title: Pph_3

city: Nanjing

first: Bowen

last: Wang

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Assembly: GRCm39
Supplementary files format and content: Excel files include counts and tpm values for each sample.

source_name: mouse embryonic stem cell

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: mouse embryonic stem cell

value: Pph


title: HK2 cell，si-FGF9-3

status: Public on Nov 13 2025

type: SRA

city: Guangzhou

first: wen

middle: qing

last: chen

address: Huangpu Avenue, Tianhe District, Guangzhou City

country: China

institute: Jinan University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence,then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
TPM were calculated using a protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-dalimited text files include TPM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: kidney

extract_protocol:
Total RNA was extracted from the samples, and the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. The total amount of RNA required for a single library construction is 1ug, the concentration is ≥50ng/μL, and the OD260/280 is between 1.8 and 2.2.
RNA library were prepared for sequencing using standard illumina protocols

treatment_protocol: HK2 cells (Human renal tubular epithelial cells ) were procured from Chinese Academy of Sciences Cell Bank (Shanghai，China). These HK2 cells were cultured in DMEM/F-12(Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12)  from Gibco (Gaithersburg, MD, USA), supplemented with 5.5mM glucose, 10% fetal bovine serum obtained from ExCell Bio, 100 U/ml of penicillin, and 100 μg/ml of streptomycin. The cells were maintained in a humidified incubator at 37°C with 5% CO2 and cultured in six-well plates at a concentration of 1×106 cells/ml. They were subjected to 50mM glucose (designated as the High Glucose group, HG) treatment 26. For gene transfection, the HK2 cells were transfected using control vector (NG) or FGF9-overexpressing lentivirus vector (HG+OE-FGF9), and si-FGF9 (5＇-CUAUGUUGCAUUAAAUAAATT-3) with the assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA)  26, 29. The transfection procedure was conducted following the manufacturer's instructions.

tag: tissue

value: kidney

tag: cell line

value: HK2 cell

tag: cell type

value: Human renal proximal tubular epithelial cells


title: HK2 cell，si-FGF9-2


title: Pph_2

organism: Mus musculus

tag: genotype


title: RChIP_DMSO8h_rep1

city: Copenhagen

first: Zhong

last: Han

address: Blegdamsvej 3B

department: ICMM, Institut for Cellulær og Molekylær Medicin

country: Denmark

institute: University of Copenhagen

library_source: genomic

data_processing:
single-end reads  were aligned with STAR, Version 2.7.11a
bigwig files were produced with bamcoverage from deeptools, Version 3.5.4
mean bigwig files were produced with bigwigaverage from deeptools, Version 3.5.4
Assembly: GRCh38
Supplementary files format and content: bigwig (mean value of replicates, and log2 fold change of mean bigwig files)

molecule: genomic DNA

source_name: Flp-In T-REx HEK293

growth_protocol: Flp-In T-REx HEK293 cells (R78007, Thermo Fisher Scientific, human embryonic kidney epithelial, female origin) were cultured in DMEM, high glucose, GlutaMAX (10566016, Thermo Fisher Scientific) supplemented with 10% v/v FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, at 37°C with 5% CO2 and routinely passaged 2-3 times a week.

extract_protocol:
Nuclei were isolated and sonicated using a Bioruptor Pico (Diagenode). RNaseH1Mut-V5 was immunoprecipitated, and the cross-linked DNA was reversed by overnight incubation at 65°C.
After treatment with RNase A and proteinase K, DNA was recovered by ethanol precipitation. Phi29 DNA polymerase was used to synthesize second-strand DNA, followed by dA tailing and adaptor ligation. The library was amplified and sequenced with single-end 50 bp reads on the Illumina NextSeq 2000, generating approximately 50 million reads per sample.

treatment_protocol: HEK293 Flp-In T-Rex SETX-dTAG: RNaseH1Mut(D210N)-V5 cells (cZH21) were seeded at a density of 4 million cells per 15 cm plate. The next day, 100 ng/mL doxycycline was added to induce the expression of RNaseH1Mut(D210N)-V5. On the third day, cells were treated with DMSO or 1 µM dTAG for 2, 4, and 8 hours. Cells were crosslinked on the plate by adding formaldehyde to a final concentration of 1% and incubating at room temperature for 10 minutes. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M.

value: Flp-In T-REx HEK293

value: SETX-dTAG, flpin RNaseH1Mut(D210N)-V5

tag: treatment


title: HK2 cell，HG+OE-FGF9-3


title: HK2 cell，si-FGF9-1


title: RChIP_dTAG4h_rep2


title: V_24h_3

city: Exeter

first: Rhys

last: Farrer

state: Devon

address: Stocker Road

department: MRC Center for Medical Mycology

country: United Kingdom

institute: University of Exeter

description: AK Yolksac

data_processing:
Reads were trimmed with fastp v.0.23.1 to remove reads < 75 bases and trim based from the 3’ end with q-score < 22. Alignment and calculation of normalised gene expression were performed with the Trinity pipeline v2.15.1.
Reads were aligned to the GJEY01 AK de novo adult gill transcriptome or to the B8441 v2 C. auris reference genome.
Assembly: Aphanius dispar GJEY00000000.1, Candida auris Cand_auris_B8441_V2
Supplementary files format and content: Tab-separated text files include Fragments per Kilobase per Million (FPKM).

organism:
Candidozyma auris
Aphanius dispar

source_name: Whole organism + yeast cells

growth_protocol: Arabian Killifish were hatched overnight and reared at 28 °C for 72 h with day and night cycles before microinjection, after which point they were kept at 37 °C in 35 ppt artificial seawater.

extract_protocol:
Total RNA was extracted using the Monarch® Total RNA Miniprep Kit (NEB, USA). Embryos were flash frozen in liquid nitrogen, re-suspended in DNA/RNA Protection Reagent and disrupted with an autoclaved plastic micropestle. Bead beating was performed in a FastPrep 24 homogenizer (MP Biomedicals) with 0.5 mm zirconia/silica beads for 8 cycles of 35 s plus 45 s on ice. Lysate was recovered and incubated for 5 min. at 55 °C with proteinase K before addition of lysis buffer and RNA purification following manufacturer’s instructions.
Samples were normalised and prepared using the NEBNext Ultra II Directional RNA Library Prep - Poly(A) mRNA Magnetic Isolation Module following the standard protocol.

