the two groups using unpaired Student’s t-test. Differences were considered significant at p < 0.05.
Assembly: as above
Supplementary files format and content: The xlsx file contains raw counts for each Sample.

molecule: other

source_name: white adipose tissue

extract_protocol:
Total RNA was extracted from tissue using the TRIzol reagent following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer
All RNAs were extracted from injured mice WAT of the CIH models. The extracted RNA samples were subjected to agarose gel electrophoresis and NanoDrop quality inspection and quantification, after which RNA-seq library was constructed. The mixed sequencing libraries of different samples were denatured with 0.1M NaOH to generate single-stranded DNA, which was then sequenced on an Illumina sequencer following the manufacturer’s instructions.

value: white adipose tissue

value: CIH


title: XGIC67R_D_P5


title: XGIC39_C_P6


title: MLE12_Rnf20_Het_shHIF1A_Pol2_chipseq_INPUT

value: Rnf20+/- shHif1a


title: KC2_1


title: KC1_2


title: CIH group replicate2

address: 福建省泉州市鲤城区中山北路34号

description:
Library name: T9
F


title: XGIC39R_E_P6

description:
Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39
Illumina Infinium MethylationEPIC v1


title: XGIC39R_E_P5

source_name: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: KC1_1


title: MLE12_Rnf20_Het_shHIF1A_Pol2_chipseq_IP

value: Pol II antibody Rpb1 NTD (D8L4Y) Cell Signalling


title: Normal_Liver_Ctrl_3

source_name: normal liver cells in mice

value: normal liver cells in mice

value: normal liver cells

value: Normal


title: CIH group replicate1

address: 福建省泉州市鲤城区中山北路34号

description:
Library name: T8
E


title: Control group replicate3

address: 福建省泉州市鲤城区中山北路34号

description:
Library name: C10
D

value: Control


title: MLE12_Rnf20_Het_PLKO_Pol2_chipseq_IP


title: XGIC39R_D_P6

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: Normal_Liver_Ctrl_2


title: C1 replicate 2 Day9

description: organoids developed from hESCs under glutamine-deprived conditions

value: glutamine-deprived conditions


title: MLE12_Rnf20_CTR_PLKO_Pol2_chipseq_IP

value: control PLKO


title: XGIC39R_D_P5


title: Normal_Liver_Ctrl_1


title: C1 Day23

value: Day 23


title: MLE12_Rnf20_HET_Pol2_chipseq_INPUT_rep3

data_processing:
Raw reads using Trimmomatic (Bolger et al. 2014), min length of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3.
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
samtools were used to convert sam files to bam files, after sorted bam files
PCR duplicates were removed using MarkDuplicates.jar from picard-tools-1.119
bam files were merged with bamtools merge (default settings).
bamCoverage was used to create bigWig files with the following settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Pausing index was calculated according to the enrichtment of the Pol2 at the TSS (-50 to 300) divided by the enrichment of Pol2 to the gene body plus 3kb from the end ot the transctiptional termination site (TTS) according to (https://github.com/MiMiroot/PIC)
Peaks were annotated with annotatePeaks.pl default setting
Assembly: mm10
Supplementary files format and content: bigWig


title: Control group replicate1

address: 福建省泉州市鲤城区中山北路34号

description:
Library name: C8
B


title: Control group replicate2

address: 福建省泉州市鲤城区中山北路34号

description:
Library name: C9
C


title: MLE12_Rnf20_HET_Pol2_chipseq_INPUT_rep2


title: MEF2D_WT3_eHCC

source_name: early HCC cells  from DEN-induced mice

value: early HCC cells  from DEN-induced mice

value: early HCC cells

value: WT


title: XGIC39R_C_P5


title: MLE12_Rnf20_CTR_PLKO_Pol2_chipseq_INPUT


title: MLE12_Rnf20_HET_Pol2_chipseq_INPUT_rep1


title: BMDM_chipseq_p65_A_23

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

data_processing:
Reads from Illumina paired end fastq files were mapped to the mouse genome (mm10) using Bowtie2 with the command “bowtie2 -q --end-to-end --very-sensitive” to generate SAM files.
Read duplicates were removed and BAM files were generated with the Picard toolkit.
Bigwig files were generated using deeptools software using the bamCoverage tool with the options “--binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2864785220  --extendReads”
Assembly: mm10
Supplementary files format and content: BigWig

source_name: bone marrow-derived macrophage

growth_protocol: Bone marrow-derived macrophages are differentiated from bone marrow cells and cultured in macrophage growth medium (MGM) (RPMI + 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 200 U/mL penicillin/streptomycin, 10% FBS, 50 µM 2-mercaptoethanol and 30% L929-conditioned media).

extract_protocol:
The chromatin from approximately 10 million cells (25-30 g) were used for histone modification ChIP and 30 million cells (~100 g) were used for the transcription factor ChIP. Cell pellets were sonicated to an average chromatin fragment of 300-400 bp. The following antibodies were used for each ChIP experiment based on instructions: 10 g anti-H3K4me3 (ab4729), 10 g anti-H3K27Ac (ab8580), 1:100 anti-IRF3 (D83B9) and 10 g anti-p65 (sc-372). 100L of Protein G dynabeads (10003D) were used for each ChIP.
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: pH medium was prepared using special RPMI-1640 without sodium bicarbonate. The media pH was adjusted to desired pH value using HCl (1 M) or NaOH (1 M). The cells were incubated at the indicated pH for at least 4 hours, followed by treatment with 10 ng/mL LPS or PBS for 4 hours in the respective conditions. mature BMDMs were plated at 15 million cells in 150 mm TC-treated plates. Cells were conditioned with pH 7.4 or 6.5 growth medium for 4 hours and stimulated with 10 ng/mL LPS for another 4 hours. In these experiments, cells were crosslinked with 200 mM DSG-PBS for 30 minutes with continuous mixing, followed by 1% formaldehyde for 10 minutes, and quenched with 0.125 M glycine for 5 minutes.

