title: 60_JRX147: HT29_ORF_FOS_60

source_name: HT-29 FOS transduction, UniqueID 60

value: FOS


title: 351_JRX223: HT29_ORF_RNF186_351

status: Public on Oct 20 2021

type: RNA

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

country: Canada

institute: Montreal Heart Institute

hyb_protocol: The labeled cRNA was  normalized to 1050 ng and hybridized on HumanHT-12. Hyb Chambers were incubated in Illumina Hybridization Oven for 16 hours at 58C at rocking speed of 5 according to Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide. Beadchips were washed according to Illumina's protocol

scan_protocol: Illumina iScan Reader

data_processing:
Beadarray v2.20.1 and illuminaHuman4.db v1.24.0 packages (R Bioconductor v3.0) were used to load and annotate (readBeadSummary and add FeatureData) the fluorescence intensity data into R-3.2.0. After normalization of the array data (normaliseIllumina, method=”neqc”), data was converted and handled using Limma package v3.26.9 (Bioconductor v3.0).
Probes annotated as “Bad” or “No match” were removed. Manual quality control of each array was performed. Quality control was performed within each batch of arrays. Duplicated probes were combined.
Batch effects were then corrected using ComBat for known batches and sva v3.18.0 for unknown systematic artefacts. Given the chips were performed in five batches, each with at least two processing date, the dates from each batch were combined first before merging the batches.
To reduce impact of residual noise or batch effects on very low expression values, the fluorescence intensity values were truncated at 2^3.5, and translated down by the same amount. Repeated samples were removed. Data provided includes only samples included in the final dataset.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HT-29 RNF186 transduction, UniqueID 351

label_protocol: Biotin-labeled cRNA corresponding to poly A RNA using Illumina® TotalPrep RNA Amplification Kit, according to manufacturer’s instructions (Life Technologies)

growth_protocol: The colorectal adenocarcinoma cell line HT-29 (ATCC HTB-38) was maintained at confluence between 20% and 80% at all times in McCoy’s 5A (Wisent, 317-010CL) 10% FBS. All experiments described herein were performed in cell at passages below 25.

extract_protocol:
The RNeasy Plus Mini kit (#74036, Qiagen Inc Canada) according to manufacturer’s protocol.
The RNA samples were quantified, and quality controlled using an Agilent RNA 6000 Nano kit (Agilent, Cat No./ID 5067-1511) on 2100 Bioanalyzer system.
Number (RIN) below 8 were discarded; RIN values were routinely in the range of 9.2-10

treatment_protocol:
ORFs for IBD gene candidates were cloned into a GATEWAY® compatible polycistronic lentiviral expression vector, pLVX-EF1a-IRES-PURO/eGFP expressing an enhanced green fluorescent protein (eGFP) and puromycin N-acetyl-transferase fusion protein.
Proliferative HT-29 cells at 50% confluency in 12 well plate (Corning) were transduced in triplicate with the different ORFs (multiplicity of infection) MOI of 40-100 with 8µg/ml of polybrene (Sigma, Cat: H-9268).
Twenty-four hours post-transduction, media was changed and 3ug/ml puromycin (Millipore Sigma) was added.
The appearance and confluence of the cultures were recorded daily, and cells were grown for an average of 8 days (with a range of 5-27 days) to select successfully transduced cells and reach confluence before RNA extraction.
Transduction of the whole set of IBD gene candidate ORFs was performed in batches of about 15 ORFs, each done in triplicate, and including an empty vector control.

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate

tag: subset


title: 349_JRX221: HT29_ORF_RNF186_349

source_name: HT-29 RNF186 transduction, UniqueID 349


title: 350_JRX222: HT29_ORF_RNF186_350

source_name: HT-29 RNF186 transduction, UniqueID 350


title: 65_JRX150: HT29_ORF_FOSL2_65

source_name: HT-29 FOSL2 transduction, UniqueID 65


title: 2CLC-RNA-seq-rep4

type: SRA

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

description:
2C-Pos2-2
Smart-seq2

library_source: transcriptomic

data_processing:
ChIP-seq and ATAC-seq data analysis. Raw reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using bowtie2 (version 2.3.4.1) with default parameters. All unmapped reads and PCR duplicates were removed. Peaks were called using MACS2 (version 2.1.1.20160309) with the parameters “-q 0.05 --nomodel --nolambda --broad --extsize 300 -B --SPMR -g mm” and signal tracks for each sample were generated with wigToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
CTCF CUT&TAG data analysis. Raw reads were trimmed using trim_galore (verion 0.4.4) with default parameters and aligned to the mouse genome build mm9 using bowtie2 (version 2.3.4.1) with parameters “--local --very-sensitive -I 10”. All multiple hits and PCR duplicates were removed. Peaks were called using GEM (version 3.4) with the default parameters and signal tracks for each sample were generated with wigToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
RNA-seq data analysis. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (version 2.1.1) with default parameters. All unmapped reads and non-uniquely mapped reads were removed. Gene counts were generated using HTSeq-count (version 0.9.1). For each sample, the gene count matrices were merged together and then the ‘Trimmed Mean of M values’ normalization (TMM) method from the R/Bioconductor package edgeR package (version 3.5.0) was used to calculate the normalized expression.
Genome_build: mm9
Supplementary_files_format_and_content: txt

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol: After FACS sorting in DPBS, mESCs were incubated in lysis buffer.  RNA-seq libraries were prepared using Smart-seq2 developed by Picelli et al., Nat Protoc 2014 (PMID: 24385147).

treatment_protocol: mESCs containing a stably integrated transgene (MERVL::tdTomato) were cultured on 0.1% gelatin in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, ESCs (non-2CLCs) and 2CLCs were sorted using the fluorescent reporters. The cells were then lysed for ATAC-seq, ULI-NChIP-seq or Smart-seq2.

tag: stain

value: 129/Ola, XY

tag: transgene


title: 50_JRX142: HT29_ORF_DUSP16_50

source_name: HT-29 DUSP16 transduction, UniqueID 50


title: 59_JRX146: HT29_ORF_FOS_59

source_name: HT-29 FOS transduction, UniqueID 59


title: 2CLC-RNA-seq-rep3

description:
2C-Pos2-1
Smart-seq2


title: Sample 1- 104624 GFP+ cells, Dorsal Region Organoid Fusion Day 90

city: Vienna

first: Sunanjay

last: Bajaj

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute for Molecular Biotechnology of the Austrian Academy of Sciences

data_processing:
Adapter were clipped with trimgalore (v0.5.0)
Abudant sequences (Rrna, mitochondrion, phiX, adapter, polyA/C) were removed with bowtie2 (v2.3.4.1)
Cleaned reads were aligned against the genome (GRCh38) with STAR (v.6.0c)
Reads were counted towards their corresponding gene (ENSEMBL 94) with featureCounts (v1.6.2)
Differentially expressed genes were detected with DESeq2 (v1.18.1) and coverage tracks were created with deepTools (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Txt, Files contain gene counts for each sample

source_name: Cerebral Organoid Fusion

growth_protocol: Cerebral organoid fusions (Fusions) were generated with a modified protocol, expanding upon previous organoid generation protocols from our lab (Lancaster et al., 2013, 2017). Please see methods of manuscript for details.

extract_protocol:
Organoid Fusions were manually dissected, single organoids were kept whole. Tissue was then dissociated using a gentleMACS dissociator (Miltenyi). GFP+ and GFP- cells were then obatiend via FACS.
Libraries were generated with the SmartSeq-2 protocol 2 (Illumina ). Libraries were pooled and sequenced on a HiSeq V4 flow cell (Illumina) with up to 4 billion single-end reads.
We sequenced all samples twice to improve the yield and then combined the samples using samtools (htslib.org). Raw files for both sequencing runs are included in this upload.

tag: stem cell type

value: H9 Feeder Free Human ESCs


title: 32_JRX136: HT29_ORF_CPEB4_32

source_name: HT-29 CPEB4 transduction, UniqueID 32


title: 2CLC-RNA-seq-rep1

description:
2C-Pos1-1
Smart-seq2


title: 284_JRX213: HT29_ORF_CDC37_284

source_name: HT-29 CDC37 transduction, UniqueID 284


title: Sample 2- 104625 GFP- cells, Dorsal Region Organoid Fusion Day 90


title: hRPE-2

first: jin

middle: ying

last: li

state: -- Select State/Province --

address: No. 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep kit for Illumina® (NEB) following the manufacturer’s recommendations, and the quality of libraries was assessed on an Agilent 2100 Bioanalyzer system and ABI StepOnePlus Real-Time PCR System.
After cluster generation, the library preparations were sequenced on an Illumina HiSeqTM 4000 platform, and 150 bp single-end reads were generated. Reads per kb per million reads (RPKM) were used to estimate gene expression levels.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human fetal RPE cells

extract_protocol:
Total RNA was extracted from hfRPE-1, hfRPE-2, and hfRPE-3 cells using TRIzol (Invitrogen) and was provided as a kind gift from Army Medical University (Chongqing, China); and RNA was similarly extracted from hAESCs-RPE-1, hAESCs-RPE-2, and hAESCs-RPE-3 cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: fetal RPE cells


title: hRPE-3


title: 283_JRX212: HT29_ORF_CDC37_283

source_name: HT-29 CDC37 transduction, UniqueID 283


title: 2CLC-RNA-seq-rep2

description:
2C-Pos1-2
Smart-seq2


title: 33_JRX137: HT29_ORF_CPEB4_33

source_name: HT-29 CPEB4 transduction, UniqueID 33


title: ESC-RNA-seq-rep4

description:
2C-Neg2-2
Smart-seq2


title: hAEC-RPE1-3

description: 10 mM NIC (Sigma-Aldrich, Cat# N3376) and 1 μM TSA (APExBIO, Cat# A8183) were added for approximately two weeks

source_name: human amniotic epithelial stem cells

value: amniotic epithelial stem cells


title: hRPE-1


title: 268_JRX210: HT29_ORF_ACTL6B_268

source_name: HT-29 ACTL6B transduction, UniqueID 268


title: Sample 3- 104626 GFP+ cells, Dorsal Region Organoid Fusion Day 90


title: 266_JRX208: HT29_ORF_TMED10_266

source_name: HT-29 TMED10 transduction, UniqueID 266


title: 269_JRX211: HT29_ORF_ACTL6B_269

source_name: HT-29 ACTL6B transduction, UniqueID 269


title: 263_JRX206: HT29_ORF_SSR2_263

source_name: HT-29 SSR2 transduction, UniqueID 263


title: 267_JRX209: HT29_ORF_TMED10_267

source_name: HT-29 TMED10 transduction, UniqueID 267


title: 261_JRX205: HT29_ORF_AUH_261

source_name: HT-29 AUH transduction, UniqueID 261

value: AUH


title: hAEC-RPE1-2


title: ESC-RNA-seq-rep2

description:
2C-Neg1-2
Smart-seq2


title: ESC-RNA-seq-rep3

description:
2C-Neg2-1
Smart-seq2


title: ESC-RNA-seq-rep1

description:
2C-Neg1-1
Smart-seq2


title: 264_JRX207: HT29_ORF_SSR2_264

source_name: HT-29 SSR2 transduction, UniqueID 264


title: 2CLC-H3K9me3

description: ULI-NChIP-seq for H3K9me3

library_source: genomic

molecule: genomic DNA

source_name: mouse embryonic stem cells

extract_protocol: After FACS sorting in DPBS, mESCs were incubated in lysis buffer.  ChIP-seq libraries were prepared using ULI-NChIP-seq developed by Brind’Amour et al., Nat Commun 2015 (PMID: 25607992)  with slightly modification.