treatment_protocol: Yolk sac microinjection with 10 nl solution of ~500 yeasts in phenol red and deionised water, or sham injection, or no injection.

value: Whole organism + yeast cells

value: Wild type

value: V

value: A. dispar infected with C. auris

tag: time point

value: 24 hours


title: Pph_1


title: HK2 cell，HG3


title: RChIP_dTAG4h_rep1


title: IV_24h_3

description: AK Yolksac

value: IV


title: RChIP_DMSO4h_rep1


title: III_24h_3

description: AK Yolksac

value: III


title: Tas_1

value: Tas


title: HK2 cell，HG2


title: RChIP_DMSO4h_rep2


title: Tas_3


title: Tas_2


title: HK2 cell，NG3


title: HK2 cell，HG1


title: MP8_3


title: RChIP_dTAG2h_rep1


title: HK2 cell，NG1


title: RChIP_dTAG2h_rep2


title: HK2 cell，NG2


title: I_24h_3

description: AK Yolksac

value: I


title: IV_24h_2

description: AK Yolksac


title: V_24h_2

description: AK Yolksac


title: II_24h_1

description: AK Yolksac

value: II


title: MP8_2

value: mouse embryonic stem cell


title: RChIP_DMSO2h_rep2


title: WT_3

value: WT


title: Empty_DAP, rep3

city: Taipei

first: Lavakau

last: Thalimaraw

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plants and Microbial biology, Academia Sinica

description:
Library name: sample 6
narrowPeaks calling in None-_22CY5FLT4.bw

data_processing:
Raw DAP-seq reads were processed to remove adapters and perform quality control using fastp (v0.24.0) and FastQC (v0.11.9). The reads were then aligned to the reference genome (Marchantia genome v6.1r1) using Bowtie2 (v2.4.4)51 with the following parameters: --mp 6 -L 22 --dovetail. Low-quality alignments (mapping quality < 2), reads aligned to mitochondrial and chloroplast genomes, and PCR duplicates were flagged and removed using the Samtools view function (v1.14). DAP-seq peaks were called using the MACS2 callpeak function with the following parameters: -f BAM -g 1.6e7 -B -q 0.05 -m 2 50. Bigwig files were generated from DAP-seq BAM files using the deepTools (v3.5.5) bamCoverage function with a bin size of 10 bp, normalized via RPKM.
Assembly: Marchantia genome MpTak_v6.1r1
Supplementary files format and content: Bigwig coverage tracks from BAM files
Library strategy: DAP-seq

organism: Marchantia polymorpha

source_name: gemmalings

growth_protocol: Marchantia polymorpha wild type (Tak-1) were grown on 1/2× Gamborg B5 medium (pH 5.5) with 1% agar under continuous light (50–60 µmol m⁻²s⁻¹) at 22°C.

extract_protocol:
For protein expression and purification, the coding sequences (CDS) for Marchantia HSFA1 and the N-terminal of HaloTag, along with the sequences for the SP6/T7 promoter and T7 terminator, were synthesized by Gene Universal, USA. These sequences were sub-cloned using BbsI into pAGM9121 as level 0 modules and further assembled via Golden Gate cloning into the level 1 expression vector pICH47732 to generate an SP6/T7 promoter-driven CDS with a N-terminal HaloTag and a T7 terminator. Recombinant proteins were expressed using the TNT SP6/T7 High-Yield Wheat Germ Protein Expression System (Promega) following the manufacturer’s protocol. 2.5 μg of plasmid was used to translate protein in vitro at 30°C for 2 hours using a reagent mixture. Protein purity and integrity were confirmed by analyzing 10% of the final mixture via SDS-PAGE confirmed protein purity and integrity. For genomic DNA, approximately 1 g of 14-day-old Marchantia gemmalings were collected and homogenized under liquid nitrogen. Genomic DNA was extracted using the phenol/chloroform method and sheared mechanically to an average size of 100-500 bp. The DNA fragments were end-polished, A-tailed, and ligated with a truncated Y-shaped adapter to prepare them for the protein-DNA binding assay.
In vitro translated proteins were incubated with HaloTag beads (Promega) for 1 hour at room temperature and purified using a magnetic separator with three washes in binding buffer (PBS with 0.1% NP-40). The purified beads-TF complexes were then incubated with the sheared, adapter-ligated DNA in the binding buffer to facilitate protein-DNA interactions. The mixture was incubated at room temperature for one hour to form TF-DNA complexes. Bead-TF-DNA complexes were captured using a magnetic base and washed three times to remove non-specifically bound DNA. Bound DNA was eluted from the beads by heating the mixtures to 98°C for 10 minutes. PCR was used to enrich the protein-bound DNA, incorporating a unique index for each sample to prepare them for multiplex sequencing.

value: gemmalings

value: Tak-6, wt

value: Cntr

tag: batch


title: MP8_1


title: RChIP_DMSO2h_rep1

value: Flp-In T-REx HEK293


title: HSFA1_DAP, rep3

description:
Library name: sample 5
narrowPeaks calling in HSFA_22CY5FLT4.bw

value: Tak-5, wt


title: PROseq_dTAG_rep2

data_processing:
fastq.gz file single reads trim 7nt from 5'end, adaptor trim followed by 7nt trim at 3'end, with minimum length of 25 nt filter,  using cutadapt, Version 4.9
the filtered-trimmed reads  were aligned with STAR, Version 2.7.11a
bigwig files were produced with bamcoverage from deeptools, Version 3.5.4
mean bigwig files were produced with bigwigaverage from deeptools, Version 3.5.4
Assembly: GRCh38
Supplementary files format and content: bigwig (mean value of replicates, and log2 fold change of mean bigwig files)
Library strategy: PRO-seq

growth_protocol: Flp-In T-REx HEK293 cells (R78007, Thermo Fisher Scientific, human embryonic kidney epithelial, female origin) were cultured in DMEM, hihg glucose, GlutaMAX (10566016, Thermo Fisher Scientific) supplemented with 10% v/v FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, at 37°C with 5% CO2 and routinely passaged 2-3 times a week.