value: bone marrow-derived macrophage

value: wild-type

value: pH 7.4, 4 hrs LPS


title: XGIC39R_B_P6


title: BMDM_chipseq_p65_B_24

value: pH 6.5, 4 hrs LPS


title: MEF2D_WT2_eHCC


title: MLE12_Rnf20_CTR_Pol2_chipseq_INPUT_rep3

value: control


title: MEF2D_WT1_eHCC


title: MLE12_Rnf20_CTR_Pol2_chipseq_INPUT_rep2


title: BMDM_chipseq_IRF3_B_26


title: MEF2D_KO3_eHCC

value: KO


title: BMDM_chipseq_IRF3_A_25


title: MLE12_Rnf20_CTR_Pol2_chipseq_INPUT_rep1


title: MEF2D_KO2_eHCC


title: XGIC39R_C_P6


title: GBM67

description:
Primary GBM tumor patient 67
Illumina Infinium MethylationEPIC v1

source_name: Primary GBM tumor patient 67

value: Primary GBM tumor patient 67


title: BMDM_chipseq_k4me3-ph74-LPS


title: MLE12_Rnf20_HET_Pol2_chipseq_IP_rep3

value: Pol II antibody Rpb1 NTD (D8L4Y) Cell Signalling


title: MEF2D_KO1_eHCC


title: BMDM_chipseq_k4me3-ph74

value: pH 7.4, untreated


title: GBM39

description:
Primary GBM tumor patient 39
Illumina Infinium MethylationEPIC v1

source_name: Primary GBM tumor patient 39

value: Primary GBM tumor patient 39


title: MLE12_Rnf20_HET_Pol2_chipseq_IP_rep2


title: GIC67_p9

description:
Primary GICs patient 67
Illumina Infinium MethylationEPIC v2

source_name: Primary GICs patient 67

value: Primary GICs patient 67


title: GIC67_p10


title: GBM39R

description:
Recurrent GBM tumor patient 39
Illumina Infinium MethylationEPIC v1

source_name: Recurrent GBM tumor patient 39

value: Recurrent GBM tumor patient 39


title: BMDM_chipseq_k4me3-ph65-LPS


title: GIC67R_p8

description:
Recurrent GICs patient 67
Illumina Infinium MethylationEPIC v1

source_name: Recurrent GICs patient 67

value: Recurrent GICs patient 67


title: MLE12_Rnf20_CTR_Pol2_chipseq_IP_rep3


title: BMDM_chipseq_k4me3-ph65

value: pH 6.5, untreated


title: XRGIC67_D_P8

description:
Xenograft derived GICs; modelled-recurrence, PDX seeded with primary GICs; patient 67
Illumina Infinium MethylationEPIC v2


title: GIC39R_p8

description:
Recurrent GICs patient 39
Illumina Infinium MethylationEPIC v1

source_name: Recurrent GICs patient 39

value: Recurrent GICs patient 39


title: BMDM_chipseq_K27ac-ph74-LPS


title: MLE12_Rnf20_CTR_Pol2_chipseq_IP_rep2


title: XGIC39R_B_P5

value: Xenograft derived GICs; PDX seeded with recurrent GICs; patient 39


title: GBM67R

description:
Recurrent GBM tumor patient 67
Illumina Infinium MethylationEPIC v1

source_name: Recurrent GBM tumor patient 67

value: Recurrent GBM tumor patient 67


title: XRGIC67_D_P7

source_name: Xenograft derived GICs; modelled-recurrence, PDX seeded with primary GICs; patient 67


title: BMDM_chipseq_K27ac-ph74

value: bone marrow-derived macrophage


title: GIC39_p9

description:
Primary GICs patient 39
Illumina Infinium MethylationEPIC v1

source_name: Primary GICs patient 39

value: Primary GICs patient 39


title: XRGIC67_A_P6

value: Xenograft derived GICs; modelled-recurrence, PDX seeded with primary GICs; patient 67


title: GIC39R_p6


title: BMDM_chipseq_K27ac-ph65-LPS

value: wild-type

value: pH 6.5, 4 hrs LPS


title: MLE12_Rnf20_CTR_Pol2_chipseq_IP_rep1

value: control


title: XRGIC67_A_P5


title: A549 cells, STAT1g1 H1N1 18h, rep3

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

description:
Library name: KJ186
DNBSEQ-G400C

data_processing:
Complete Genomics RNA-seq reads were mapped against the human genome assembly version 38 (Hg38) using STAR version 2.7.9a. Custom STAR parameters were set as follows: limitOutSAMoneReadBytes: 1000000, outSAMprimaryFlag: AllBestScore, outFilterType: BySJout, alignSJoverhangMin: 8, alignSJDBoverhangMin: 3, outFilterMismatchNmax: 999, alignIntronMin: 20, alignIntronMax: 1000000, alignMatesGapMax: 1000000, outFilterMultimapNmax: 20; otherwise, default STAR parameters were used.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample as generated by STAR

growth_protocol: A549 cell lines were maintained in F-12K media with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from cells following the TRIzol isolation method (Invitrogen). All samples were quantified and assayed to confirm minimum RNA integrity number of at least 9.4 using an Agilent TapeStation 4150.
500 ng of total RNA per sample underwent mRNA capture and was then fragmented at 94°C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using eleven cycles of final amplification (KAPA mRNA HyperPrep Kit, catalog no. KK8580 and KAPA UDI Adapter Kit, catalog no. KK8727). Libraries underwent QC prior to sequencing using an Agilent TapeStation 4150.

treatment_protocol: A549 cells were seeded overnight at 175,000 cells per well in 12-well plates in 1.5 mL media to reach ~80-90% confluency the next day. The cell monolayer was washed twice with 1X DPBS and then incubated with IAV CA/09 H1N1 at MOI 0.1 or mock inoculum in serum-free media for one hour at 37°C, 5% CO2. After one hour, the inoculum was removed, and the cells were washed again with 1X DPBS. Additional serum-free media containing 0.2% bovine albumin fraction V and 0.5 μg/mL TPCK-trypsin was added, and the cells were incubated at 37°C, 5% CO2 for 18 hours.

value: epithelial cell

value: STAT1 knockdown

value: IAV CA/09 H1N1


title: HX Male WT rep. 14

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

data_processing:
R1 is a single end read file. UMI files contain the UMI of each read in R1.
Quality and adaptor trimming with cutadapt
Read mapping with STAR
Read counting and UMI counting with HTSeq
Assembly: mm10
Supplementary files format and content: TSV matrix raw counts
Supplementary files format and content: TSV matrix umi corrected counts

source_name: Brain

extract_protocol:
Qiagen RNAeasy minikit according to the manufacturer's protocol
INCPM Bulk-MARSSeq: RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019) was used to generate RNA-Seq libraries for expression profiling of XXX. Briefly, (30 ng of input) RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR  as previously described (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019).
Poly-A and 3' UTR targeting