tag: chip antibody

value: H3K9me3 (Active Motif, 39161)


title: 251_JRX202: HT29_ORF_ZFP36L1_251

source_name: HT-29 ZFP36L1 transduction, UniqueID 251


title: 252_JRX203: HT29_ORF_ZFP36L1_252

source_name: HT-29 ZFP36L1 transduction, UniqueID 252


title: 260_JRX204: HT29_ORF_AUH_260

source_name: HT-29 AUH transduction, UniqueID 260


title: C3

city: Changchun

first: Yingshuang

last: Wang

state: Jilin

address: NO.1163 Xinmin Street

institute: Jilin University School of Public Health

data_processing:
Illumina HiSeq 4000 software used for basecalling.
The clean reads were mapped to the reference using Hisat2 and the reference-based assembly of transcripts was performed using Stringtie
Then transcripts including mRNAs, lncRNAs and TUCPs (transcripts of unknown coding potential) were quantified by StringTie-eB
Differential expression analyses were performed by “ballgown” package of R softwore.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM for every transcript and every sample

source_name: Peripheral blood

extract_protocol:
Total RNA was isolated and purified using standard TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manual. RNA concentration and purity, RNA integrity were then assessed using the Nanodrop2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The cDNA library was constructed using the Truseq RNA sample Prep Kit (Illumina, Inc., San Diego, CA). RNA sequencing (2*150 bp) was conducted on the Illumina HiSeq 4000 sequencing system (Illumina, Inc.).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy control

tag: race

value: Asian

tag: age

tag: diabetes

value: No

tag: hypertension

tag: gender

value: male

tag: tissue

value: Peripheral blood


title: 24_JRX135: HT29_ORF_CEBPB_24

source_name: HT-29 CEBPB transduction, UniqueID 24

tag: orf

value: CEBPB


title: C2


title: ESC-H3K9me3

description: ULI-NChIP-seq for H3K9me3


title: 2CLC-H3K27me3-rep2

description: ULI-NChIP-seq for H3K27me3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: 245_JRX201: HT29_ORF_USP12_245

source_name: HT-29 USP12 transduction, UniqueID 245

tag: uniqueid


title: ESC-H3K27me3-rep2

description: ULI-NChIP-seq for H3K27me3


title: IS3

value: ischemic stroke (IS) patient


title: 233_JRX198: HT29_ORF_TRIB1_233

source_name: HT-29 TRIB1 transduction, UniqueID 233

tag: arraybatch


title: C1


title: 23_JRX134: HT29_ORF_CEBPB_23

source_name: HT-29 CEBPB transduction, UniqueID 23

tag: transductiondate


title: 228_JRX197: HT29_ORF_TMEM17_228

source_name: HT-29 TMEM17 transduction, UniqueID 228

tag: subset


title: 234_JRX199: HT29_ORF_TRIB1_234

source_name: HT-29 TRIB1 transduction, UniqueID 234


title: 227_JRX196: HT29_ORF_TMEM17_227

source_name: HT-29 TMEM17 transduction, UniqueID 227


title: hAEC-RPE1-1

source_name: human amniotic epithelial stem cells


title: ESC-H3K27me3-rep1

description: ULI-NChIP-seq for H3K27me3

tag: stain


title: 244_JRX200: HT29_ORF_USP12_244

source_name: HT-29 USP12 transduction, UniqueID 244


title: IS1


title: 2CLC-H3K4me1-rep2

description: ULI-NChIP-seq for H3K4me1

tag: transgene

value: H3K4me1 (Active Motif, 39297)


title: 221_JRX192: HT29_ORF_TM9SF4_221

source_name: HT-29 TM9SF4 transduction, UniqueID 221


title: 2CLC-H3K4me1-rep1

description: ULI-NChIP-seq for H3K4me1


title: 218_JRX191: HT29_ORF_SPRED2_218

source_name: HT-29 SPRED2 transduction, UniqueID 218


title: SnubarHighAK

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

country: USA

institute: MDACC

description:
SnubarHighAK_ATAC and SnubarHighAK_BC
SnubarATAC-HighAK: 2 cell line mixture (A20-K562)-scATAC and sample_barcode sample
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: SnubarHighAK

growth_protocol: The A20 and K562 cell lines were purchased from the American Type Culture Collection and cultured based on ATCC guidelines. The MDA-MB-231 and MDA-MB-436  cell lines were obtained from the MD Anderson Characterized Cell Line Core Facility and were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose medium supplemented with 10% FBS  and 1X penicillin-streptomycin. Mice were purchased from the Jackson Laboratory and housed in the Research Animal Support Facility at MD Anderson Cancer Center.

extract_protocol:
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits,  CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)
single cell ATAC-seq, single cell RNA&ATAC co-assay, and barcode libraries

treatment_protocol: 28 mice were treated under 7 different conditions (4 mice in each group): 1) Control; 2) Chemotherapy + 2 Gy Radiotherapy; 3) 4 Gy Radiotherapy; 4) Chemotherapy + 2 Gy Radiotherapy + Talazoparib; 5) Chemotherapy + 2 Gy Radiotherapy + PD-L1 Blockade; 6) 4Gy Radiotherapy + PD-L1 Blockade; 7) 4Gy Radiotherapy + Talazoparib + PD-L1 Blockade.

tag: cell lines


title: 217_JRX190: HT29_ORF_SPRED2_217

source_name: HT-29 SPRED2 transduction, UniqueID 217


title: 21_JRX133: HT29_ORF_C1orf106_21

source_name: HT-29 C1orf106 transduction, UniqueID 21


title: 216_JRX189: HT29_ORF_SMURF1_216

source_name: HT-29 SMURF1 transduction, UniqueID 216


title: 212_JRX187: HT29_ORF_SMAD7_212

source_name: HT-29 SMAD7 transduction, UniqueID 212


title: 2CLC-H3K27me3-rep1

description: ULI-NChIP-seq for H3K27me3

source_name: mouse embryonic stem cells


title: ESC-H3K4me1-rep2

description: ULI-NChIP-seq for H3K4me1


title: 2CLC-H3K4me3-rep2

description: ULI-NChIP-seq for H3K4me3

value: H3K4me3 (Diagenode, C15410003)


title: 215_JRX188: HT29_ORF_SMURF1_215

source_name: HT-29 SMURF1 transduction, UniqueID 215


title: IS2

source_name: Peripheral blood


title: 211_JRX186: HT29_ORF_SMAD7_211

source_name: HT-29 SMAD7 transduction, UniqueID 211


title: ESC-H3K4me1-rep1

description: ULI-NChIP-seq for H3K4me1


title: 2CLC-H3K4me3-rep1

description: ULI-NChIP-seq for H3K4me3


title: ESC-H3K4me3-rep2

description: ULI-NChIP-seq for H3K4me3


title: 20_JRX132: HT29_ORF_C1orf106_20

source_name: HT-29 C1orf106 transduction, UniqueID 20


title: 209_JRX185: HT29_ORF_SMAD3_209

source_name: HT-29 SMAD3 transduction, UniqueID 209


title: ESC-H3K4me3-rep1

description: ULI-NChIP-seq for H3K4me3


title: 185_JRX182: HT29_ORF_RORC_185

source_name: HT-29 RORC transduction, UniqueID 185

value: RORC


title: 18_JRX131: HT29_ORF_ARHGEF2_18

source_name: HT-29 ARHGEF2 transduction, UniqueID 18


title: 208_JRX184: HT29_ORF_SMAD3_208

source_name: HT-29 SMAD3 transduction, UniqueID 208


title: 177_JRX179: HT29_ORF_RIPK2_177

source_name: HT-29 RIPK2 transduction, UniqueID 177


title: 186_JRX183: HT29_ORF_RORC_186

source_name: HT-29 RORC transduction, UniqueID 186


title: osmotic_shock_RPE_t_180m_Dam_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_180m; target: Dam.
pADamID_185

data_processing:
library strategy: pA-DamID
1. pA-DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 1.30.1 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for pA-DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Genome_build: hg38
Supplementary_files_format_and_content: 1. pA-DamID: BigWig files of log2-normalized pADamID scores for 50 kb genomic bins, tsv files with genomic coordinates and all scores per replicate / average scores per condition (including previously published pA-DamID data used in this study), tsv file with complete metadata that includes target/Dam control combinations; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios.

source_name: hTERT-RPE (ATCC CRL-4000)

growth_protocol: hTERT-RPE, HCT116 and K562 cells (all from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. pA-DamID: 1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a primary antibody and for a Dam control condition, to specifically deposit m6A marks at chromatin nearby the primary antibody. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested as for pA-DamID and immediately fixed in ice-cold ethanol.
1. pA-DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.