extract_protocol:
DMSO or dTAG-treated cells were permeabilized and counted. For each sample, around 1 million permeabilized cells (nuclei) were processed for Run-On reaction containing two biotin-tagged NTPs (PerkinElmer, NEL542001EA, NEL545001EA), which was carried out at 37°C for 6 minutes. The reaction was terminated by adding TRIzol LS, followed by total RNA extraction.
Total RNA was denatured by adding NaOH to a final concentration of 200 mM and purified using Bio-Rad RNase-free P-30 columns according to the manufacturer’s instructions. The 3′ RNA adaptor was ligated, and the biotin-labeled RNA was enriched using Streptavidin beads. On-bead 5′ hydroxyl repair and de-capping reactions were performed, followed by 5′ RNA adaptor ligation. The biotin-labeled RNA was released from the Streptavidin beads using TRIzol/chloroform extraction and ethanol precipitation. Reverse transcription was performed off-bead to generate cDNA. The resulting libraries were amplified, cleaned up using SPRI beads, and sequenced with single-end 50 bp reads on the Illumina NextSeq 2000, generating approximately 50 million reads per sample.

treatment_protocol: DMSO vs dTAG

value: SETX-dTAG


title: PROseq_dTAG_rep3


title: II_24h_3

description: AK Yolksac

value: Whole organism + yeast cells

value: Wild type


title: WT_1


title: Empty_DAP, rep2

description:
Library name: sample 4
narrowPeaks calling in N_22HML7LT3.bw

value: Tak-4, wt


title: PROseq_dTAG_rep1


title: Pex5cKO, CPZ, rep 3, snRNAseq

city: Houston

first: Jian

last: Hu

state: TX

address: 1881 East Rd, South Campus Research Building 3

department: Cancer Biology

country: USA

institute: University of Texas MD Anderson Cancer Center

description: 10X Genomics 3', Dual Index, v3.1

library_source: transcriptomic single cell

data_processing:
After demultiplexing, the 10X Cell Ranger pipeline (cellranger v7.0.0) was used for read alignment and annotation, barcode processing, and gene counting using cellranger count command. Introns were included during read mapping.
Assembly: mm10
Supplementary files format and content: Filtered features and barcodes per sample are provided in tab-separated files. Corresponding UMI counts are provided in matrix files.

source_name: Brain

extract_protocol:
2-3 mm^3 sample, including the corpus callosum, was dissected from frozen mouse brain. Samples were homogenized on ice to extract nuclei using a glass Dounce homogenizer. Nuclei stained with DAPI and PI were purified via fluorescence activated nuclei sorting. Purified nuclei were collected to generate droplet-based, single nuclei RNA seq libaries using the 10X Genomics 3' Dual Index kit (v3.1).
Libraries were generated using the 10X Genomics 3' Dual Index kit (v3.1) per manufacturer's instructions. In brief, nuclei were loaded onto a Chromium Chip G and partitioned into gel-bead emulsions using the 10X Chromium Controller. Poly-A mRNA captured from nuclei-bead emulsions were retrotranscribed into cDNA using poly(dT) primers and tagged with an Illumina R1 primer sequence, 10X barcode, and unique molecular identifier. cDNA was cleaned using Silane Dynabeads and was amplified via PCR. cDNA underwent size selection and fragmentation, followed by end repair, A-tailing, and adapter ligation to add P5 and P7 sequences, and i7 and i5 sample indeces to enable dual index, pair-end sequencing. Libraries were sequenced via 50nt paired-end sequencing on an Illumina NovaSeq 6000 using the following sequencing parameters: R1, 28 cylces; R2, 90 cycles; i7 index, 10 cycles; i2 index, 10 cycles.
single nuclei RNA seq

treatment_protocol: Adult mice (8 to 12-weeks, all males) received 100 uL of tamoxifen (20 mg/mL dissolved in corn oil) via intraperitoneal injection daily for five consecutive days. 1 week post injection, mice were fed 0.2% cuprizone diet  (CPZ) or standard chow (baseline) for 6 weeks. After 6 weeks, the mice were perfused with PBS transcardially and the brain was excised and flash frozen in liquid nitrogen.

value: Brain

value: Single nuclei

value: Cx3cr1^CreEYFP/wt, Pex5^lox/lox


title: Tumor pancreas T4_6

type: RNA

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: The data were analyzed using Bioconductor and package Affy, using the rma() function with default settings.

label: biotin

source_name: Tumor pancreas, sample 3

label_protocol: Total mRNA was RNase H reduced and labelled with the SuperScript One-Cycle cDNA Kit following manufacturer's instructions (Invitrogen).

extract_protocol: Chirgwin's extraction of total RNA (Chirgwin JM et al., 1979) performed on fresh tissues.

treatment_protocol: No treatment.

value: pancreas

value: Ink4a/Arffl/fl; LSL-KrasG12D; Pdx1-Cre

tag: gender

value: Male

tag: age

value: 4 weeks old


title: HSFA1_DAP, rep2

description:
Library name: sample 3
narrowPeaks calling in 50_22HML7LT3.bw

value: Tak-3, wt


title: PROseq_DMSO_rep3


title: Pex5cKO, CPZ, rep 2, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1


title: Tumor pancreas T4_4

source_name: Tumor pancreas, sample 1


title: PROseq_DMSO_rep2


title: Tumor pancreas T4_5

source_name: Tumor pancreas, sample 2


title: HSFA1_DAP, rep1

description:
Library name: sample 1
narrowPeaks calling in A_22CV7GLT4.bw

value: gemmalings

value: Tak-1, wt


title: Empty_DAP, rep1

description:
Library name: sample 2
narrowPeaks calling in E_22CV7GLT4.bw

value: Tak-2, wt

value: Cntr


title: PROseq_DMSO_rep1

value: Flp-In T-REx HEK293


title: Control_pancreas_C4_3

source_name: Control pancreas, sample 3

value: Ink4a/Arffl/fl; LSL-KrasG12D


title: Wheat Straw , end of the exponential phase, rep3

city: MARSEILLE

first: Nicolas

last: VITA

address: 31 ch Joseph Aiguier

institute: CNRS

description:
Library name: WS3
Column name in RNAseq_lignin_CDScount.csv : PailleE-R3