value: Brain

value: Microglia


title: A549 cells, STAT1g1, mock 18h, rep3

description:
Library name: KJ185
DNBSEQ-G400C

value: mock


title: MLE12_Rnf20_HET_Pol2_chipseq_IP_rep1

extract_protocol:
107 control, Rnf20+/-, and Rnf20+/-HIF1   KD MLE12 cells were fixed with 1% methanol-free formaldehyde for 10 min at room temperature. 125 mM glycine was added to quench the fixation. After three washes with PBS, cells were suspended in cold PBS at a concentration of 5  106/ml. Equal volume of 2   lysis buffer (100 mM Tris-HCl pH8, 300 mM NaCl, 2% Triton X-100, 10 mM CaCl2) was added for 10 min on ice with gentle shaking. The nuclei were washed with cold PBS and centrifuged at 2500 g, 4   C for 5 min. Chromatin was sheared using a Covaris Ultrasonicator (10% duty factor, 200 cycles, 75 A) for 6 min and the samples were clarified at 16 000g for 15 min. Next, the extracts were pre-cleaned with 75   l protein G beads for 2 h at 4  C, then incubated with 0.5   g Pol II antibody (14958S, Cell Signalling), 1   g Pol II p-Ser5 (ab5131, Abcam), 1   g Pol II p-Ser2 (13499s, Cell Signalling), 1   g H2Bub1 (5546S, Cell Signalling) or 1   g H3K4me3 (ab8580, Abcam) antibodies overnight at 4  C, followed by binding to 75   l BSA-coated protein G beads. Immunoprecipitates were washed twice with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 150 mM NaCl), three times with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH7.5, 500 mM NaCl), twice with LiCl buffer (10 mM Tris-HCl pH7.5, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 20 mM EDTA) and then eluted with Elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA pH8.0, 1% SDS). Samples were treated with RNase A for 1 h at 37   C, followed by Protein K digestion for 2 h at 37   C, and cross-linking was reversed by incubation at 65   C overnight. DNA was purified by using the Qiagen mini elute PCR purification kit (Qiagen, 28004).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S/L, E7103S/L) according to the manufacturer's instructions.

value: Pol II antibody Rpb1 NTD (D8L4Y) Cell Signalling


title: A549 cells, VILMIRg2, H1N1 18h rep3

description:
Library name: KJ184
DNBSEQ-G400C

value: VILMIR knockdown


title: H3K27Ac-AB1-E7.5 replicate 2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA.
BWA (version 0.5.9-r26-dev, default parameter) to align the ChIP-Seq reads to mouse genome mm9(MGSCv37 from Sanger), Picard(version 1.65(1160)) then have been used for marking duplicated reads.
Then only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)).
We followed the ENCODE criterion to quality control (QC) the data that non-duplicated version of SPP (version 1.11) have been used to draw cross-correlation and calculated relative strand correlation value (RSC) under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6) and estimated the fragment size.
We required > 10M unique mapped reads
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: E7.5 mouse embryos

extract_protocol:
Embryos were collected at E7.5. At least three litters derived from inbred NMRI mouse were pooled together for each sample. Each sample contained at least 40 embryos. The embryos were snap frozen immediately after collection and dissociated mechanically with a protase inhibitor buffer solution.
ChIP-Seq was performed using the Diagenode Low Cell kit

tag: developmental stage

value: E7.5 mouse embryos

tag: number of embryos

value: 35-40 embryos pooled

value: NMRI

tag: chip antibody

value: H3K27ac (Active Motif Ref39135)


title: BMDM_chipseq_K27ac-ph65

value: bone marrow-derived macrophage

value: pH 6.5, untreated


title: GIC39_p8

tag: tissue

value: Primary GICs patient 39


title: H3K27Ac-AB1-E7.5 replicate 1


title: A549 cells, Ctrl, H1N1 18h, rep3

description:
Library name: KJ180
DNBSEQ-G400C

value: GFP knockdown


title: A549 cells, VILMIRg1, mock 18h, rep3

description:
Library name: KJ181
DNBSEQ-G400C


title: A549 cells, VILMIRg1, H1N1 18h rep3

description:
Library name: KJ182
DNBSEQ-G400C


title: HX Male WT rep. 13


title: HX Male WT rep. 10


title: HX Male WT rep. 37


title: Elongated spermatids, Tent5c wt/wt, rep3

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

description:
Library name: ES_TENT5c_WT_3
poly(A) tail and terminal modifications

data_processing:
Reads base calling was done with Guppy (version 5.0.10., Oxford Nanopore Technologies)
The length of the poly(A) tail for each read was determined using Nanopolish (Loman et al., 2015)
To run the Nanopolish poly(A) pipeline, reads were indexed with Nanopolish and mapped reads were sorted and indexed with SAMtools (Danecek et al., 2021)
Reads were demultiplexed using Deeplexicon (Smith et al., 2020).
Count matrix obtained from direct RNA sequencing using the DESeqDataSetFromMatrix function from DESeq2 - Bioconductor package (Love et al., 2014).
Assembly: Reads were then aligned to the mm10 assembly annotated with GENCODE vM17 genes using Minimap2 software v2.20-r1061
Supplementary files format and content: Comma separated value file with mapping transcript, polyA tail length, modification and replicate information for each read. File used as an input for poly(A) tail analysis and differential transcript accumulation (DESeq2, Bioconductor package, Love et al., 2014).
Supplementary files format and content: Comma separated value file with count matrix. File used as an input for Cell Population Mapping (Frishberg at al. 2019).
Supplementary files format and content: Comma separated value file showing differential transcript accumulation between round spermatids and elongated spermatids from wt/wt mice. Output from DESeq2 analysis (Bioconductor package, Love et al., 2014).
Supplementary files format and content: Comma separated value file showing differential transcript accumulation between round spermatids of Tent5c dcat/dcat and wt/wt mice. Output from DESeq2 analysis (Bioconductor package, Love et al., 2014).
Supplementary files format and content: Comma separated value file showing differential transcript accumulation between elongated spermatids of Tent5c dcat/dcat and wt/wt mice. Output from DESeq2 analysis (Bioconductor package, Love et al., 2014).

source_name: Testis

growth_protocol: Round (RS) and elongated (ES) spermatids were obtained from adult male mice.

extract_protocol:
Total RNA was isolated using TRIzol. Poly(A) RNAs were purified with oligoT beads.
Direct RNA sequencing libraries were built according to the Oxford Nanopore Technologies protocol (Direct RNA Sequencing Kit- SQK-RNA002) with modifications to incorporate barcoded oligonucleotides.
This analysis include 3 libraries per condition considered here as replicate (rep1-3). Each library is built with a pool of mRNAs isolated from the spermatids of 3 independant mice. Each library include four distinct barcodes to detect 3'end residues. Libraries were run on Nanopore R9 chips with a GridIon instrument.

treatment_protocol:
Spermatids were isolated from wt/wt male mice or mice expressing a catalytically inactive TENT5C (Tent5cdcat/dcat).
Single cell suspensions of total testis were double stained with Hoescht and PI. Round and elongated spermatids were isolated based on their DNA content, red fluorescence and side and forward scatter.