treatment_protocol: 1. Wildtype: no treatment; 2. Cell cycle: cells were synchronized with a sequential treatment of G2 enrichment (16 hours, with RO-3306) and metaphase blocking (90 minutes, with nocodazole). Synchronized cells were harvested with a mitotic shake-off, and immediately processed for pA-DamID or replated for interphase time points; 3. Ki67-AID: protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich, in DMSO, 24 h depletion), a similar amount of DMSO was used as control; 4. Actinomycin D: nucleoli were disrupted with a low dose of actinomycin D (50 ng/mL, in DMSO, 3 h treatment), a similar amount of DMSO was used as control; 5. Osmotic shock: nucleoli were disrupted with a short osmotic shock (0.2x PBS, 15 minutes), cells were harvested at two time points during nucleolar recovery; 6. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

tag: cell type

value: hTERT-immortalized retinal pigment epithelial cells

tag: library type

value: pA-DamID

tag: experiment

tag: condition

tag: target

value: Dam


title: 176_JRX178: HT29_ORF_RIPK2_176

source_name: HT-29 RIPK2 transduction, UniqueID 176


title: 179_JRX180: HT29_ORF_RIT1_179

source_name: HT-29 RIT1 transduction, UniqueID 179


title: 2CLC-H3K27ac-rep1

description: ULI-NChIP-seq for H3K27ac

value: 129/Ola, XY

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: osmotic_shock_RPE_t_180m_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_180m; target: Dam.
pADamID_184


title: 17_JRX130: HT29_ORF_ARHGEF2_17

source_name: HT-29 ARHGEF2 transduction, UniqueID 17


title: 180_JRX181: HT29_ORF_RIT1_180

source_name: HT-29 RIT1 transduction, UniqueID 180


title: 154_JRX174: HT29_ORF_PARK7_154

source_name: HT-29 PARK7 transduction, UniqueID 154


title: 15_JRX129: HT29_ORF_ARFRP1_15

source_name: HT-29 ARFRP1 transduction, UniqueID 15


title: 173_JRX177: HT29_ORF_PUSL1_173

source_name: HT-29 PUSL1 transduction, UniqueID 173


title: 172_JRX176: HT29_ORF_PUSL1_172

source_name: HT-29 PUSL1 transduction, UniqueID 172


title: 14_JRX128: HT29_ORF_ARFRP1_14

source_name: HT-29 ARFRP1 transduction, UniqueID 14


title: ESC-H3K27ac-rep2

description: ULI-NChIP-seq for H3K27ac

source_name: mouse embryonic stem cells


title: 149_JRX173: HT29_ORF_ORMDL3_149

source_name: HT-29 ORMDL3 transduction, UniqueID 149


title: osmotic_shock_RPE_t_30m_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_30m; target: Dam.
pADamID_183


title: 222_JRX193: HT29_ORF_TM9SF4_222

source_name: HT-29 TM9SF4 transduction, UniqueID 222


title: 155_JRX175: HT29_ORF_PARK7_155

source_name: HT-29 PARK7 transduction, UniqueID 155


title: osmotic_shock_RPE_t_30m_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_30m; target: Dam.
pADamID_182


title: 143_JRX171: HT29_ORF_NXPE1_143

source_name: HT-29 NXPE1 transduction, UniqueID 143


title: 148_JRX172: HT29_ORF_ORMDL3_148

source_name: HT-29 ORMDL3 transduction, UniqueID 148


title: 140_JRX168: HT29_ORF_NUPR1_140

source_name: HT-29 NUPR1 transduction, UniqueID 140


title: 2CLC-ATAC-rep1

description: ATAC-seq

extract_protocol: After FACS sorting in DPBS, mESCs were incubated in lysis buffer.  ATAC-seq libraries were prepared using the protocol developed by  Buenrostro et al., Nat Methods 2013 (PMID: 24097267)  with slightly modification.


title: 131_JRX166: HT29_ORF_NR5A2_131

source_name: HT-29 NR5A2 transduction, UniqueID 131


title: ESC-ATAC-rep2

description: ATAC-seq


title: 2CLC-ATAC-rep2

description: ATAC-seq


title: Ki67_aid_HCT116_RO_IAA_Dam_r4

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: Dam.
pADamID_181

source_name: HCT116 (ATCC CCL-247)

value: Colorectal carcinoma cells

tag: genetic modification

value: OsTir1; Ki67-miniAID-mClover


title: ESC-H3K27ac-rep1

description: ULI-NChIP-seq for H3K27ac


title: Ki67_aid_HCT116_RO_Dam_r4

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Dam.
pADamID_177

value: RO


title: SAMPLE098

first: Shervin

last: Assassi

address: 6431 Fannin

department: Division of Rheumatology

institute: The University of Texas Health Science Center at Houston

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile-quantile normalized and restricted to the overlap between probes mapped to Entrez Gene (by “re-annotated” mapping in Bioconductor package illuminaHumanv4.db) and those with average detection p-value equal to or below 0.01.

label: biotin

source_name: PBC

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

extract_protocol: Whole blood was extracted from PAXgene Tubes. RNA quality was checked with Agilent Bioanalyser.

value: Control

tag: gender

value: Female

tag: age

tag: race

value: Caucasian


title: 141_JRX169: HT29_ORF_NUPR1_141

source_name: HT-29 NUPR1 transduction, UniqueID 141

tag: orf

tag: uniqueid


title: SAMPLE097


title: SAMPLE101


title: SAMPLE096


title: NMuMG overexpressing empty vector replicate 2

city: Mobile, AL

first: Simon

last: Grelet

state: Alabama

address: 1660 Spring Hill Ave - USA Drive North,

institute: University of South Alabama - Mitchell Cancer Institute

data_processing:
Alignement with Bowtie 2 (2.2.5)
Quantification to mouse (Gencode Comprehensive gene annotation)
Normalization by CPM (counts per million)
Add: 1.0E-4 for each value
Genome_build: M18 (GRCm38.p6)
Supplementary_files_format_and_content: Normalized_counts.txt (normalized reads in CPM)

source_name: In vitro cell culture

growth_protocol: Cells are routinely cultivated in DMEM 10% FBS

extract_protocol:
Trizol extraction of 2D in vitro cultures
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells are : treated with TGF-beta or Silenced for PCBP1 and silenced or overexpressing Platr18

tag: cell line

value: NMuMG

tag: treatment

value: Empty vector overexpression

tag: origin

value: Mouse Mammary Gland


title: Ki67_aid_HCT116_RO_IAA_Dam_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: Dam.
pADamID_180


title: SAMPLE093

value: systemic sclerosis patient

value: Male


title: Ki67_aid_HCT116_RO_IAA_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: Dam.
pADamID_178


title: ESC-ATAC-rep1

description: ATAC-seq

tag: stain

tag: transgene


title: NMuMG overexpressing Platr18 cl16 replicate 2

value: Platr 18 overexpression


title: 132_JRX167: HT29_ORF_NR5A2_132

source_name: HT-29 NR5A2 transduction, UniqueID 132

tag: arraybatch

tag: transductiondate

tag: subset


title: NMuMG overexpressing empty vector replicate 1


title: Ki67_aid_HCT116_doublethy_IAA_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: Dam.
pADamID_173

tag: cell type

tag: library type

tag: experiment

tag: condition


title: SAMPLE090

tag: gender


title: SAMPLE092

tag: age


title: SAMPLE099

tag: race


title: SAMPLE095

value: African American


title: SAMPLE094


title: NMuMG overexpressing Platr18 cl12 replicate 1


title: Ki67_aid_HCT116_doublethy_IAA_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: Dam.
pADamID_172

value: pA-DamID

tag: genetic modification

tag: target


title: 142_JRX170: HT29_ORF_NXPE1_142

source_name: HT-29 NXPE1 transduction, UniqueID 142

tag: orf

tag: uniqueid


title: Ki67_aid_HCT116_RO_IAA_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: Dam.
pADamID_179

value: Dam


title: 107_JRX162: HT29_ORF_KIF3B_107

source_name: HT-29 KIF3B transduction, UniqueID 107


title: SAMPLE082


title: SAMPLE081


title: SAMPLE075


title: Ki67_aid_HCT116_RO_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Dam.
pADamID_175


title: NMuMG cells replicate 2

tag: cell line

tag: treatment

value: WT cells

tag: origin


title: SAMPLE074


title: Ki67_aid_HCT116_control_IAA_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: Dam.
pADamID_169


title: NMuMG cells replicate 1


title: Ki67_aid_HCT116_RO_Dam_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Dam.
pADamID_176


title: 2CLC-H3K27ac-rep2

description: ULI-NChIP-seq for H3K27ac

tag: stain

value: 129/Ola, XY

tag: transgene

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: SAMPLE085

value: Hispanic


title: SAMPLE072


title: NMuMG cells treated with TGFbeta replicate 2

value: WT cells Treated with Tgfbeta


title: Ki67_aid_HCT116_doublethy_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: Dam.
pADamID_171

tag: cell type

value: Colorectal carcinoma cells

value: OsTir1; Ki67-miniAID-mClover

value: doublethy


title: SAMPLE083

value: Control

value: Caucasian


title: 108_JRX163: HT29_ORF_KIF3B_108

source_name: HT-29 KIF3B transduction, UniqueID 108

tag: arraybatch

tag: transductiondate

tag: subset


title: Ki67_aid_HCT116_control_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: Dam.
pADamID_167

tag: library type

tag: experiment

tag: condition

value: control


title: NMuMG silenced for PCBP1 primary tumor replicate 2

source_name: Mouse primary tumor

value: NMuMG

value: shRNA hnRNP E1

value: Mouse primary tumor


title: Ki67_aid_HCT116_RO_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Dam.
pADamID_174

tag: genetic modification

value: RO


title: NMuMG overexpressing Platr18 cl12 replicate 2

value: Platr 18 overexpression

value: Mouse Mammary Gland


title: Ki67_aid_HCT116_doublethy_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: Dam.
pADamID_170

value: pA-DamID

tag: target

value: Dam


title: SAMPLE076

tag: gender

value: Female

tag: age

tag: race


title: SAMPLE067


title: SAMPLE066


title: SAMPLE088

value: systemic sclerosis patient

value: Male

value: African American


title: NMuMG silenced for PCBP1 directed on the lungs replicate 2

source_name: Mouse Lung metasasis

tag: cell line

tag: treatment

value: Mouse Lung metasasis


title: SAMPLE078


title: actinomycin_K562_50ng_Dam_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_163

value: Chronic myeloid leukemia cells

value: actinomycin


title: NMuMG overexpressing Platr18 cl16 replicate 1

tag: origin


title: SAMPLE060

value: Control


title: SAMPLE062


title: PATIENT58

value: Hispanic

tag: disease duration


title: NMuMG silenced for PCBP1 expressing platr18 shRNA replicate 2

value: NMuMG

value: shRNA hnRNP E1 & shRNA platr18


title: SAMPLE071


title: PATIENT55


title: Ki67_aid_HCT116_control_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: Dam.
pADamID_166