data_processing:
Sequence reads were trimmed for adaptor or low-quality sequences with the  trimommatic software (v0.39). Parameters : -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 ILLUMINACLIP:TruSeq3-PE-2.fa:2:20:10
Read count mapping the CDS features were performed through the htseq_count v2.0.3 software. Parameters: --mode=intersection-strict --stranded=reverse –minaqual=10 (default)
Control quality report, nomalisation and differential analysis data were obtained by the using the DESeq2 package (v1.34.0) through the SARTools pipeline (v1.7.4) on R. The reference condition is the Wheat Straw (WS). Parameters: featuresToRemove=alignment_not_unique, ambiguous, no_feature, not_aligned, too_low_aQual
Up-regulated genes were filtered according these criteria: adjusted p-value (padj) < 0.05 ; expression Fold Change (FC) > 2
Assembly: GCF_000022065.1_ASM2206v1_genomic.fna (NCBI 2022-03-30)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (RNAseq_lignin_CDScount.csv)

organism: Ruminiclostridium cellulolyticum

source_name: prokaryotic cell

growth_protocol: Anaerobic cultures (90-400 mL) of Ruminiclostrium cellulolyticum H10 were performed in triplicates at 32°C in H10 rich medium supplemented with cellobiose (4 g.L-1), Sigmacell cellulose (4 g.L-1), a mix of  polysaccharides (Sigmacell cellulose 2g.L-1 [Sigma] + insoluble wheat arabinoxylan 1.5 g.L-1 [WAXYi, Megazyme]+  xyloglucan 0.2 g.L-1 [Megazyme]) or hatched straw at 5 g.L-1 (chips ~4-6 mm).

extract_protocol:
After thawing of bacterial pellets, cells were treated with lysozyme (1g.L-1) in TE buffer and incubated for 20 minutes at 37°C. After lysis, total RNA were extracted using the "Maxwell® 16 miRNA Tissue Kit" (Promega) and treated with the TURBO DNA-free™ kit (Invitrogen) following the supplier protocols. After quality control using TapeStation microfluidic electrophoresis with RNA ScreenTape (Agilent Technologies), the samples were stored at -80°C.
Illumina RNA-seq libraries were prepared using the Zymo-Seq RiboFree® Total RNA Library Kit (ZYMO RESEARCH) using 250 ng of total RNA and following manufacturer's protocols. After quality control using TapeStation microfluidic electrophoresis with High Sensitivity D1000 ScreenTape (Agilent Technologies) and DNA quantification using a Qubit fluorometer (Thermo Fisher Scientific), the sequencing was performed using an Illumina NextSeq 500 sequencer (TGML sequencing platform, Marseille, France) and following manufacturer's protocols.

treatment_protocol: Cell growth was followed by metabolic profiling. Collection of the cells at the mid and/or the end of the exponential growth phase was performed as follow: filtration of the culture (cut off: 2.7 µm); washing of the residual substrate and further filtration; pool of both filtrates and centrifugation to pellets the cells (4,000 g, 4°C, 10 min); washing of the pellet with deionized water; additional centrifugation  (8,000 g, 4°C, 5 min) and pellet quick freezing in liquid nitrogen; storage at -80°C. Since the collection of the cells grown on insoluble substrates (Sigmacell cellulose, mix of polysaccharides and hatched wheat straw) lasts 1 hour, cells collected from cultures on soluble substrate (cellobiose) were collected the same way and were kept at room temperature in water for 1 h in total in order to be exposed to the same oxidative stress time.

value: prokaryotic cell

value: wild type

tag: growth substrate

value: hatched wheat straw (chips ~4-6 mm) 5 g.L-1

tag: growth phase_sampling

value: end of the exponential phase


title: WT_2

value: mouse embryonic stem cell

value: WT


title: Pex5cKO, CPZ, rep 1, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1

value: Brain

value: Single nuclei

value: Cx3cr1^CreEYFP/wt, Pex5^lox/lox


title: Control, CPZ, rep 3, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1

value: Cx3cr1^CreEYFP/wt, Pex5^wt/lox


title: Wheat Straw , end of the exponential phase, rep2

description:
Library name: WS2
Column name in RNAseq_lignin_CDScount.csv : PailleE-R2


title: dko_ABA_ATAC, rep2

description:
Library name: sample 32
Column name in counts_ABA_ATAC.txt: dko-CK2
counts_ABA_ATAC.txt
dko-Mock.merge_RPKM.bw

data_processing:
Raw ATAC-seq sequence data were trimmed to remove adapters and were quality-checked using fastp (v0.24.0) and FastQC (v0.11.9). Processed reads were aligned to the Marchantia reference genome (v6.1r1) with Bowtie2 (v2.4.4). Alignments with low quality (mapping quality < 2), those mapped to mitochondrial or chloroplast genomes, and PCR duplicates were identified and removed using Samtools view (v1.14). ATAC-seq peaks were identified across biological replicates with MACS2 (v2.2.7.1) using the following parameters: -f BAMPE -g 1.6e7 --cutoff-analysis --nomodel --shift -100 --extsize 200. Identified peaks were consolidated using BEDtools merge to generate a consensus peak list. ATAC-seq alignments were assigned and quantified at these peak regions using the featureCounts function from subread (v2.0.6). Bigwig coverage tracks for data visualization in the Integrated Genome Browser (IGV) were created from merged replicate BAM files using deepTools49 (v3.5.5) bamCoverage with a 10-bp bin size and Reads Per Kilobase Million (RPKM) normalization.
Assembly: Marchantia genome MpTak_v6.1r1
Supplementary files format and content: Tab-delimited text file includes peak raw counts for each sample, Bigwig coverage tracks from merged replicate BAM files

growth_protocol: Marchantia polymorpha wild type (Tak-1) and knockout mutants (hsfa1, hsfb1, and hsfa1/hsfb1 double knockout) were grown on 1/2× Gamborg B5 medium (pH 5.5) with 1% agar under continuous light (50–60 µmol m⁻²s⁻¹) at 22°C.