value: Testis

value: Elongated spermatids (ES)

value: Tent5c wt/wt

tag: age

value: Adult


title: Elongated spermatids, Tent5c dcat/dcat, rep2

description:
Library name: ES_TENT5c_dCAT_2
poly(A) tail and terminal modifications

value: Tent5c dcat/dcat


title: HX Male KO rep. 17

value: Brain

value: Microglia


title: HX Male WT rep. 11


title: A549 cells, VILMIRg2, mock 18h rep3

description:
Library name: KJ183
DNBSEQ-G400C

value: epithelial cell

value: mock


title: Elongated spermatids, Tent5c dcat/dcat, rep3

description:
Library name: ES_TENT5c_dCAT_3
poly(A) tail and terminal modifications


title: HX Male KO rep. 40


title: Elongated spermatids, Tent5c wt/wt, rep1

description:
Library name: ES_TENT5c_WT_1
poly(A) tail and terminal modifications


title: A549 cells, STAT1g1 H1N1 18h, rep2

description:
Library name: KJ178
DNBSEQ-G400C

value: STAT1 knockdown

value: IAV CA/09 H1N1


title: A549 cells, Ctrl, mock 18h, rep3

description:
Library name: KJ179
DNBSEQ-G400C


title: Elongated spermatids, Tent5c dcat/dcat, rep1

description:
Library name: ES_TENT5c_dCAT_1
poly(A) tail and terminal modifications


title: A549 cells, STAT1g1, mock 18h, rep2

description:
Library name: KJ177
DNBSEQ-G400C


title: HX Male KO rep. 9


title: HX Male KO rep. 6


title: Round spermatids, Tent5c dcat/dcat, rep3

description:
Library name: RS_TENT5c_dCAT_3
poly(A) tail and terminal modifications

value: Round spermatids (RS)


title: A549 cells, VILMIRg2, H1N1 18h rep2

description:
Library name: KJ176
DNBSEQ-G400C

value: VILMIR knockdown


title: HX Male KO rep. 36


title: Round spermatids, Tent5c dcat/dcat, rep2

description:
Library name: RS_TENT5c_dCAT_2
poly(A) tail and terminal modifications


title: A549 cells, VILMIRg2, mock 18h rep2

description:
Library name: KJ175
DNBSEQ-G400C


title: Round spermatids, Tent5c dcat/dcat, rep1

description:
Library name: RS_TENT5c_dCAT_1
poly(A) tail and terminal modifications


title: A549 cells, VILMIRg1, mock 18h, rep2

description:
Library name: KJ173
DNBSEQ-G400C


title: Round spermatids, Tent5c wt/wt, rep3

description:
Library name: RS_TENT5c_WT_3
poly(A) tail and terminal modifications


title: Elongated spermatids, Tent5c wt/wt, rep2

description:
Library name: ES_TENT5c_WT_2
poly(A) tail and terminal modifications


title: HX Female WT rep.39


title: Round spermatids, Tent5c wt/wt, rep2

description:
Library name: RS_TENT5c_WT_2
poly(A) tail and terminal modifications


title: HX Female WT rep.34


title: A549 cells, Ctrl, H1N1 18h, rep2

description:
Library name: KJ172
DNBSEQ-G400C


title: Round spermatids, Tent5c wt/wt, rep1

description:
Library name: RS_TENT5c_WT_1
poly(A) tail and terminal modifications


title: A549 cells, Ctrl, mock 18h, rep2

description:
Library name: KJ171
DNBSEQ-G400C


title: Testis, Tent5c dcat/dcat, busulfan, rep2

description:
Library name: DCAT_bsf_2
poly(A)

data_processing:
Reads base calling was done with Guppy (version 5.0.10., Oxford Nanopore Technologies)
The length of the poly(A) tail for each read was determined using Nanopolish (Loman et al., 2015)
To run the Nanopolish poly(A) pipeline, reads were indexed with Nanopolish and mapped reads were sorted and indexed with SAMtools (Danecek et al., 2021)
Reads were demultiplexed using Deeplexicon (Smith et al., 2020).
Count matrix obtained from direct RNA sequencing using the DESeqDataSetFromMatrix function from DESeq2 - Bioconductor package (Love et al., 2014).
Assembly: Reads were then aligned to the mm10 assembly annotated with GENCODE vM17 genes using Minimap2 software v2.20-r1061
Supplementary files format and content: Comma separated value file with mapping transcript, polyA tail length, modification and replicate information for each read. File used as an input for poly(A) tail analysis and differential transcript accumulation (DESeq2, Bioconductor package, Love et al., 2014).
Supplementary files format and content: Comma separated value file showing the count matrix. File used as an input for Cell Population Mapping (Frishberg at al. 2019).
Supplementary files format and content: Comma separated value file showing differential transcript accumulation between Tent5c dcat/dcat and Tent5c wt/wt mice, all treated with vehicle. Output from DESeq2 analysis (Bioconductor package, Love et al., 2014).
Supplementary files format and content: Comma separated value file showing differential transcript accumulation between Tent5c dcat/dcat and Tent5c wt/wt mice, all treated with busulfan. Output from DESeq2 analysis (Bioconductor package, Love et al., 2014).

growth_protocol: Testis were collected from adult male mice.

extract_protocol:
Total RNA was isolated from total testis using TRIzol. Poly(A) RNAs were purified with oligoT beads.
Direct RNA sequencing libraries were built according to the Oxford Nanopore Technologies protocol (Direct RNA Sequencing Kit- SQK-RNA002) with modifications to incorporate barcoded oligonucleotides for multiplexing.
This analysis include 2 libraries considered here as replicate (rep1 and rep2). Each library was prepared by multiplexing 4 mRNA extracts (BC 1-4) representative of 1 mouse in each of the 4 conditions. Libraries were run on Nanopore R9 chips with a GridIon instrument.

treatment_protocol: Mice were injected with a single dose of busulfan 20mg/kg or the corresponding vehicle 4 weeks prior testis collection.

value: busulfan


title: HX Female KO rep.7


title: Testis, Tent5c dcat/dcat, busulfan, rep1

description:
Library name: DCAT_bsf_1
poly(A)


title: A549 cells, STAT1g1 H1N1 18h, rep1

description:
Library name: KJ170
DNBSEQ-G400C


title: A549 cells, STAT1g1, mock 18h, rep1

description:
Library name: KJ169
DNBSEQ-G400C


title: HX Female KO rep.16


title: Testis, Tent5c dcat/dcat, vehicle, rep2

description:
Library name: DCAT_veh_2
poly(A)

value: vehicle


title: HX Female KO rep.33


title: A549 cells, VILMIRg2, H1N1 18h rep1

description:
Library name: KJ168
DNBSEQ-G400C


title: A549 cells, VILMIRg2, mock 18h rep1

description:
Library name: KJ167
DNBSEQ-G400C


title: HX Female WT rep. 30


title: Testis, Tent5c dcat/dcat, vehicle, rep1

description:
Library name: DCAT_veh_1
poly(A)


title: A549 cells, VILMIRg1, H1N1 18h rep2

description:
Library name: KJ174
DNBSEQ-G400C


title: Testis, Tent5c wt/wt, busulfan, rep2

description:
Library name: WT_bsf_2
poly(A)


title: A549 cells, VILMIRg1, H1N1 18h rep1

description:
Library name: KJ166
DNBSEQ-G400C


title: HX Female WT rep. 31


title: A549 cells, VILMIRg1, mock 18h, rep1

description:
Library name: KJ165
DNBSEQ-G400C


title: Round spermatids, rep2

description:
Library name: round_2
poly(A) tail

data_processing:
Reads base calling was done with Guppy (version 5.0.10., Oxford Nanopore Technologies)
The length of the poly(A) tail for each read was determined using Nanopolish (Loman et al., 2015)
To run the Nanopolish poly(A) pipeline, reads were indexed with Nanopolish and mapped reads were sorted and indexed with SAMtools (Danecek et al., 2021)
Reads were demultiplexed using Deeplexicon (Smith et al., 2020).
Count matrix obtained from direct RNA sequencing using the DESeqDataSetFromMatrix function from DESeq2 - Bioconductor package (Love et al., 2014).
Assembly: Reads were then aligned to the mm10 assembly annotated with GENCODE vM17 genes using Minimap2 software v2.20-r1061
Supplementary files format and content: Comma separated value file with mapping transcript, polyA tail length, modification and replicate information for each read. File used as an input for poly(A) tail analysis.
Supplementary files format and content: Comma separated value file with count matrix. File used as an input for Cell Population Mapping (Frishberg at al. 2019).