value: Colorectal carcinoma cells

value: OsTir1; Ki67-miniAID-mClover

value: control


title: SAMPLE065


title: SAMPLE068


title: PATIENT53

value: Caucasian


title: NMuMG cells treated with TGFbeta replicate 1

value: WT cells Treated with Tgfbeta

value: Mouse Mammary Gland


title: PATIENT54

value: Female


title: PATIENT50

value: systemic sclerosis patient


title: PATIENT51

value: Male


title: NMuMG silenced for PCBP1 directed on the lungs replicate 1

value: shRNA hnRNP E1


title: SAMPLE064


title: actinomycin_K562_50ng_Dam_r4

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_165

value: pA-DamID

value: Dam


title: actinomycin_K562_50ng_Dam_r3

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_164

value: Chronic myeloid leukemia cells

value: actinomycin


title: NMuMG silenced for PCBP1 expressing platr18 shRNA replicate 1


title: Ki67_aid_HCT116_control_IAA_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: Dam.
pADamID_168


title: actinomycin_K562_DMSO_Dam_r4

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_161

value: DMSO


title: actinomycin_K562_50ng_Dam_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_162


title: actinomycin_K562_DMSO_Dam_r3

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_160


title: actinomycin_K562_DMSO_Dam_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_159


title: PATIENT48


title: NMuMG silenced for PCBP1 replicate 1

value: NMuMG


title: NMuMG silenced for PCBP1 primary tumor replicate 1

value: Mouse primary tumor


title: PATIENT46


title: PATIENT56


title: PATIENT45


title: PATIENT57


title: PATIENT49


title: Sept20_Cell_90

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
For gene expression quantification, pseudo-alignment of the RNA-Seq reads was performed using the software Kallisto in AltAnalyze with mm10 EnsMart72 as a reference.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited-text

source_name: T cells

growth_protocol: Mice were place on a highfat diet for 20 weeks, Th17 cells were isolated from the liver by FACS sorting the TCRb+CD4+IL-17A-GFP+ cells.

extract_protocol:
cDNA was generated using the SMART-Seq2 version 2 chemistry as recommended by the manufacturer
RNA libraries were generated for sequencing using standard Illumina protocols

treatment_protocol: HFD

tag: strain

tag: tissue

value: Liver

tag: Sex

tag: genotype

tag: housing temperature

value: TCRb+CD4+IL-17A-GFP+ cells


title: PATIENT40

value: Hispanic


title: Sept20_Cell_88

tag: cell type


title: PATIENT38

value: Caucasian


title: PATIENT37


title: Sept20_Cell_85


title: NMuMG silenced for PCBP1 expressing scrambled shRNA replicate 2


title: actinomycin_HCT116_50ng_Dam_r4

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_156

value: Colorectal carcinoma cells

tag: library type

tag: experiment


title: NMuMG silenced for PCBP1 expressing scrambled shRNA replicate 1

value: Mouse Mammary Gland


title: actinomycin_K562_DMSO_Dam_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_158

tag: condition


title: PATIENT34

value: Female


title: PATIENT52

value: systemic sclerosis patient


title: PATIENT42


title: actinomycin_HCT116_50ng_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_154

tag: target


title: Sept20_Cell_83


title: actinomycin_HCT116_50ng_Dam_r5

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_157


title: PATIENT32

tag: gender


title: Sept20_Cell_81


title: NMuMG silenced for PCBP1 replicate 2


title: PATIENT44

tag: age


title: PATIENT47

tag: race


title: actinomycin_HCT116_DMSO_Dam_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_150


title: PATIENT43


title: PATIENT35


title: Sept20_Cell_78


title: PATIENT36


title: PATIENT33


title: Sept20_Cell_76


title: actinomycin_HCT116_DMSO_Dam_r5

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_152


title: actinomycin_HCT116_DMSO_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_148


title: PATIENT21


title: actinomycin_HCT116_50ng_Dam_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_155


title: PATIENT18

value: SE  Asian


title: Sept20_Cell_75


title: actinomycin_HCT116_DMSO_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_149


title: Sept20_Cell_87


title: Sept20_Cell_74


title: PATIENT15


title: Sept20_Cell_80


title: Sept20_Cell_73


title: PATIENT13

value: African American


title: PATIENT28

value: Male


title: actinomycin_RPE_50ng_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_146

source_name: hTERT-RPE (ATCC CRL-4000)

value: hTERT-immortalized retinal pigment epithelial cells

value: pA-DamID

value: Dam


title: actinomycin_RPE_DMSO_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_145

value: actinomycin

value: DMSO


title: PATIENT10


title: PATIENT08


title: actinomycin_RPE_DMSO_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_144


title: actinomycin_HCT116_DMSO_Dam_r4

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Dam.
pADamID_151


title: cell_cycle_RPE_t_10h_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_10h; target: Dam.
pADamID_143


title: PATIENT05


title: PATIENT04


title: cell_cycle_RPE_t_10h_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_10h; target: Dam.
pADamID_142


title: PATIENT26


title: PATIENT22


title: PATIENT24


title: Sept20_Cell_63


title: cell_cycle_RPE_t_6h_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_6h; target: Dam.
pADamID_141


title: actinomycin_HCT116_50ng_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_153


title: PATIENT27


title: PATIENT25


title: LPS/2D216 1

city: La Jolla

first: Tomoko

last: Hayashi

state: California

address: 9500 GIlman Drive

institute: UC San Diego

hyb_protocol: NanoString Mouse Immunology pannel

scan_protocol: NanoString Mouse Immunology pannel

data_processing: Data were acquired in triplicates, and the expression values were normalized using positive controls to eliminate platform related variation, negative controls to eliminate background effect, and housekeeping genes to remove variation due to sample input. Genes with zero counts were removed from group comparisons, linear models for microarray with the trend method were used to compare log2 expression values among groups.  The Benjamini-Hochberg procedure was applied to control the false discovery rate (FDR). A gene was considered significantly changed if FDR < 0.05. Principal component analysis (PCA) was performed and plotted using Prism 9 software (GraphPad Software, San Diego, CA) to assess similarity or dissimilarity between the datasets.

label: NanoString

source_name: Mouse BMDC

label_protocol: NanoString Mouse Immunology pannel

growth_protocol: BMDCs were cultured with 10% FCS/RPMI.

extract_protocol: Total RNAs were prepared with Qiagen RNA mini kit and subjected to NanoString analysis.

treatment_protocol: BMDCs were treated with 0.05% DMSO, 5 mM 2D216, 1 ng/mL LPS, and 1 ng/mL LPS with 5 mM 2D216 for 5 hr (n = 3 for each treatemt).

value: LPS 1 ng/mL and 2D216 5 mM for 5 hr


title: LPS 3

value: LPS 1 ng/mL for 5 hr


title: Sept20_Cell_62

value: Liver

value: TCRb+CD4+IL-17A-GFP+ cells


title: Sept20_Cell_72


title: Sept20_Cell_64


title: PATIENT30

value: Hispanic


title: Sept20_Cell_69


title: LPS/2D216 3


title: PATIENT16


title: Sept20_Cell_61


title: LPS/2D216 2


title: Sept20_Cell_60


title: PATIENT12


title: Sept20_Cell_38


title: Vehicle 3

value: DMSO 0.05% for 5 hr


title: PATIENT07

value: Caucasian


title: actinomycin_RPE_50ng_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: Dam.
pADamID_147


title: Vehicle 2


title: cell_cycle_RPE_t_6h_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_6h; target: Dam.
pADamID_140


title: PATIENT03

value: Female


title: cell_cycle_RPE_t_3h_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_3h; target: Dam.
pADamID_138


title: cell_cycle_RPE_t_0h_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_0h; target: Dam.
pADamID_135


title: Sept20_Cell_91


title: Sept20_Cell_68


title: PATIENT02

value: systemic sclerosis patient


title: ATAC-seq arp8Δ Rep1

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

country: France

institute: Institute Pasteur

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016).
For MNase-Seq, paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options. For ATAC-Seq, default options were used.
Bam files were generated using samtools (Li et al., 2009). Mitochondrial and rDNA reads were removed from the bam files for MNase-Seq.
Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: Signal intensity in bigWig file format

organism: Saccharomyces cerevisiae

source_name: colony 1

growth_protocol: For anchor-away experiments, yeast strains were grown in YPAD media to OD 0.2-0.3 . For histone depletion experiments, cells were grown in SC + 2% galactose to OD 1.0. For deletion strains, cells were grown in YPAD to OD 1-0-2.0. For ATAC-seq, cells were grown to OD 0.4 in YPAD media.

extract_protocol:
Yeast nuclei was prepared according to (Almer and Horz, 1986). Cells were harvested  and incubated in 2 volume of preincubation solution (0.7 M ß-mercaptoethanol, 28 mM EDTA) for 25-30 mins. After washing with 1M sorbitol, cell wall was digested with Zymolyase. Spheroplasts were washed with 1M sorbitol and lysed with Ficoll buffer (18 % Ficoll, 20 mM KH2PO4 pH 6.8, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA). Nuclei was centrifuged and stored at -80 ̊C before use. For MNase digestion, nuclei was washed and dissolved in MNase digestion buffer (15 mM Tris-Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, 0.2 mM EDTA, 5 mM ß-mercaptoethanol). Equal volume of nuclei was digested with increasing amount of MNase for 20 mins at 37 ̊C. Reaction was stopped with 10 mM EDTA, 1% SDS and 50 mM Tris-Cl pH 8.5, followed by Proteinase K incubation for 30 mins at 37 ̊C. DNA was isolated by Phenol:Chloroform extraction and precipitation with 100% ethanol. Pellet was dissolved in TE buffer and RNA was removed with RNAse A incubation at 37 ̊C for 60 mins. DNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 μl TE. 25 μl DNA was loaded on 1.7% agarose gel and resolved for 4 hours at 2 V/cm. Appopriately digested sample with 70% mono-, 20% di- and 10% tri-nucleosome bands were used for library preparation without cutting mononucleosome band.
Libraries were prepared from whole MNase digested DNA. DNA fragments longer than 500 bp were removed using ampure size selection. 50 ng of size-selected DNA was used for library preparation with NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s protocol. For PCR amplification step, 3 or 4 cycles were performed. Quality control on final libraries was performed using DNA 1000 Bioanalyzer and fragment length of ~270-280 bp was consistently observed, corresponding to ~150-160 bp insert length. For ATAC-seq, libraries were prepared using Nextera DNA Library Prep Kit in 25 ul reaction. Final fragment size of 100-600 bp were retained during Ampure purification.

treatment_protocol: For anchor-away background strains: Vehicle (90% ethanol, 10% Tween-20) or Rapamycin (1 μg/ml final concentration) dissolved in Vehicle. For histone depletion strain: Cells were washed with pre-warmed SC media and dissoved in SC media + 2% Galactose (control) or 2% Glucose (histone depletion).