extract_protocol:
Whole Marchantia gemmalings (1.5 g) were finely chopped with a razor blade in 4 mL of ice-cold Galbraith buffer (45 mM MgCl₂, 20 mM MOPS, 30 mM sodium citrate, 0.2% Triton X-100, and cOmplete Protease Inhibitor Cocktail) for 2-5 minutes in a chilled petri dish, followed by 10 minutes of incubation at 4°C. The lysate was then filtered twice through a 40 µm filter and transferred to an ice-cold 15 mL tube. Nuclei were pelleted by centrifugation at 500 × g for 10 minutes at 4°C, and the supernatant was carefully removed. The pellet was gently resuspended in 2 mL of Galbraith buffer and centrifuged again under the same condition. After removing the supernatant, the nuclei were resuspended in 1 mL of Galbraith buffer in a 5 mL round-bottom tube and stained with 10 µg/mL DAPI. Flow cytometry was performed on a BD FACS Aria II using a 100 µm nozzle at a pressure below 20 psi. Sorting gates were set based on FSC and SSC to exclude debris and potential doublets. Baseline fluorescence was established by running unstained control samples before sorting DAPI-stained nuclei. 50,000 sorted nuclei were collected into 500 µL of Galbraith buffer (without Triton X-100) in 1.5 mL Eppendorf tubes per sample.
The nuclei were pelleted by centrifugation at 1000 × g for 10 minutes at 4°C. The sorted nuclei were resuspended in a 50 µL tagmentation reaction mixture consisting of 25 µL of 2x TD buffer, 2.5 µL of TDE1 enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits), and 22.5 µL of nuclease-free water. The reaction was incubated at 37°C for 30 minutes, followed by DNA purification with Zymo CHIP DNA Clean and Concentrator (Cat# D5205). The eluted DNA was amplified with dual-indexed Nextera primers using NEBNext 2x HiFi PCR Master Mix (New England Biolabs) for library construction. For library amplification, 10 µL of transposed DNA fragments were mixed with 25 µL of NEBNext 2x HiFi PCR Master Mix, 6.25 µL of 10 µM T5 primer, and 2.5 µL of nuclease-free water. The corresponding T7 primer (6.25 µL) was added, and PCR amplification was performed with the following conditions: 72°C for 5 minutes (initial denaturation), 98°C for 30 seconds, then 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Additional cycles were optimized via qPCR using PowerSYBR™ Green Master Mix on 5 µL of the amplified library. Amplified libraries underwent dual size selection using a 1.2x SPRIselect magnetic bead ratio (Beckman Coulter). Library quality was assessed with a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).

treatment_protocol: Marchantia gemmalings were grown in 1/2× Gamborg B5 medium for seven days under continuous light, then exposed to heat stress at 37°C for 0 or 1 hour or treated with 0 (mock, 20% EtOH) or 50 µM ABA.

value: hsfa1/hsfb1, ko

value: ABA


title: DRBR30m_dTAG_rep3

data_processing:
single-end reads were aligned with STAR, Version 2.7.11a
bigwig files were produced with bamcoverage from deeptools, Version 3.5.4
mean bigwig files were produced with bigwigaverage from deeptools, Version 3.5.4
Assembly: GRCh38
Supplementary files format and content: bigwig (mean of replciates)
Library strategy: TTseq

extract_protocol:
Cells were incubated with 4SU for 15 minutes, after which the medium was removed, and 1 mL of TRIzol was added per dish to terminate labeling. The TRIzol-cell mixture was collected, and total RNA was extracted via TRIzol/chloroform extraction followed by isopropanol precipitation. RNA concentration was measured using the Qubit RNA BR Assay Kit (Thermo Fisher, Q10210). For each sample, 1 µg of S. cerevisiae 4TU-labeled RNA was mixed with 100 µg of purified 4SU-labeled RNA. The total volume was adjusted to 100 µL with RNase-free water, and 20 µL of 1 M NaOH was added per sample. Samples were incubated on ice for 20 minutes to fragment the RNA, and RNA fragmentation was stopped by adding 80 µL of 1 M Tris-HCl, pH 6.0. The samples were purified using Micro Bio-Spin P-30 gel columns (Bio-Rad, 7326250) to neutralize NaOH and prevent further fragmentation. The column-purified RNA was biotinylated in a 250 µL reaction containing 10 mM Tris-HCl, pH 7.4, 1 mM EDTA, and 5 mg of MTSEA biotin-XX linker (Biotium, BT90066) for 30 minutes at room temperature in the dark. Biotinylated RNA was purified by phenol-chloroform extraction and isopropanol precipitation. The RNA was then denatured at 65°C for 10 minutes and purified using the μMACS Streptavidin Kit (Miltenyi, 130-074-101) according to the manufacturer’s instructions. The purified nascent RNA was further cleaned using the RNeasy MinElute kit (QIAGEN, 74204) and used to prepare sequencing libraries.
TTchem-seq libraries were generated using the KAPA RNA HyperPrep Kit (Roche, 08098093702) with the fragmentation step omitted. A total of 75 ng of nascent RNA was denatured at 65°C for 5 minutes. The rest of the library preparation followed the manufacturer’s instructions, with two SPRI bead purifications (Beckman Coulter, A63881) performed using bead-to-sample ratios of 0.95x and 1x.

treatment_protocol: Cells were treated with DMSO or 1 µM dTAGv1 for one hour, followed by a 3-hour pre-treatment with 100 µM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole). After this, cells were released from DRB inhibition for 15, 20, or 30 minutes, which included a 15-minute pulse with 1 mM 4-thiouridine, while still under DMSO or dTAG.