growth_protocol: Pachytene spermatocytes and round spermatids were obtained from adult C57BL/6J/B6 male mice.

extract_protocol:
Total RNA was isolated from germcells using TRIzol. Poly(A) RNAs were purified with oligoT beads.
Direct RNA sequencing libraries were built according to the Oxford Nanopore Technologies protocol (Direct RNA Sequencing Kit- SQK-RNA002) with modifications to incorporate barcoded oligonucleotides for multiplexing.
This analysis include 2 libraries, one for pachytene spermatocytes and one for round spermatids. The two libraries were prepared in parallel. Each library was built to multiplex 3 mRNA extracts (BC 1-3, here considered as replicate rep1-3), each representative of a pool of mRNAs from 3 independant mice.Libraries were run on Nanopore R9 chips with a GridIon instrument.

treatment_protocol: Single cell suspensions of total testis were double stained with Hoescht and PI. Pachytene spermatocytes and round spermatids were isolated based on their DNA content, red fluorescence and side and forward scatter.

value: Round spermatids


title: Round spermatids, rep1

description:
Library name: round_1
poly(A) tail


title: Testis, Tent5c wt/wt, vehicle, rep2

description:
Library name: WT_veh_2
poly(A)


title: A549 cells, Ctrl, H1N1 18h, rep1

description:
Library name: KJ164
DNBSEQ-G400C

value: GFP knockdown


title: Testis, Tent5c wt/wt, vehicle, rep1

description:
Library name: WT_veh_1
poly(A)

value: Testis


title: HX Female KO rep.1


title: Pachytene spermatocytes, rep3

description:
Library name: pachytene_3
poly(A) tail

value: Pachytene/Diplotene Spermatocytes


title: A549 cells, Ctrl, mock 18h, rep1

description:
Library name: KJ163
DNBSEQ-G400C


title: Slide1 (5x UUO, 2x Healthy)

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

institute: University of Edinburgh

hyb_protocol: The 6000-plex ISH probe panel previously described was prepared by denaturing at 95°C for 2min and placing on ice. The ISH probe mix was prepared using 1nM ISH probes in 1X Buffer R and 0.1U/μL SUPERaseIn RNase Inhibitor (Thermo Fisher, AM2696). Samples were then incubated with the probe mix at 37°C overnight. On the next day slides were washed with 50% formamide (VWR) in 2X SSC at 37°C for 25 min, rinsed twice with 2X SSC for 2 min at room temperature. Before antibody incubation slides were treated with blocking buffer with DAPI nuclear stain for 15min. For visualization of cell morphology antibodies against PanCK, CD45 and CD3 from the CosMx Segmentation and Supplemental Markers Kit were chosen and incubated at room temperature for 1 hours. Finally, after washing with 2X SSC for 2 min at room temperature a custom-made slide covers were attached to the sample slide to form a flow cell.

scan_protocol: RNA readouts were acquired used previously described by manufacturer protocols. Briefly, the assembled flow cells were loaded onto the SMI instrument and washed with reporter was buffer. Initially the flow cell was washed and a median of 12 and total of 141 field of views (FOVs) were defined inside which RNA was detected. The imaging procedure was repeated in 16 reporter pools, with each imaging repeated 8 times to increase RNA detection sensitivity. Each cycle was initiated with flowing 100µL of the Reporter Pool into the flow cell and incubating for 15min followed by flushing with 1ml of Reporter Wash Buffer. The wash buffer was replaced with imaging buffer and nine Z-stack images (0.8 um step size) of each FOV were acquired. Each cycle was completed with UV cleavage of fluorophores on the reporter probes and washing using Strip Wash buffer. Following RNA readouts DAPI and the 3 membrane antibodies were acquired by capturing nine Z-stack images after washing with Reporter Washing Buffer.

data_processing: Image processing and feature extraction followed the Nanostring pipeline which first extracts XYZ locations of individual transcripts. After image registration, feature detection and localisation the Z-stack images of nuclear and cell membrane markers were used define cell boundaries using a machine learning algorithm. Cell segmentation boundaries were used to assign transcripts to cells and subcellular compartments from which a count matrix was generated. Pipeline outputs included a cell by gene matrix, cell segmentation polygons, and cell meta data.

source_name: Kidney nephrectomy

extract_protocol: 5mm sections were cut from FFPE embedded tissue blocks and adhered to Superfrost Plus slides (VWR, 631-0108). Slides were deparaffinized with two 5min Xylene washed and two 2min 100% ethanol washes followed by proteinase K (3μg/ml; Thermo Fisher, AM2546) digestion (40°C for 30 min) and heat induced epitope retrieval at 100°C for 15 min in buffer ER1 (Leica, AR9961). After rinsing with nuclease free water and incubated with 1:1000 diluted fiducials (Bangs Laboratory) in 2X SSCT (2X saline sodium citrate, 0.001% Tween 20) for 5min at room temperature. After PBS washes were fixed with 10% neutral buffered formalin for 5min at room temperature. After rinsing with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base) and a 5min wash with PBS samples were blocked using 100 mM N-succinimidyl acetate (Thermo Fisher, 464750250) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8) for 15 min at room temperature. Samples were rinsed with 2X saline sodium citrate (SSC) for 5 min and samples were covered with an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs).

treatment_protocol: Nephrectomy tissue was fixed with in neutral buffered formalin and embedded in paraffin. 5µm sections  were cut.

value: Ureteral obstruction (UUO, n=5) and healthy kidneys (n=2)


title: Pachytene spermatocytes, rep1

description:
Library name: pachytene_1
poly(A) tail


title: MAVER1 response, Ibrutinib condition

status: Public on Mar 19 2025

city: Montpellier

first: Jerome

last: MOREAUX

address: 141, rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE

country: France

institute: IGH

data_processing:
RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner.
All of the statistical analyses were performed with the R statistics software (version 4.3.0; available from https://www.r-project.org) and with R packages developed by the BioConductor project (available from https://www. bioconductor.org/).
The expression level of each gene was summarized and normalized using the DESeq2 R/Bioconductor package.
Assembly: GRCh37
Supplementary files format and content: Text file with values separated with tabs

growth_protocol: JEKO1 and MAVER1 cells were cultured at 5x10e5 cells/ml in RPMI 1640 medium + 20% FCS. JVM2 cells were cultured at 3x10e5 cells/ml in RPMI 1640 medium + 10% FCS. All cell lines were culture in T25 flasks.