tag: depletion or deletion

value: Gene deletion

tag: protein tagged or deleted


title: ATAC-seq TKO Rep2

value: isw1delta, isw2delta, chd1delta background

tag: treatment


title: Vehicle 1


title: 2D216 2

value: 2D216 5 mM for 5 hr


title: ATAC-seq WT Rep2

value: Wild type


title: LPS 1


title: cell_cycle_RPE_t_0h_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_0h; target: Dam.
pADamID_134

value: hTERT-immortalized retinal pigment epithelial cells

value: pA-DamID


title: cell_cycle_RPE_t_3h_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_3h; target: Dam.
pADamID_139

value: Dam


title: LPS 2


title: 2D216 3


title: Sept20_Cell_86


title: Sept20_Cell_84


title: TKO TBP Vehicle 60 min MNase high Rep2

source_name: TKO TBP depletion control MNase high, colony 2

value: Depletion by anchor-away

value: TBP tagged with FRB and isw1delta, isw2delta and chd1delta

value: anchor-away background

value: Vehicle control in OD 0.2-0.3 cells for 60 mins


title: PATIENT01

value: African American

tag: disease duration


title: TKO TBP Vehicle 60 min MNase low Rep2

source_name: TKO TBP depletion control MNase low, colony 2


title: wildtype_K562_wt_Dam_r3

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_132

value: Chronic myeloid leukemia cells

value: wildtype

value: wt


title: Sept20_Cell_89

tag: strain

value: Liver

value: Female

value: TCRb+CD4+IL-17A-GFP+ cells


title: TKO TBP Rapamycin 60 min Rep1

source_name: TKO TBP depletion, colony 1

value: Rapamycin 1 microg/ml final concentration in OD 0.2-0.3 cells for 60 mins


title: wildtype_K562_wt_Dam_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_131


title: cell_cycle_RPE_t_1h_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_1h; target: Dam.
pADamID_136


title: TKO G1 arrest Rapamycin 60 min Rep1

source_name: TKO G1 arrest depletion, colony 1

value: Rpb1 tagged with FRB and isw1delta, isw2delta and chd1delta

value: G1 arrest for 2 h, Rapamycin for 60 mins


title: TKO G1 arrest Vehicle 60 min Rep2

source_name: TKO G1 arrest depletion control, colony 2

value: G1 arrest for 2 h, Vehicle control for 60 mins


title: TKO G1 arrest Rapamycin 60 min Rep2

source_name: TKO G1 arrest depletion, colony 2


title: TKO G1 arrest Vehicle 60 min Rep1

source_name: TKO G1 arrest depletion control, colony 1


title: cell_cycle_RPE_t_1h_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_1h; target: Dam.
pADamID_137

value: hTERT-immortalized retinal pigment epithelial cells

value: pA-DamID


title: ATAC-seq TKO

data_processing:
Fastq files were demiltiplexed using Je demultiplex suite (Girardot et al., 2016).
For Mnase-Seq, paired-end reads were mapped to sacCer3 R64-1-1 genome using Bowtie2 ((Langmead and Salzberg, 2012) with default setting except -X 500, --no-discordant, --no-mixed options. For ATAC-Seq, default options were used.
Bam files were generated using samtools (Li et al., 2009). Mitochondrial and rDNA reads were removed from the bam files for MNase-Seq.
Nucleosome dyad coverage and bigWig files were generated using 140-160 bp reads and resizing to 50 bp at the dyad center for MNase-Seq.
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: Signal intensity in bigWig file format

extract_protocol:
Yeast nuclei was prepared according to (Almer and Horz, 1986). Cells were harvested  and incubated in 2 volume of preincubation solution (0.7 M ß-mercaptoethanol, 28 mM EDTA) for 25-30 mins. After washing with 1M sorbitol, cell wall was digested with Zymolyase. Spheroplasts were washed with 1M sorbitol and lysed with Ficoll buffer (18 % Ficoll, 20 mM KH2PO4 pH 6.8, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA). Nuclei was centrifuged and stored at -80 ̊C before use. For MNase digestion, nuclei was washed and dissolved in MNase digestion buffer (15 mM Tris-Cl pH 7.5, 50 mM NaCl, 1.4 mM CaCl2, 0.2 mM EGTA, 0.2 mM EDTA, 5 mM ß-mercaptoethanol). Equal volume of nuclei was digested with increasing amount of MNase for 20 mins at 37 ̊C. Reaction was stopped with 10 mM EDTA, 1% SDS and 50 mM Tris-Cl pH 8.5, followed by Proteinase K incubation for 30 mins at 37 ̊C. DNA was isolated by Phenol:Chloroform extraction and precipitation with 100% ethanol. Pellet was dissolved in TE buffer and RNA was removed with RNAse A incubation at 37 ̊C for 60 mins. DNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50 μl TE. 25 μl DNA was loaded on 1.7% agarose gel and resolved for 4 hours at 2 V/cm. Appopriately digested sample with 70% mono-, 20% di- and 10% tri-nucleosome bands were used for library preparation without cutting mononucleosome band.
Libraries were prepared from whole MNase digested DNA. DNA fragments longer than 500 bp were removed using ampure size selection. 50 ng of size-selected DNA was used for library preparation with NEBNext Ultra II DNA Library Prep Kit, according to the manufacturer’s protocol. For PCR amplification step, 3 or 4 cycles were performed. Quality control on final libraries was performed using DNA 1000 Bioanalyzer and fragment length of ~270-280 bp was consistently observed, corresponding to ~150-160 bp insert length. Fro ATAC-seq, libraries were prepared using Nextera DNA Library Prep Kit in 25 ul reaction. Final fragment size of 100-600 bp were retained during Ampure purification.

value: Gene deletion

tag: strain background

value: isw1Δ, isw2Δ, chd1Δ background


title: TKO TBP Rapamycin 60 min MNase high Rep2

source_name: TKO TBP depletion MNase high, colony 2

value: Depletion by anchor-away

value: TBP tagged with FRB and isw1delta, isw2delta and chd1delta

value: anchor-away background


title: wildtype_HCT116_wt_Dam_r6

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_128

source_name: HCT116 (ATCC CCL-247)

value: Colorectal carcinoma cells

value: Dam


title: Sept20_Cell_70

tag: tissue

tag: Sex


title: 2D216 1

value: 2D216 5 mM for 5 hr


title: Sept20_Cell_77

value: Liver

tag: genotype

tag: housing temperature


title: wildtype_HCT116_wt_Dam_r7

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_129

tag: cell type

tag: library type

value: wildtype

value: wt


title: TKO pRS413 Gal1-10 HHT2-HHF2 Glucose Rep 1

source_name: Histone genes under Gal1-10 promoter, colony 1

value: Depletion by promoter shut-off, 3 hours

value: Histone depletion and isw1Δ, isw2Δ, chd1Δ background

value: Glucose media


title: wildtype_K562_wt_Dam_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_130

value: Chronic myeloid leukemia cells

tag: experiment

tag: condition


title: Sept20_Cell_82

value: Female

value: TCRb+CD4+IL-17A-GFP+ cells


title: TKO pRS413 Gal1-10 HHT2-HHF2 Galactose Rep 2

source_name: Histone genes under Gal1-10 promoter, colony 2

value: Gene deletion

value: Galactose media


title: ATAC-seq arp8Δ Rep2

source_name: colony 2


title: Sept20_Cell_67


title: wildtype_K562_wt_Dam_r7

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_133

value: pA-DamID

tag: target


title: TKO TBP Vehicle 60 min Rep1

source_name: TKO TBP depletion control, colony 1

value: Depletion by anchor-away

value: TBP tagged with FRB and isw1delta, isw2delta and chd1delta

value: Vehicle control in OD 0.2-0.3 cells for 60 mins


title: TKO YCP50 HHT2-HHF2 Galactose

source_name: Histone native promoter

value: Mock depletion control, 3 hours


title: WT pRS413 Gal1-10 HHT2-HHF2 Glucose Rep 2

value: Histone depletion background


title: TKO pRS413 Gal1-10 HHT2-HHF2 Galactose Rep 1


title: ATAC-seq WT

value: Wild type


title: wildtype_HCT116_wt_Dam_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_124

value: Colorectal carcinoma cells

value: wildtype

value: Dam


title: Sept20_Cell_79

source_name: T cells

value: Liver


title: TKO pRS413 Gal1-10 HHT2-HHF2 Glucose Rep 2

value: Depletion by promoter shut-off, 3 hours

value: Histone depletion and isw1Δ, isw2Δ, chd1Δ background

value: Glucose media


title: WT pRS413 Gal1-10 HHT2-HHF2 Galactose Rep 2


title: Sept20_Cell_71

value: Female

value: TCRb+CD4+IL-17A-GFP+ cells


title: TKO YCP50 HHT2-HHF2 Glucose

value: Gene deletion


title: TKO TBP Rapamycin 60 min MNase low Rep2

source_name: TKO TBP depletion MNase low, colony 2

value: anchor-away background

value: Rapamycin 1 microg/ml final concentration in OD 0.2-0.3 cells for 60 mins


title: wildtype_HCT116_wt_Dam_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_123

value: pA-DamID

value: wt


title: wildtype_HCT116_wt_Dam_r4

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_126


title: wildtype_HCT116_wt_Dam_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_125


title: WT pRS413 Gal1-10 HHT2-HHF2 Glucose Rep 1


title: Jun9_Cell_34

value: Male


title: 42

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

data_processing:
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.
Reads were aligned to the human genome (GRch38.p13) using STAR  (-runThreadN 2 --genomeDir ../../../star/genome --readFilesIn *.fq.gz *.fq.gz --readFilesCommand gunzip -c --outFileNamePrefix ../STAR/*_ --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /star/genome/Homo_sapiens.GRCh38.86.gtf --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Raw counts using HTSeq

source_name: Vastus Lateralis Muscle

extract_protocol:
Subjects were fasted and refrained from exercise and alcohol 24 hours prior to testing. Biopsies from vastus lateralis were collected using the suction modified Bergström technique from the non-dominant leg under local anaesthesia using a using a 5-mm Bergström o needle. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 30 mg in 1 mL Trizol reagent in Tissue lyser II (Qiagen) for 2 min at 30 Hz. 240 µL of cold chloroform was added to the lysates, shaken thoroughly for 30 seconds and incubated on ice for 5 min before centrifugation at 12,000 RPM for 15 min at 4˚C (Mikro 200R, Hettich, Germany). The aqueous layer was transferred to a new tube and 700 µL of ice-cold isopropanol was added, mixed with RLT buffer (Qiagen) and loaded onto RNAeasy spin columns (Qiagen). RNA purification was done according to manufacturers’ protocol. RNA concentration was measured using NanoDrop spectrophotometer (Thermofisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.