value: SETX-dTAG


title: Control, CPZ, rep 2, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1


title: Wheat Straw , end of the exponential phase, rep1

description:
Library name: WS1
Column name in RNAseq_lignin_CDScount.csv : PailleE-R1


title: Control_pancreas_C4_2

source_name: Control pancreas, sample 2

value: pancreas

value: Male

value: 4 weeks old


title: DRBR30m_dTAG_rep2

value: Flp-In T-REx HEK293


title: Control, CPZ, rep 1, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1


title: Control_pancreas_C4_1

source_name: Control pancreas, sample 1

value: Ink4a/Arffl/fl; LSL-KrasG12D


title: Pex5cKO, baseline, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1


title: DRBR30m_dTAG_rep1


title: Wheat Straw , mid of the exponentiel phase, rep3

description:
Library name: Wsm3
Column name in RNAseq_lignin_CDScount.csv : PailleM-R3

value: prokaryotic cell

value: wild type

value: mid of the exponential phase


title: dko_Mock_ATAC, rep2

description:
Library name: sample 30
Column name in counts_ABA_ATAC.txt: dko-ABA2
counts_ABA_ATAC.txt
dko-ABA.merge_RPKM.bw

value: gemmalings

value: Mock


title: DRBR30m_DMSO_rep3


title: dko_Mock_ATAC, rep1

description:
Library name: sample 29
Column name in counts_ABA_ATAC.txt: dko-ABA1
counts_ABA_ATAC.txt
dko-ABA.merge_RPKM.bw


title: Wheat Straw , mid of the exponentiel phase, rep2

description:
Library name: Wsm2
Column name in RNAseq_lignin_CDScount.csv : PailleM-R2

value: hatched wheat straw (chips ~4-6 mm) 5 g.L-1


title: dko_ABA_ATAC, rep1

description:
Library name: sample 31
Column name in counts_ABA_ATAC.txt: dko-CK1
counts_ABA_ATAC.txt
dko-Mock.merge_RPKM.bw


title: Control, baseline, snRNAseq

description: 10X Genomics 3', Dual Index, v3.1

value: Brain

value: Single nuclei


title: Wheat Straw , mid of the exponentiel phase, rep1

description:
Library name: WSm1
Column name in RNAseq_lignin_CDScount.csv : PailleM-R1


title: hsfb1_Mock_ATAC, rep2

description:
Library name: sample 26
Column name in counts_ABA_ATAC.txt: hsfb-ABA2
counts_ABA_ATAC.txt
hsfb-ABA.merge_RPKM.bw

value: hsfb1, ko


title: Mix, end of the exponential phase, rep2

description:
Library name: Mix2
Column name in RNAseq_lignin_CDScount.csv : Mix-R2

value: mix of polysaccharides 4 g.L-1 (Sigmacell cellulose 2g.L-1 [Sigma] + insoluble wheat arabinoxylan 1.5 g.L-1 [WAXYi, Megazyme]+  xyloglucan 0.2 g.L-1 [Megazyme])

value: end of the exponential phase


title: DRBR20m_dTAG_rep3

value: SETX-dTAG


title: hsfb1_Mock_ATAC, rep1

description:
Library name: sample 25
Column name in counts_ABA_ATAC.txt: hsfb-ABA1
counts_ABA_ATAC.txt
hsfb-ABA.merge_RPKM.bw


title: DRBR30m_DMSO_rep2


title: DRBR30m_DMSO_rep1


title: p53cKO_1

city: Seattle

first: Valeri

last: Vasioukhin

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
nf-core/rnaseq  v1.4.2 in Nextflow  v20.04.1 was utilized to process the data. Sequencing reads were mapped to the GRCm38 mouse genomes using STAR.v2.6.1d and gene level abundance was quantitated using featureCounts v1.6.4 ancd analyzed using DESeq2 v2.11.40.8.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file which includes gene counts for each sample

source_name: skin epidermis

extract_protocol:
Total RNA was extracted with QIAzol (QIAGEN) followed by RNase-free DNAase treatment (QIAGEN) and purification using RNeasy kit (QIAGEN).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: skin epidermis

value: K14-Cre/Trp53 +/flox


title: DRBR20m_dTAG_rep2


title: Mix, end of the exponential phase, rep1

description:
Library name: Mix1
Column name in RNAseq_lignin_CDScount.csv : Mix-R1


title: p53cKO_3


title: hsfb1_ABA_ATAC, rep1

description:
Library name: sample 27
Column name in counts_ABA_ATAC.txt: hsfb-CK1
counts_ABA_ATAC.txt
hsfb-Mock.merge_RPKM.bw

value: ABA


title: Mix, end of the exponential phase, rep3

description:
Library name: Mix3
Column name in RNAseq_lignin_CDScount.csv : Mix-R3


title: p53cKO_2


title: hsfa1_ABA_ATAC, rep2

description:
Library name: sample 24
Column name in counts_ABA_ATAC.txt: hsfa-CK2
counts_ABA_ATAC.txt
hsfa-Mock.merge_RPKM.bw

value: hsfa1, ko


title: DRBR20m_dTAG_rep1

value: Flp-In T-REx HEK293


title: L1L2p53cKO_3

value: K14-Cre/Llgl1/2 flox/flox/Trp53 +/flox


title: Cellulose, end of the exponential phase, rep2

description:
Library name: C2
Column name in RNAseq_lignin_CDScount.csv : Cellulo-R2

value: prokaryotic cell

value: wild type

value: Sigmacell cellulose 4 g.L-1 (Sigma)


title: DRBR20m_DMSO_rep3


title: L1L2p53cKO_1


title: Cellulose, end of the exponential phase, rep1

description:
Library name: C1
Column name in RNAseq_lignin_CDScount.csv : Cellulo-R1


title: hsfb1_ABA_ATAC, rep2

description:
Library name: sample 28
Column name in counts_ABA_ATAC.txt: hsfb-CK2
counts_ABA_ATAC.txt
hsfb-Mock.merge_RPKM.bw

value: gemmalings


title: hsfa1_ABA_ATAC, rep1

description:
Library name: sample 23
Column name in counts_ABA_ATAC.txt: hsfa-CK1
counts_ABA_ATAC.txt
hsfa-Mock.merge_RPKM.bw


title: hsfa1_Mock_ATAC, rep2

description:
Library name: sample 22
Column name in counts_ABA_ATAC.txt: hsfa-ABA2
counts_ABA_ATAC.txt
hsfa-ABA.merge_RPKM.bw