extract_protocol:
A Total RNA was extreated using Qiagen AllPrep DNA/RNA/miRNA Universal Kit (ref 80224)
The RNA-seq library preparation was completed with 150 ng of input RNA using DNBSEQ Eukaryotic Strand resequencing. Paired end RNA-seq was performed with an DNBSEQ Eukaryotic Strand resequencing (BGI Genomics, China).

treatment_protocol: Cell lines were treated with ironomycin (JEKO1: 50 nM; JVM2/MAVER1: 250 nM) and ibrutinib (JEKO1: 0.5 μM; JVM2: 1.5 μM; MAVER1: 6.25 μM) for 48h

value: cell line

value: Ibru


title: MAVER1 response, Ironomycin + Ibrutinib condition

value: Irono+Ibru


title: MAVER1 response,  Ironomycin condition

value: Irono


title: Eberryi Isoseq Visual system

city: Onna

first: Daria

last: Gavriouchkina

state: Kunigami District, Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

description: Eberryi Isoseq Visual system

data_processing:
RNA-seq reads were aligned to the genome using STAR (v2.5.2b)
RNA-seq counts were obtained using featureCounts v1.6.1
scRNA-seq: scRNA-seq reads were aligned to the genome using STAR Solo (v.2.5.2b)
scRNA-seq: scRNA-seq analysis was carried out using Seurat v.4
Supplementary files format and content: RNA-seq: bam files
Supplementary files format and content: RNA-seq: bigwig file for signal visualisation
Supplementary files format and content: RNA-seq: tab-delimited file containing raw counts
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files
Supplementary files format and content: scRNA-seq: Robject files containing Seurat Objects
Supplementary files format and content: scRNA-seq: bigwig file for signal visualisation
Assembly: The genome of the animal  (E.berryi) has been submitted to ENA under project name PRJEB52690

organism: Euprymna berryi

source_name: Retinas, Optic Lobes

extract_protocol:
RNA-seq: Total RNA extraction was carried  out using TRIzol reagent (Invitrogen) for lysis followed by on-column purification using PureLink RNA Mini Kit (Invitrogen)  as described in TRIzol Plus RNA Purification instructions from manufacturer. RNA extraction was followed by Turbo DNase treatment (Thermo Fisher Scientific) to remove genomic DNA according to manufacturer’s instructions.
RNA-seq: For organ-specific transcriptomes, library preparation was achieved by using TruSeq Stranded mRNA Library Prep for NeoPrepTM (Illumina). For stage-specific transcriptomes,  NEBNExt Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used.
RNA-seq
scRNA-seq: Tissues were dissociated using a 1%  Papain solution in filtered natural seawater containing 0.1% sodium thioglycolate for retinas, and a 1% Pronase solution for non-retinal tissues on a nutator with gentle trituration. Cell clumps were filtered out using either  30µm MACS SmartStrainers (Miltenyi Biotec) for v2 sample  or using 40µm and 70µm cell strainers (flowmi). Cells were resuspended in a 50% L15 medium in sterile-filtered natural seawater.
scRNA-seq:single cell transcriptomes were obtained using 10x Genomics v.2 and v.3.1 protocols as per manufacturer's instructions
scRNA-seq

value: Retinas, Optic Lobes

tag: Sex

value: Male

value: Adult - Over 100 days post hatching

tag: 10x genomics_chemistry

value: Wild-type


title: Round spermatids, rep3

description:
Library name: round_3
poly(A) tail

tag: cell type

tag: genotype


title: JVM2 response, Ibrutinib condition

tag: cell line


title: JVM2 response, Ironomycin + Ibrutinib condition

tag: treatment


title: MAVER1 response, control condition

value: Ctrl


title: JVM2 response,  Ironomycin condition


title: JEKO1 response, Ibrutinib condition


title: JEKO1 response, Ironomycin + Ibrutinib condition


title: Testis, Tent5c wt/wt, busulfan, rep1

description:
Library name: WT_bsf_1
poly(A)

value: Tent5c wt/wt


title: JEKO1 response, control condition


title: APOBEC1_MAVS-FL_RepC

city: Seattle

first: Nandan

middle: S

last: Gokhale

state: WA

address: 750 Republican St., E320

department: Immunology

institute: University of Washington

data_processing:
Data processesing was performed using the SOAPnuke platform by BGI Genomics using patameters " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 100"
Adapter filtering: If the sequencing read matched 25.0% or more of the adapter sequence (2 base mismatch maximum allowed), adapter was cut.
Read length filtering: If the length of the sequencing read was than 100 bp, the read was discarded
N removal: If the N content in the sequencing read accounts for 0.1% or more of the entire read, the read was discarded
Low-quality data filtering: If the bases with a quality value of less than 20 in the sequencing read account or 40% or more of the sequencing read, the read was discarded
Clean reads: output read quality value system is set to Phred + 33
The Bullseye pipeline was used to detect C-to-T editing at sites with at least 10 reads of coverage per sample, with an edit ratio between 2% and 95% (minEdit=5), and an edit ratio at least 1.5-fold higher than control samples (editFoldThreshold=1.5)
Assembly: hg38
Supplementary files format and content: Table of Bulleye pipeline output ("APOBEC1-mediated profiling of MAVS-associated RNA.xls"). This is a single file with tabs for comparison across conditions.

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS, 1X non-essential amino acids, 25 mM HEPES, and 1X P/S/G.

extract_protocol:
RNA was isolated using TRIzol. DNA was eliminated using Turbo DNase I, and RNA was cleaned by phenol-chloroform extraction and ethanol precipitation.
Library construction was performed through BGI Genomics. Briefly, rRNA was eliminated by digestion with RNase H and RNA was fragmented. First strand cDNA synthesis was performed using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. After end repair, A-addition, and adaptor ligation, U-labeled second strand cDNA was digested with UDG and samples were amplified by PCR. After QC, library was cyclized using a splint oligonucleotide and DNA ligase. DNA nanoball libraries were then synthesized and sequenced on the DNBseq platform.

treatment_protocol: HEK293T cells seeded in 12-well plates were transfected with 0.5 µg plasmid encoding FLAG-APOBEC1, FLAG-APOBEC1-MAVS-Cterm, or FLAG-APOBEC1-MAVS-FL using the Mirus X2 transfection reagent.