value: Vastus Lateralis Muscle

tag: age group

value: Older


title: Sept20_Cell_66


title: WT pRS413 Gal1-10 HHT2-HHF2 Galactose Rep 1

value: Histone depletion background

value: Galactose media


title: 41


title: 40


title: WT YCP50 HHT2-HHF2 Glucose

value: Mock depletion control, 3 hours


title: Sept20_Cell_65

value: Liver


title: 39


title: wildtype_RPE_wt_Dam_r3

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_121

source_name: hTERT-RPE (ATCC CRL-4000)

value: hTERT-immortalized retinal pigment epithelial cells

value: wildtype

value: Dam


title: wildtype_RPE_wt_Dam_r4

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_122


title: Jun9_Cell_3


title: Jun9_Cell_4


title: wildtype_RPE_wt_Dam_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_120


title: WT YCP50 HHT2-HHF2 Galactose


title: 38


title: Jun9_Cell_29


title: 37

value: Young


title: TKO swr1Δ Rpb1 Vehicle 60 min Rep 2

source_name: TKO swr1Δ Rpb1 depletion control, colony 2

value: Depletion by anchor-away

value: Rpb1 tagged with FRB and isw1Δ, isw2Δ, chd1Δ and swr1Δ

value: Vehicle control in OD 0.2-0.3 cells for 60 mins


title: wildtype_HCT116_wt_Dam_r5

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_127

value: Colorectal carcinoma cells


title: wildtype_RPE_wt_Dam_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Dam.
pADamID_119

value: pA-DamID


title: Jun9_Cell_31

value: TCRb+CD4+IL-17A-GFP+ cells


title: TKO swr1Δ Rpb1 Rapamycin 60 min Rep 2

source_name: TKO swr1Δ Rpb1 depletion, colony 2

value: anchor-away background

value: Rapamycin 1 μg/ml final concentration in OD 0.2-0.3 cells for 60 mins


title: osmotic_shock_RPE_t_180m_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_180m; target: Ki67.
pADamID_118


title: osmotic_shock_RPE_t_180m_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_180m; target: Ki67.
pADamID_117


title: TKO swr1Δ Rpb1 Rapamycin 60 min Rep 1

source_name: TKO swr1Δ Rpb1 depletion, colony 1


title: 35

value: Male

value: Vastus Lateralis Muscle

value: Older


title: 36


title: Jun9_Cell_25


title: Jun9_Cell_23


title: TKO swr1Δ Rpb1 Vehicle 60 min Rep 1

source_name: TKO swr1Δ Rpb1 depletion control, colony 1


title: osmotic_shock_RPE_t_30m_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_30m; target: Ki67.
pADamID_116


title: TKO htz1Δ Rpb1 Rapamycin 60 min Rep 2

source_name: TKO htz1Δ Rpb1 depletion, colony 2

value: Rpb1 tagged with FRB and isw1Δ, isw2Δ, chd1Δ and htz1Δ


title: Jun9_Cell_18

value: Liver


title: 32


title: osmotic_shock_RPE_t_30m_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: osmotic_shock; condition: t_30m; target: Ki67.
pADamID_115

value: hTERT-immortalized retinal pigment epithelial cells


title: 33


title: Jun9_Cell_17


title: TKO htz1Δ Rpb1 Vehicle 60 min Rep 2

source_name: TKO htz1Δ Rpb1 depletion control, colony 2


title: 31


title: Jun9_Cell_28


title: Jun9_Cell_12


title: Ki67_aid_HCT116_RO_IAA_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: H3K9me3.
pADamID_113

tag: genetic modification

value: OsTir1; Ki67-miniAID-mClover


title: 30


title: TKO htz1Δ Rpb1 Rapamycin 60 min Rep 1

source_name: TKO htz1Δ Rpb1 depletion, colony 1

tag: depletion or deletion


title: 29


title: Ki67_aid_HCT116_RO_IAA_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: H3K27me3.
pADamID_111

source_name: HCT116 (ATCC CCL-247)


title: Jun9_Cell_1


title: 28


title: Aug31_Cell_92


title: Aug31_Cell_93


title: TKO htz1Δ Rpb1 Vehicle 60 min Rep 1

source_name: TKO htz1Δ Rpb1 depletion control, colony 1

tag: protein tagged or deleted


title: Aug31_Cell_90


title: 27


title: TKO arp8Δ Rpb1 Rapamycin 60 min Rep 2

source_name: TKO arp8Δ Rpb1 depletion, colony 2

value: Rpb1 tagged with FRB and isw1Δ, isw2Δ, chd1Δ and arp8Δ

tag: treatment


title: TKO arp8Δ Rpb1 Rapamycin 60 min Rep 1

source_name: TKO arp8Δ Rpb1 depletion, colony 1


title: Ki67_aid_HCT116_RO_IAA_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: H3K27me3.
pADamID_112


title: Ki67_aid_HCT116_RO_IAA_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: LMNB1.
pADamID_110


title: TKO arp8Δ Rpb1 Vehicle 60 min Rep 2

source_name: TKO arp8Δ Rpb1 depletion control, colony 2


title: 26


title: Aug31_Cell_86


title: TKO arp8Δ Rpb1 Vehicle 60 min Rep 1

source_name: TKO arp8Δ Rpb1 depletion control, colony 1


title: Aug31_Cell_85

source_name: T cells


title: Ki67_aid_HCT116_RO_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: H3K9me3.
pADamID_108

value: RO


title: TKO arp8Δ Vehicle 60 min

source_name: TKO arp8Δ control

value: Mock depletion control

value: Mock depletion control in isw1Δ, isw2Δ, chd1Δ and arp8Δ


title: 25

source_name: Vastus Lateralis Muscle


title: Aug31_Cell_84


title: 24


title: TKO nhp10Δ Rpb1 Rapamycin 60 min Rep 2

source_name: TKO nhp10Δ Rpb1 depletion, colony 2

value: Depletion by anchor-away

value: Rpb1 tagged with FRB and isw1Δ, isw2Δ, chd1Δ and nhp10Δ


title: Ki67_aid_HCT116_RO_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: H3K9me3.
pADamID_107

value: Colorectal carcinoma cells

value: pA-DamID


title: Aug31_Cell_83

value: TCRb+CD4+IL-17A-GFP+ cells


title: 23


title: Ki67_aid_HCT116_RO_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: H3K27me3.
pADamID_106


title: Ki67_aid_HCT116_RO_IAA_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: LMNB1.
pADamID_109


title: Aug31_Cell_77


title: Ki67_aid_HCT116_RO_IAA_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO_IAA; target: H3K9me3.
pADamID_114


title: TKO nhp10Δ Rpb1 Rapamycin 60 min Rep 1

source_name: TKO nhp10Δ Rpb1 depletion, colony 1

value: anchor-away background

value: Rapamycin 1 μg/ml final concentration in OD 0.2-0.3 cells for 60 mins


title: Ki67_aid_HCT116_RO_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: H3K27me3.
pADamID_105


title: TKO nhp10Δ Rpb1 Vehicle 60 min Rep 2

source_name: TKO nhp10Δ Rpb1 depletion control, colony 2

value: Vehicle control in OD 0.2-0.3 cells for 60 mins


title: Aug31_Cell_82

value: Male


title: TKO nhp10Δ Rpb1 Vehicle 60 min Rep 1

source_name: TKO nhp10Δ Rpb1 depletion control, colony 1


title: 21

value: Vastus Lateralis Muscle

value: Young


title: 20


title: Ki67_aid_HCT116_RO_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Ki67.
pADamID_102


title: 22


title: TKO arp8Δ deletion Rep 2

source_name: Colony 2

value: Gene deletion

value: isw1Δ, isw2Δ, chd1Δ background


title: Ki67_aid_HCT116_RO_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: LMNB1.
pADamID_104

value: OsTir1; Ki67-miniAID-mClover


title: TKO nhp10Δ Vehicle 60 min

source_name: TKO nhp10Δ control

value: Mock depletion control in isw1Δ, isw2Δ, chd1Δ and nhp10Δ


title: Ki67_aid_HCT116_RO_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: LMNB1.
pADamID_103

value: RO


title: Aug31_Cell_75

value: Liver


title: Aug31_Cell_74


title: Aug31_Cell_73


title: TKO arp8Δ deletion Rep 1

source_name: Colony 1


title: Ki67_aid_HCT116_doublethy_IAA_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: H3K9me3.
pADamID_100


title: TKO nhp10Δ ΔN ino80 Rep 2


title: Ki67_aid_HCT116_doublethy_IAA_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: H3K9me3.
pADamID_99


title: 15


title: Aug31_Cell_72


title: Aug31_Cell_69


title: 19


title: TKO nhp10Δ ΔN ino80 Rep 1


title: Ki67_aid_HCT116_doublethy_IAA_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: H3K27me3.
pADamID_98


title: Ki67_aid_HCT116_RO_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: RO; target: Ki67.
pADamID_101


title: 14


title: Aug31_Cell_68


title: 17


title: TKO ΔN ino80 Rep 2


title: Aug31_Cell_67


title: Ki67_aid_HCT116_doublethy_IAA_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: H3K27me3.
pADamID_97


title: TKO nhp10Δ Rep 2


title: Aug31_Cell_65


title: 13


title: Ki67_aid_HCT116_doublethy_IAA_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: LMNB1.
pADamID_95


title: 12

value: Older


title: 16


title: Aug30_Cell_95


title: TKO ΔN ino80 Rep 1


title: TKO nhp10Δ Rep 1


title: 10


title: Aug30_Cell_93


title: Ki67_aid_HCT116_doublethy_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: H3K9me3.
pADamID_93

value: doublethy


title: Ki67_aid_HCT116_doublethy_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: H3K9me3.
pADamID_94

value: Colorectal carcinoma cells


title: TKO Rep 2


title: Aug30_Cell_62


title: 11


title: Aug30_Cell_61


title: Ki67_aid_HCT116_doublethy_IAA_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy_IAA; target: LMNB1.
pADamID_96