value: Mock


title: L1L2p53cKO_2


title: hsfa1_Mock_ATAC, rep1

description:
Library name: sample 21
Column name in counts_ABA_ATAC.txt: hsfa-ABA1
counts_ABA_ATAC.txt
hsfa-ABA.merge_RPKM.bw


title: DRBR20m_DMSO_rep2


title: Cellobiose, end of the exponential phase, rep3

description:
Library name: Cb3
Column name in RNAseq_lignin_CDScount.csv : CB-R3

value: cellobiose 4 g.L-1 (Sigma)


title: L1L2cKO_3

value: K14-Cre/Llgl1/2 flox/flox


title: L1L2cKO_2


title: Tak-1_ABA_ATAC, rep2

description:
Library name: sample 20
Column name in counts_ABA_ATAC.txt: Tak1-CK2
counts_ABA_ATAC.txt
Tak1-Mock.merge_RPKM.bw

value: Tak-1, wt


title: Cellobiose, end of the exponential phase, rep2

description:
Library name: Cb2
Column name in RNAseq_lignin_CDScount.csv : CB-R2


title: Tak-1_ABA_ATAC, rep1

description:
Library name: sample 19
Column name in counts_ABA_ATAC.txt: Tak1-CK1
counts_ABA_ATAC.txt
Tak1-Mock.merge_RPKM.bw


title: Cellulose, end of the exponential phase, rep3

description:
Library name: C3
Column name in RNAseq_lignin_CDScount.csv : Cellulo-R3


title: DRBR15m_dTAG_rep1


title: Control_3


title: HCT116 RAD21-mAC cells, 120 min 1 uM auxin, biol rep3

city: Davis

first: Henriette

last: O'Geen

state: CA

address: 451 Health Sciences Drive, GBSF 4617A

department: Genome Center

institute: UC Davis

description: Library name: 4C_AIDT3_R1.fastq.gz

data_processing:
Libraries were analyzed following previously published protocol using the pipe4C pipeline in R developed by the de Laat lab (https://github.com/deLaatLab/pipe4C).
Briefly, demultiplexed reads were trimmed from the 5’ end to the start of the DpnII motif and mapped to the reference genome (hg19) using Bowtie 2.5.1. No mismatches were tolerated and unmapped reads were removed. The reference genome was then digested in silico and the fragment ends were mapped against the reference genome. Read counts were normalized (max total sum of mapped reads = 1 million) and smoothed (running mean window size = 21), and processed data files were generated.
4C peaks were called using the previously published peakC R package developed by the de Wit Lab (https://github.com/deWitLab/peakC).
Briefly, this package computes non-parametric statistics based on ranks of coverage of 4C fragment ends with respect to a background model. This model estimates the background contact frequency of both the region upstream and downstream of the viewpoint independently for each 4C-seq experiment individually and uses a statistical model to identify genomic regions that are significantly contacted.
Assembly: hg19
Supplementary files format and content: WIG
Library strategy: 4C-Seq

source_name: cell line

growth_protocol: HCT116 cells were cultured in McCoy′s 5a supplemented with 2mM Glutamine, 10% Fetal Bovine Serum (FBS), and 1x penicillin/streptomycin. K562 cells were cultured in RPMI 1640 supplemented with 2mM Glutamine, 10% Fetal Bovine Serum (FBS), and 1x penicillin/streptomycin. All cultures were maintained in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
For each replicate, approximately 5 million cells were crosslinked in 2% formaldehyde and 10% FBS in PBS for 10 min while rotating at room temperature. Glycine was added to a final concentration of 0.125 M to quench crosslinking reaction and cells were centrifuged at 500 x g for 5 min. Cells were washed twice with PBS, transferred to an Eppendorf tube, and lysed on ice for 20 min with 1 mL lysis buffer (50 mM Tris-HCl (pH 7.5), 10 mM NaCl, 5 mM EDTA, 0.5% NP-40 and 1% Triton X-100) supplemented with 1X protease inhibitors (Roche). Cells were then washed once with 450 µL of 1.2X DpnII buffer and resuspended in 500 µL 1.2X DpnII buffer and 15 µL of 10% SDS (final: 0.3% SDS) and incubated in a thermoshaker at 37 °C for 1 h at 750 RPM. Then, 75 µL of 20% Triton X-100 (final: 2.5% Triton-X-100) were added, nuclear aggregates were resuspended with a pipet, and tubes were incubated at 37°C for 1 h while shaking at 750 RPM. A 5 µL aliquot of undigested control was stored, and nuclei were incubated overnight with 250 U of DpnII restriction enzyme (New England Biolabs). A fresh 250 U of DpnII was added the following morning, and samples were digested for an additional 3 h. After this, digestion was checked for completion by running 5 μl of sample on a 0.6% agarose gel next to undigested lysates. DpnII was inactivated by incubating the reaction tubes for 20 min at 65 °C, and a proximity ligation reaction was performed in a 7 mL volume with 3200 U of T4 DNA ligase (New England Biolabs) for 16 h at room temperature followed by an overnight period at 16 °C and finally a 500 U T4 DNA ligase spike-in and another 36 h incubation at room temperature. After this, ligation was checked for completion by running 5 μl of sample on a 0.6% agarose gel next to the digested control. Cross-links were reversed at 65 °C overnight after adding 300 μg proteinase K. Samples were then treated with 300 μg RNase A for 30 min at 37 °C, and DNA was purified using MagMax DNA binding beads (Thermo Fisher Scientific) and a magnetic bead-based protocol described in a previous reference 50. A second restriction digest was performed overnight at 37 °C while shaking at 500 RPM in a 500 μL reaction with 200 U of NlaIII (New England Biolabs). After this, digestion was checked for completion by running 5 μl of sample on a 0.6% agarose gel next to the samples from the first ligation. NlaIII was inactivated at 65 °C for 25 min, and a proximity ligation reaction (5 ng/μL DNA concentration) was performed in a 5 mL volume with 2000 U of T4 DNA ligase for 16 h at room temperature followed by an overnight period at 16 °C and finally a 400 U T4 DNA ligase spike-in and another 36 h incubation at room temperature. After ligation, DNA was again purified using MagMax DNA binding beads (Thermo Fisher Scientific)
To generate the 4C–seq library, several viewpoint-specific inverse PCR primer sets targeting the MYC promoter conserved CTCF binding site were compared for efficiency and the primer pair that produced the strongest product was selected for the 1st round PCR in library preparation. 200 ng of prepared 4C template was amplified with 16 PCR cycles in 4 separate 50 μL reactions using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs). Next, these 4 reactions were mixed and 50 μL of 1st round PCR product was purified using ChargeSwitch PCR Clean- Up Kit (Thermo Fisher Scientific) to remove primer dimers. 5 μL purified 1st round PCR product was used as a template in a 2nd round of PCR for 20 cycles in a 50 μL reaction using Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs) to add Illumina P5/P7 flow cell adapters, Illumina sequencing primer sites, and unique 6 bp indexes to all replicates. These 2nd round reactions were then purified with the QIAquick PCR purification kit (QIAGEN), the purity was measured with a Nanodrop 2000 Spectrophotometer (Thermo Fisher Scientific), the concentration was more accurately determined using the Qubit dsDNA HS Assay (Thermo Fisher Scientific), and all replicates were run on the Bioanalyzer 2100 (Agilent) to check for any remaining primer dimers and determine average library size. After final quality control and Element library circularization, the 4C-seq libraries were sequenced on the Element Biosciences AVITI for 150 bases in paired-end read mode at 300 cycles.