value: HEK293T cells

value: Transformed human embryonic kidney cells

value: WT

value: Transfection of pEFTak FLAG-APOBEC1-MAVS-FL


title: JEKO1 response, Ironomycin condition


title: APOBEC1_MAVS-FL_RepA


title: APOBEC1_MAVS-FL_RepB


title: Pachytene spermatocytes, rep2

description:
Library name: pachytene_2
poly(A) tail

value: Testis


title: APOBEC1_MAVS-Cterm_RepA

value: Transfection of pEFTak FLAG-APOBEC1-MAVS-Cterm


title: APOBEC1_MAVS-Cterm_RepB


title: APOBEC1_CTRL_RepC

value: Transfection of pEFTak FLAG-APOBEC1


title: APOBEC1_CTRL_RepB


title: APOBEC1_CTRL_RepA


title: JVM2 response, control condition

value: cell line


title: APOBEC1_MAVS-Cterm_RepC


title: WT preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 20

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from WT preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.3.14 was used for the normalization, summarization and quality control of the microarray data.

label: biotin

source_name: Wild type-50

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

growth_protocol: The animals were bred and maintained in the SPF (specific pathogen-free) area of the animal house.  At the age of 2 months, they were exposed to a single low-dose irradiation (2 Gy).

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

treatment_protocol: Exposed to a single low-dose irradiation (2 Gy)

value: Bone marrow


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 22

description: Gene expression data from Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy)


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 13


title: WT preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 19

source_name: Wild type-44


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 23


title: Leukemic pro-B cells WT-IR (2 Gy), SAMPLE 14

description: Gene expression data from WT leukemic bone marrow cells

source_name: Wild type-1


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 10

description: Gene expression data from Pax5+/- leukemic bone marrow cells


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 9


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 11


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 7


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 8


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 6


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 21


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 24


title: Leukemic pro-B cells WT-IR (2 Gy), SAMPLE 15

source_name: Wild type-4


title: Leukemic pro-B cells WT-IR (2 Gy), SAMPLE 17

source_name: Wild type-16


title: Leukemic pro-B cells WT-IR (2 Gy), SAMPLE 16

source_name: Wild type-17


title: Pax5+/- preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 12


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 3


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 5


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 4


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 2


title: WT preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy), SAMPLE 18

source_name: Wild type-42


title: Atopic_dermatitis_involved_skin_chronic_4

city: Kobe

first: Hayao

last: Ebise

address: 1-5-2 Minatojima Minamimachi, Chuo-ku

institute: Racthera Co., Ltd.

description: Gene expression data from chronic skin lesion of Atopic dermatitis

hyb_protocol: Labeled cRNA were hybridization on Gene Chip arrays at 45C for 16h. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip arrays were scanned using GeneArray Scanner G2500A (Afffymetrix).

data_processing: The data was summarized by pmonly-liwong method on Affy 1.1 package of R environment.

source_name: Biopsy specimen from chronic skin lesion of Atopic dermatitis

label_protocol: mRNA were amplified by reverse transcription with oligo-dT primers and in vitro transcription and then labeled cRNA were prepared as described in Gene Chip Expression Analysis Technical Manual (Affymetrix)

extract_protocol: Total RNA was prepared from each biopsy specimen section using TRIzol (Invitrogen, Carlsbad, CA) and an RNeasy Kit (Qiagen, Valencia, CA), according to the manufacturer's protocols.

value: Skin

tag: patient diagnosis

value: Atopic Dermatitis (AD)

tag: disease state

value: chronic


title: Atopic_dermatitis_involved_skin_chronic_2


title: Atopic_dermatitis_involved_skin_chronic_1


title: Atopic_dermatitis_involved_skin_chronic_5


title: Atopic_dermatitis_involved_skin_chronic_6


title: Leukemic pro-B cells Pax5 +/- IR (2 Gy), SAMPLE 1


title: Atopic_dermatitis_involved_skin_subacute_9

description: Gene expression data from subacute skin lesion of Atopic dermatitis

source_name: Biopsy specimen from subacute skin lesion of Atopic dermatitis

value: subacute


title: Atopic_dermatitis_involved_skin_subacute_7


title: Atopic_dermatitis_involved_skin_subacute_8


title: Atopic_dermatitis_involved_skin_subacute_5


title: Atopic_dermatitis_involved_skin_subacute_6


title: Atopic_dermatitis_involved_skin_subacute_3


title: Atopic_dermatitis_involved_skin_subacute_2


title: Atopic_dermatitis_involved_skin_subacute_1


title: Atopic_dermatitis_involved_skin_acute_8

description: Gene expression data from acute skin lesion of Atopic dermatitis

source_name: Biopsy specimen from acute skin lesion of Atopic dermatitis

value: acute


title: Atopic_dermatitis_involved_skin_acute_2


title: Atopic_dermatitis_involved_skin_chronic_3


title: Atopic_dermatitis_involved_skin_acute_7


title: Atopic_dermatitis_involved_skin_acute_1


title: Atopic_dermatitis_involved_skin_acute_3


title: Atopic_dermatitis_involved_skin_acute_6


title: Atopic_dermatitis_involved_skin_acute_5


title: Atopic_dermatitis_involved_skin_acute_4


title: Atopic_dermatitis_uninvolved_skin_4

description: Gene expression data from uninvolved skin from a patient with Atopic dermatitis

source_name: Biopsy specimen from uninvolved skin from a patient with Atopic dermatitis