value: pA-DamID


title: TKO Rep 1


title: 8


title: 9


title: Aug30_Cell_60

value: TCRb+CD4+IL-17A-GFP+ cells


title: arp8Δ + pRS416 ΔN arp8 Rep 2

value: pRS416 plasmid with Δ2-197 Arp8 gene

value: Complementation with Δ2-197 arp8 plasmid

value: Arp8 deleted background


title: 6

value: Male


title: arp8Δ + pRS416 ΔN arp8 Rep 1


title: 7

value: Vastus Lateralis Muscle


title: Ki67_aid_HCT116_doublethy_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: LMNB1.
pADamID_90


title: Aug30_Cell_56


title: 2

value: Young


title: arp8Δ + pRS416 Arp8 Rep 1

value: pRS416 plasmid with Arp8 gene

value: Complementation with WT Arp8 plasmid


title: Aug30_Cell_53


title: arp8Δ + pRS416 Rep 2

value: pRS416 plasmid

value: Complementation with empty plasmid


title: 4


title: Ki67_aid_HCT116_doublethy_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: Ki67.
pADamID_87

value: OsTir1; Ki67-miniAID-mClover


title: Ki67_aid_HCT116_control_IAA_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: Ki67.
pADamID_86


title: Aug30_Cell_50

value: Liver


title: Ki67_aid_HCT116_doublethy_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: H3K27me3.
pADamID_92


title: Ki67_aid_HCT116_doublethy_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: H3K27me3.
pADamID_91


title: Ki67_aid_HCT116_doublethy_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: Ki67.
pADamID_88


title: Ki67_aid_HCT116_doublethy_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: doublethy; target: LMNB1.
pADamID_89


title: Aug30_Cell_45


title: arp8Δ + pRS416 Rep 1


title: Ki67_aid_HCT116_control_IAA_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: Ki67.
pADamID_85


title: arp8Δ + pRS416 Arp8 Rep 2


title: arp8Δ deletion Rep 2

value: Gene deletion

value: Wild type background


title: arp8Δ deletion Rep 1


title: Aug30_Cell_43


title: nhp10Δ ΔN ino80 Rep 2


title: Ki67_aid_HCT116_control_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: Ki67.
pADamID_84

value: Colorectal carcinoma cells

value: control


title: Aug30_Cell_44

value: TCRb+CD4+IL-17A-GFP+ cells


title: T3.9

city: Colchester

first: Liudmila

last: Mikheeva

address: Wivenhoe Park

country: United Kingdom

institute: University of Essex

data_processing:
Trimmed reads were aligned to Synechocystis sp. PCC 6803 genome (GCA_000009725.1) using TopHat v2.1.2 with Bowtie2 v2.3.4.1. We used Picard tools (http://broadinstitute.github.io/picard/) to deduplicate reads and HTseq to count reads with parameters stranded=yes and type=exon.
Genome_build: Synechocystis sp. PCC 6803
Supplementary_files_format_and_content: raw counts text files

organism: Synechocystis sp. PCC 6803

source_name: cell suspension

growth_protocol: Cultures were grown in modified liquid blue-green (BG-11) medium (Andersen, 2005) buffered with 10 mM TES–KOH, pH 7.5 and bubbled with filtered (Millex®-FG, 50mm, PTFE 0.2 µm pore size, Merck KGaA, Darmstadt, Germany) CO2-enriched air (1% (v/v); BOC Industrial Gases, UK) at a rate of ~ 200 mL s-1. Cultures were grown under continuous illumination of 150 µmol photons m2 s-1 of cool white (6500K) light supplied by light emitting diodes (LED; The Optoelectronic Manufacturing Corporation (UK) Ltd., Cornwall, UK) that were evenly spaced around the culture vessel.

extract_protocol:
Tri-Reagent as per manufacturers instructions including a DNAse treatment step
TruSeq Stranded mRNA Sample Preparation, 1. Purify and fragment mRNA, 2. Synthesize First Strand cDNA, 3. Adenylate 3' ends, 4. Ligate Adapters, 5. Enrich DNA Fragments, 6. Pooling at with a pool average size of  336bp. The raw reads were pre-processed including the removal of low-quality bases and sequencing adapters (CGR, Liverpool).

treatment_protocol: See "overall design"

tag: control (c) or treatment (t)

value: T

tag: biological replicate

tag: time point


title: T3.7


title: T3.10


title: actinomycin_K562_50ng_H3K9me3_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_82

value: Chronic myeloid leukemia cells

value: pA-DamID

value: actinomycin


title: Aug30_Cell_49

tag: strain

tag: tissue

value: Male


title: Aug30_Cell_41

tag: Sex

tag: genotype


title: 1

value: Vastus Lateralis Muscle

value: Young


title: T3.11


title: nhp10Δ ΔN ino80 Rep 1

tag: strain background


title: Ki67_aid_HCT116_control_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: Ki67.
pADamID_83

source_name: HCT116 (ATCC CCL-247)

tag: cell type

tag: library type


title: T3.8


title: ΔN ino80 Rep 1


title: Aug30_Cell_40

tag: housing temperature


title: Aug30_Cell_38


title: Aug30_Cell_37


title: T3.5


title: actinomycin_K562_50ng_H3K9me3_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_81

tag: experiment

tag: condition

tag: target


title: Aug30_Cell_36


title: ΔN ino80 Rep 2

tag: depletion or deletion


title: T3.6


title: actinomycin_K562_50ng_LMNB1_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_78


title: actinomycin_K562_50ng_H3K27me3_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_79


title: actinomycin_K562_50ng_H3K27me3_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_80


title: T3.2


title: nhp10Δ

tag: protein tagged or deleted


title: WT Ino80 Rapamycin 90 min Rep 1

source_name: WT Ino80 depletion, colony 1

value: Depletion by anchor-away

value: Ino80 tagged with FRB

value: anchor-away background

tag: treatment

value: Rapamycin 1 μg/ml final concentration in OD 0.2-0.3 cells for 90 mins


title: T3.4

tag: control (c) or treatment (t)


title: WT Ino80 Rapamycin 90 min Rep 2

source_name: WT Ino80 depletion, colony 2


title: TKO Ino80 Rapamycin 90 min Rep 2

source_name: TKO Ino80 depletion, colony 2

value: Ino80 tagged with FRB and isw1Δ, isw2Δ and chd1Δ


title: Jun9_Cell_5

value: Liver


title: T2.11

tag: biological replicate


title: T3.1

tag: time point


title: actinomycin_K562_50ng_LMNB1_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_77


title: Jun9_Cell_33

tag: strain


title: actinomycin_K562_50ng_Ki67_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_76


title: Jun9_Cell_26

tag: tissue


title: Jun9_Cell_22

tag: Sex


title: actinomycin_K562_50ng_Ki67_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_75


title: T2.10


title: T3.0


title: actinomycin_K562_DMSO_H3K9me3_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_74

value: DMSO


title: T3.3


title: TKO Ino80 Vehicle 90 min Rep 1

source_name: TKO Ino80 depletion control, colony 1

value: Vehicle control in OD 0.2-0.3 cells for 90 mins


title: actinomycin_K562_DMSO_H3K27me3_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_72


title: Jun9_Cell_14

tag: genotype


title: Jun9_Cell_13


title: T2.8


title: Jun9_Cell_20


title: T2.9


title: actinomycin_K562_DMSO_H3K27me3_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_71


title: actinomycin_K562_DMSO_LMNB1_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_70


title: actinomycin_K562_DMSO_LMNB1_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_69


title: Aug31_Cell_95


title: TKO Ino80 Rapamycin 90 min Rep 1

source_name: TKO Ino80 depletion, colony 1

tag: strain background


title: TKO Rpb1 Ino80 Vehicle 120 min Rep 2

source_name: TKO Rpb1 Ino80 depletion control, colony 2

value: Rpb1 and Ino80 tagged with FRB and isw1Δ, isw2Δ and chd1Δ

value: Vehicle control in OD 0.2-0.3 cells for 120 mins


title: Jun9_Cell_11

source_name: T cells

tag: cell type

value: TCRb+CD4+IL-17A-GFP+ cells


title: Aug31_Cell_91


title: Aug31_Cell_96


title: TKO Ino80 Vehicle 90 min Rep 2

source_name: TKO Ino80 depletion control, colony 2


title: T2.7

value: T


title: actinomycin_K562_DMSO_H3K9me3_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_73

value: Chronic myeloid leukemia cells

tag: library type

value: pA-DamID


title: TKO Rpb1 Ino80 Rapamycin 120 min Rep 2

source_name: TKO Rpb1 Ino80 depletion, colony 2

value: Rpb1 and Ino80 tagged with FRB and ΔIsw1, ΔIsw2 and ΔChd1

value: Rapamycin 1 μg/ml final concentration in OD 0.2-0.3 cells for 120 mins


title: TKO Rpb1 Ino80 Vehicle 120 min Rep 1

source_name: TKO Rpb1 Ino80 depletion control, colony 1


title: T2.6


title: Aug31_Cell_88

value: Male

tag: housing temperature


title: T2.5


title: TKO Rpb1 Ino80 Rapamycin 120 min Rep 1

source_name: TKO Rpb1 Ino80 depletion, colony 1

value: Depletion by anchor-away


title: actinomycin_K562_DMSO_Ki67_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_67

tag: experiment

value: actinomycin


title: actinomycin_K562_DMSO_Ki67_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_68

tag: condition


title: actinomycin_HCT116_50ng_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_66

value: Colorectal carcinoma cells

tag: target


title: TKO Rpb1 Rapamycin 120 min

source_name: TKO Rpb1 depletion, colony 2

tag: depletion or deletion

value: Rpb1 tagged with FRB and isw1Δ, isw2Δ and chd1Δ

value: anchor-away background


title: T2.4


title: T2.3


title: actinomycin_HCT116_50ng_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_63


title: T2.1


title: TKO Rpb1 Vehicle 120 min

source_name: TKO Rpb1 depletion control, colony 2

tag: protein tagged or deleted


title: Aug31_Cell_87

value: Liver


title: actinomycin_HCT116_50ng_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_65


title: T2.2


title: Aug31_Cell_81


title: actinomycin_HCT116_50ng_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_64


title: TKO Rpb1 Rapamycin 60 min Rep 2

tag: treatment

value: Rapamycin 1 μg/ml final concentration in OD 0.2-0.3 cells for 60 mins


title: Aug31_Cell_79


title: T2.0

tag: control (c) or treatment (t)


title: T1.11

tag: biological replicate


title: TKO Rpb1 Rapamycin 60 min Rep 1

source_name: TKO Rpb1 depletion, colony 1


title: Aug31_Cell_66


title: Aug31_Cell_71


title: Aug31_Cell_76


title: TKO Rpb1 Rapamycin 60 min Rep 3


title: T1.9

tag: time point


title: actinomycin_HCT116_50ng_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_60


title: T1.10


title: Aug31_Cell_64

tag: strain


title: actinomycin_HCT116_50ng_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_62


title: TKO Vehicle 60 min Rep 2

source_name: TKO control, colony 2

value: Mock depletion control

value: No protein tagged and isw1Δ, isw2Δ and chd1Δ

value: Vehicle control in OD 0.2-0.3 cells for 60 mins


title: TKO Rpb1 Vehicle 60 min Rep 2


title: actinomycin_HCT116_50ng_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_59


title: T1.8

source_name: cell suspension


title: actinomycin_HCT116_DMSO_H3K9me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_58

source_name: HCT116 (ATCC CCL-247)

value: DMSO


title: TKO Vehicle 60 min Rep 1

source_name: TKO control, colony 1


title: Aug30_Cell_94

tag: tissue

value: TCRb+CD4+IL-17A-GFP+ cells


title: actinomycin_HCT116_50ng_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_61


title: Aug30_Cell_92

tag: Sex


title: T1.7

value: T


title: T1.6


title: Aug30_Cell_63

tag: genotype


title: WT Rpb1 Rapamycin 120 min

source_name: WT Rpb1 depletion

value: Rpb1 tagged with FRB

tag: strain background


title: Aug30_Cell_58

tag: cell type


title: WT Rpb1 Rapamycin 60 min


title: Aug30_Cell_57


title: T1.5


title: actinomycin_HCT116_DMSO_H3K9me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_57

tag: library type

value: pA-DamID


title: actinomycin_HCT116_DMSO_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_56


title: Aug30_Cell_52

tag: housing temperature


title: T1.4


title: actinomycin_HCT116_DMSO_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_55

tag: experiment


title: T1.3


title: actinomycin_HCT116_DMSO_LMNB1_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_54

tag: condition


title: actinomycin_HCT116_DMSO_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_52

tag: target


title: Aug30_Cell_48


title: actinomycin_HCT116_DMSO_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_53


title: WT Rpb1 Vehicle 60 min

source_name: WT Rpb1 depletion control

tag: depletion or deletion


title: WT Vehicle 60 min

source_name: WT control

tag: protein tagged or deleted

value: No protein tagged


title: WT Rpb1 Vehicle 120 min

tag: treatment


title: Aug30_Cell_46

value: Male


title: T1.0

tag: control (c) or treatment (t)


title: T1.1

tag: biological replicate


title: actinomycin_RPE_50ng_H3K9me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_49

source_name: hTERT-RPE (ATCC CRL-4000)

value: hTERT-immortalized retinal pigment epithelial cells


title: C4.10

value: C

tag: time point


title: Jun9_Cell_32

tag: strain


title: TKO Rpb1 Vehicle 60 min Rep 1

source_name: TKO Rpb1 depletion control, colony 1

value: Depletion by anchor-away


title: actinomycin_RPE_50ng_H3K27me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_48

value: actinomycin


title: C4.9


title: actinomycin_RPE_50ng_H3K9me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: H3K9me3.
pADamID_50


title: Aug31_Cell_89

source_name: T cells

tag: tissue


title: Aug31_Cell_94

tag: Sex


title: actinomycin_HCT116_DMSO_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_51

value: Colorectal carcinoma cells


title: C4.7


title: Aug30_Cell_42

value: Liver

tag: genotype


title: C4.4


title: actinomycin_RPE_50ng_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_43


title: actinomycin_RPE_50ng_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: Ki67.
pADamID_44


title: LD Tfh cell rep2

city: CLAYTON

first: Aidil

last: Zaini

state: VICTORIA

address: LEVEL 3, BUILDING 77, MONASH UNIVERSITY

department: BIOCHEMISTRY AND MOLECULAR BIOLOGY

country: Australia

institute: MONASH UNIVERSITY

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al., 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GRCm38 was used
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts, text file, tab separated

source_name: mesenteric lymph node

extract_protocol:
RNA from FACS-sorted cells was extracted using Rneasy Plus Micro Kit (QIAGEN) as per manufacturers’ standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were infected with either low dose/LD/30 or high dose/HD/200 parasitic eggs and culled 21 days after infection, and mesentric lymph nodes were extracted. Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+) at d21 pi and naive Th cells (CD4+ FOXP3- CD44low CD62Lhigh ) from uninfected mice were FACS-sorted and purified for RNA extraction.

value: FIR mice

value: mesenteric lymph node

tag: post infection

value: 21 days


title: C4.11


title: LD Tfh cell rep1


title: actinomycin_RPE_DMSO_H3K9me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_42

tag: cell type


title: T1.2


title: actinomycin_RPE_DMSO_H3K9me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: H3K9me3.
pADamID_41

tag: library type


title: Sample NT4 cyto technical replicate b

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

description: PDAC Control Cytoplasm sample 4 technical replicate b

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.1. Before mapping, poly N read tail were trimmed, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 88) using the STAR mapper (version 2.5.2b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Mus musculus GTF genome annotation from Ensembl version 88. All overlapping regions between alignments and referenced exons were counted and aggregated by genes with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 88
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: PDAC

extract_protocol:
Trizol extraction
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: mPDAC cells were treated for 48 hours with N6L

tag: genetic background

value: FVB/N x C57BL6

tag: age

value: Control

tag: cellular compartment

value: Cytoplasm


title: Sample NT4 cyto technical replicate a

description: PDAC Control Cytoplasm sample 4 technical replicate a


title: actinomycin_RPE_50ng_LMNB1_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_46

tag: experiment

tag: condition

tag: target


title: Sample NT4 poly technical replicate d

description: PDAC Control Polysom sample 4 technical replicate d

tag: treatment

value: Polysom


title: C4.0

tag: control (c) or treatment (t)


title: actinomycin_RPE_50ng_H3K27me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: H3K27me3.
pADamID_47


title: Sample NT4 cyto technical replicate c

description: PDAC Control Cytoplasm sample 4 technical replicate c


title: C4.1

tag: biological replicate


title: Aug30_Cell_47

tag: housing temperature

value: TCRb+CD4+IL-17A-GFP+ cells


title: Sample NT4 poly technical replicate b

description: PDAC Control Polysom sample 4 technical replicate b


title: C3.9

tag: time point


title: Sample T3 Poly technical replicate d

description: PDAC Nucleolin Inhibitor Polysom sample 3 technical replicate d

value: Nocleolin inhibitor


title: actinomycin_RPE_DMSO_LMNB1_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_37

value: pA-DamID

value: DMSO


title: actinomycin_RPE_DMSO_H3K27me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_40

value: hTERT-immortalized retinal pigment epithelial cells


title: actinomycin_RPE_DMSO_H3K27me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: H3K27me3.
pADamID_39


title: C4.8

value: C


title: C3.8


title: Sample T3 Poly technical replicate b

description: PDAC Nucleolin Inhibitor Polysom sample 3 technical replicate b


title: actinomycin_RPE_50ng_LMNB1_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: 50ng; target: LMNB1.
pADamID_45


title: C4.6


title: Sample NT4 poly technical replicate c

description: PDAC Control Polysom sample 4 technical replicate c


title: Sample NT4 cyto technical replicate d

description: PDAC Control Cytoplasm sample 4 technical replicate d


title: C4.5


title: Sample T3 Poly technical replicate a

description: PDAC Nucleolin Inhibitor Polysom sample 3 technical replicate a


title: C4.3


title: actinomycin_RPE_DMSO_LMNB1_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: LMNB1.
pADamID_38


title: cell_cycle_RPE_t_6h_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_6h; target: Ki67.
pADamID_32


title: C3.10


title: Sample T2 Poly technical replicate c

description: PDAC Nucleolin Inhibitor Polysom sample 2 technical replicate c


title: cell_cycle_RPE_t_10h_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_10h; target: Ki67.
pADamID_34


title: actinomycin_RPE_DMSO_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_36


title: C4.2


title: C3.11


title: C3.5


title: actinomycin_RPE_DMSO_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: actinomycin; condition: DMSO; target: Ki67.
pADamID_35


title: cell_cycle_RPE_t_3h_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_3h; target: Ki67.
pADamID_30


title: Sample NT4 poly technical replicate a

description: PDAC Control Polysom sample 4 technical replicate a


title: Sample T3 Poly technical replicate c

description: PDAC Nucleolin Inhibitor Polysom sample 3 technical replicate c


title: cell_cycle_RPE_t_10h_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_10h; target: Ki67.
pADamID_33


title: C3.7


title: C3.2


title: cell_cycle_RPE_t_6h_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_6h; target: Ki67.
pADamID_31


title: Sample T2 Poly technical replicate d

description: PDAC Nucleolin Inhibitor Polysom sample 2 technical replicate d


title: C3.6


title: C3.3


title: Sample T1 Poly technical replicate d

description: PDAC Nucleolin Inhibitor Polysom sample 1 technical replicate d


title: Sample T2 Poly technical replicate b

description: PDAC Nucleolin Inhibitor Polysom sample 2 technical replicate b


title: cell_cycle_RPE_t_1h_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_1h; target: Ki67.
pADamID_27


title: cell_cycle_RPE_t_1h_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_1h; target: Ki67.
pADamID_28


title: C3.0


title: C3.4


title: C3.1


title: cell_cycle_RPE_t_3h_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_3h; target: Ki67.
pADamID_29


title: Sample T1 Poly technical replicate c

description: PDAC Nucleolin Inhibitor Polysom sample 1 technical replicate c


title: Sample T1 Poly technical replicate b

description: PDAC Nucleolin Inhibitor Polysom sample 1 technical replicate b


title: cell_cycle_RPE_t_0h_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_0h; target: Ki67.
pADamID_25


title: C2.11


title: cell_cycle_RPE_t_0h_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: cell_cycle; condition: t_0h; target: Ki67.
pADamID_26


title: wildtype_K562_wt_H3K9me3_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: H3K9me3.
pADamID_23

value: Chronic myeloid leukemia cells

value: wildtype

value: wt


title: wildtype_K562_wt_H3K9me3_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: H3K9me3.
pADamID_24


title: Sample T2 Poly technical replicate a

description: PDAC Nucleolin Inhibitor Polysom sample 2 technical replicate a


title: C2.10


title: C2.8


title: Sample T3 Cyto technical replicate a

description: PDAC Nucleolin Inhibitor Cytoplasm sample 3 technical replicate a


title: C2.6


title: Sample T1 Poly technical replicate a

description: PDAC Nucleolin Inhibitor Polysom sample 1 technical replicate a


title: wildtype_K562_wt_Ki67_r3

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_21