title: Atopic_dermatitis_uninvolved_skin_3


title: Atopic_dermatitis_uninvolved_skin_2


title: Atopic_dermatitis_involved_skin_subacute_4


title: Atopic_dermatitis_uninvolved_skin_1


title: CC,Input,Flag-CMV,rep3

city: Beer Sheva

first: Adam

last: Zaretsky

address: David Ben Gurion Blvd 1

institute: Ben Gutrion University of the Negev

data_processing:
Raw fastq files from both experiments were analyzed with nf-core/chipseq pipeline (v2.0) . In brief, reads were trimmed with TrimGalore!  and align to the hg38 reference genome using BWA algorithm . The peak calling step was performed with MACS2 software , followed by the identification of the consensus and condition-specific peak sets. Peak annotation and enrichment analysis were performed with clusterProfiler R package. Publicly available Lamin B ChIP-seq human brain data  was used to annotate LAD regions. Heterochromatin regions in SK-N-SH cells, defined using H3K27me3 and H3K9me3 peaks were downloaded from The Human Heterochromatin Chromatin Database (HHCDB). The significance of the overlap between peak sets used as a measure for REST occurrence at LAD or heterochromatin regions was calculated with regioneR package  with ‘randomizeRegions’ argument in permTest() function, aiming to preserve the size of tested regions for permutations (N = 3000).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ChIP–qPCR analysis ChIP-seq sample preparation was carried out as previously described49. Briefly, SHSY-5Y cells WT and SIRT6 KO, or WT and SIRT KO transfected with Flag-REST, K494A, K494M, K494Q were cultured up to 80% of confluence. In the case of ChIP negative controls cells were transfected with an empty vector (CMV-Flag). Cells were cross-linked with 1% formaldehyde for 10 minutes and blocked with 0.125M Glycine for 5 minutes. Cross-linked cells were scrapped on RIPA buffer (150mM NaCl, 1% NP-40, 0.5% Sodium deoxycholate, 0.1% SDS, 50mM Tris pH 8, 5mM EDTA, 0.5mM PMSF, 50mM NaF/0.2mM Sodium orthovanadate, 5uM trichostatin A), and chromatin was sonicated with a needle sonicator (VibraCell VCX130, Sonics, CT, USA) during 25 minutes, 30/30 seconds on/off cycles at 40% of amplitude. One milligram of the sonicated chromatin was incubated overnight with previously blocked SureBeads™ Protein G Magnetic Beads or Anti-FLAG® M2 Magnetic Beads. The beads were then washed 4 times with RIPA buffer, 4 times with LiCl buffer (500mM LiCl, 100mM Tris-HCl pH 8.5, 1% NP-40, 1% sodium deoxycholate), and 2 times with TE buffer (10mM Tris-HCl pH 8, 1mM EDTA). Chromatin was eluted from beads using elution buffer (70mM Tris-HCl pH 8, 1mM EDTA, 1.5% SDS) and cross-linking was reversed by adding 200mM NaCl, 1U of Proteinase K, and incubating the eluted chromatin at 65C for 5 hours. The obtained DNA was further purified using the Nucleo Spin Gel and PCR Clean-Up kit. For qPCR analysis of specific REST binding regions in the genome, we used the set of primers listed in the key resources table. qPCR was performed according to the method described. We used 1uL of Input and ChIP samples per qPCR reaction.
ChIP DNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ChIP-Seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA). NEB Next Ultra II DNA Library Preparation kit was used following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Briefly, the ChIP DNA was end repaired and adapters were ligated after adenylation of the 3’ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina Novaseq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the Novaseq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and demultiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

tag: chip-antibody

value: Neuroblastoma

value: WT (CRISPR Control)

value: CMV-Flag transfection


title: CC,Input,Flag-CMV,rep2


title: CC,Input,WT,rep2

value: REST WT transfection


title: CC,Input,WT,rep1


title: CC,Input,K494Q,rep2

value: REST K494Q transfection


title: CC,Input,K494Q,rep3


title: Normal_skin_3

description: Gene expression data from normal skin

source_name: Biopsy specimen from normal skin of a healthy volunteer

value: normal


title: Normal_skin_4

description: Gene expression data from normal skin


title: CC,Input,K494M,rep2

value: REST K494M transfection


title: Atopic_dermatitis_uninvolved_skin_7


title: CC,Input,K494M,rep1


title: CC,Input,K494M,rep3


title: Atopic_dermatitis_uninvolved_skin_5


title: Normal_skin_1

description: Gene expression data from normal skin


title: CC,Input,K494A,rep3

value: REST K494A transfection


title: Normal_skin_2

description: Gene expression data from normal skin


title: CC,Input,K494A,rep1


title: CC,Input,K494A,rep2


title: CC,ChIP,WT,rep2

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse


title: CC,ChIP,Flag-CMV,rep1


title: CC,ChIP,WT,rep3


title: CC,ChIP,K494Q,rep3


title: CC,ChIP,Flag-CMV,rep2


title: CC,ChIP,WT,rep1


title: CC,Input,Flag-CMV,rep1


title: Atopic_dermatitis_uninvolved_skin_6


title: CC,Input,WT,rep3


title: CC,ChIP,K494Q,rep2


title: CC,ChIP,K494Q,rep1


title: CC,Input,K494Q,rep1


title: CC,ChIP,K494M,rep3


title: CC,ChIP,K494A,rep1


title: CC,ChIP,K494M,rep1


title: CC,Input,REST,rep1

value: No treatment


title: CC,ChIP,K494M,rep2


title: CC,Input,REST,rep2


title: CC,Input,IgG,rep1


title: C3,Input,REST,rep2

value: SIRT6 KO


title: CC,ChIP,K494A,rep3


title: CC,Input,REST,rep3


title: CC,ChIP,K494A,rep2


title: C3,Input,REST,rep1


title: CC,Input,IgG,rep2


title: C3,Input,IgG,rep2


title: CC,ChIP,Flag-CMV,rep3


title: C3,Input,REST,rep3


title: C3,Input,IgG,rep1


title: CC,ChIP,REST,rep3

value: Anti-REST (Part No.CS207378)


title: CC,ChIP,IgG,rep3

value: Rabbit IgG (Part No. PP64B)


title: CC,ChIP,REST,rep1


title: CC,ChIP,IgG,rep2


title: CC,ChIP,REST,rep2


title: CC,ChIP,IgG,rep1


title: CC,Input,IgG,rep3


title: C3,Input,IgG,rep3


title: C3,ChIP,REST,rep3


title: C3,ChIP,REST,rep2


title: C3,ChIP,REST,rep1


title: C3,ChIP,IgG,rep2


title: C3,ChIP,IgG,rep3


title: WT_Ddx54_3

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description:
Library name: WT_Ddx54_3
microRNA-seq

data_processing:
Trimmomatic - STAR - TargetScan
Assembly: mm10
Supplementary files format and content: tsv file format

source_name: Lung cancer cell line

growth_protocol: We culture LLC1 cells in 10% FBS DMEM culture media.

extract_protocol:
We extract total using iNtron extraction kit.
microRNA-seq

treatment_protocol: We knocked down Ddx54 gene in LLC1 using shRNA

value: Lung cancer cell line

value: WT DDX54


title: Ddx54_KD_1

description:
Library name: Ddx54_KD_1
microRNA-seq

value: DDX54 KD


title: Ddx54_KD_3

description:
Library name: Ddx54_KD_3
microRNA-seq


title: WT_Ddx54_2

description:
Library name: WT_Ddx54_2
microRNA-seq


title: Ddx54_KD_2

description:
Library name: Ddx54_KD_2
microRNA-seq


title: DDX54_KD_LLC1_2

description:
Library name: DDX54_KD_LLC1_2
Bulk RNA-seq

data_processing:
Trimmomatic - STAR - HTSeq
Assembly: mm10
Supplementary files format and content: tsv file format

extract_protocol: We extract mRNA using iNtron extraction kit.


title: DDX54_KD_LLC1_3

description:
Library name: DDX54_KD_LLC1_3
Bulk RNA-seq


title: WT_Ddx54_1

description:
Library name: WT_Ddx54_1
microRNA-seq


title: WT_Ddx54_LLC1_4

description:
Library name: WT_Ddx54_LLC1_4
Bulk RNA-seq


title: WT_Ddx54_LLC1_2

description:
Library name: WT_Ddx54_LLC1_2
Bulk RNA-seq


title: WT_Ddx54_LLC1_3

description:
Library name: WT_Ddx54_LLC1_3
Bulk RNA-seq