treatment_protocol: Only for HCT116-RAD21-mAC cells, cultures were treated with either 1 µM DMSO (untreated) or 1 µM auxin (5-Ph-IAA) directly in media for 120 min prior to harvesting.

value: cell line

value: Human colorectal cancer cell-line HCT116

value: HCT116-RAD21-mAC OsTIR1(F74G)

value: 120 min 1 uM auxin


title: L1L2cKO_1

value: skin epidermis


title: DRBR15m_dTAG_rep3

value: SETX-dTAG


title: Control_2


title: Tak-1_Mock_ATAC, rep1

description:
Library name: sample 17
Column name in counts_ABA_ATAC.txt: Tak1-ABA1
counts_ABA_ATAC.txt
Tak1-ABA.merge_RPKM.bw


title: Tak-1_Mock_ATAC, rep2

description:
Library name: sample 18
Column name in counts_ABA_ATAC.txt: Tak1-ABA2
counts_ABA_ATAC.txt
Tak1-ABA.merge_RPKM.bw


title: DRBR15m_DMSO_rep3


title: HCT116 RAD21-mAC cells, 120 min 1 uM auxin, biol rep2

description: Library name: 4C_AIDT2_R1.fastq.gz


title: Control_1


title: dko_HS_ATAC, rep2

description:
Library name: sample 16
Column name in counts_HS_ATAC.txt: dko-HS2
counts_HS_ATAC.txt
dko-HS.merge_RPKM.bw

value: hsfa1/hsfb1, ko

value: HS


title: HCT116 RAD21-mAC cells, 120 min 1 uM auxin, biol rep1

description: Library name: 4C_AIDT1_R1.fastq.gz


title: Cellobiose, end of the exponential phase, rep1

description:
Library name: Cb1
Column name in RNAseq_lignin_CDScount.csv : CB-R1

value: end of the exponential phase


title: DRBR15m_DMSO_rep2

value: Flp-In T-REx HEK293


title: DRBR20m_DMSO_rep1


title: HCT116 RAD21-mAC cells, 120 min 1 uM DMSO, biol rep3

description: Library name: 4C_AIDU3_R1.fastq.gz

value: 120 min 1 uM DMSO


title: Skin, SDS_Day5, rep2

first: Kang-Yu

last: Tai

address: Yonglin Biomedical Engineering Hall, No.49, Fanglan Rd.

department: Genome and Systems Biology Degree Program

institute: National Taiwan University

data_processing:
Galaxy version 23.1.rc1
Sequence reads were trimmed for adaptors by Trim Galore ( ver0.6.7)
Trimmed sequence were mapped to mm10 using HISAT2 (ver 2.2.1)
Raw counts were extracted by featureCounts (ver 2.0.3)
Normalized counts were performed by DESeq2 (ver 2.11.40.8)
Assembly: mm10
Supplementary files format and content: tab-delimited file contains raw counts for each sample
Supplementary files format and content: tab-delimited matrix file contains normalized counts for all sample

source_name: whole skin

growth_protocol: 7 week-age mice

extract_protocol:
RNeasy Micro Kit
Agilent SureSelect Strand-Specific RNA library Prep Cat#G9691B

treatment_protocol: Topical treatment as indicated for 4 days

value: whole skin

value: 7 week

value: SDS


title: DRBR15m_DMSO_rep1


title: Skin, SDS_Day3, rep2


title: dko_HS_ATAC, rep1

description:
Library name: sample 15
Column name in counts_HS_ATAC.txt: dko-HS1
counts_HS_ATAC.txt
dko-HS.merge_RPKM.bw

value: gemmalings


title: dko_Cntr_ATAC, rep2

description:
Library name: sample 14
Column name in counts_HS_ATAC.txt: dko-CK2
counts_HS_ATAC.txt
dko-CK.merge_RPKM.bw

value: Cntr


title: DRBR15m_dTAG_rep2


title: HCT116 RAD21-mAC cells, 120 min 1 uM DMSO, biol rep2

description: Library name: 4C_AIDU2_R1.fastq.gz


title: Lipo-MK1775+NLG-2

city: Hefei

first: Peijie

last: Zhou

state: Anhui

address: Lujiang road

department: Department of Radiation Oncology, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

description: whole_transcripts_FPKM.txt column name: 5-2

data_processing:
The Fastq files were evaluated for read quality using FastQC. Subsequently, Trim-Galore was used for adapter and read quality trimming (Phred score threshold of 30).
Mapping against the Mus musculus (GRCm39) genome was performed using the HISAT2 software.
Fragments Per Kb of exon per Million mapped reads (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene using StringTie (parameters: -e -B).
Differential expression gene (DEG) analysis was performed using Ballgown R package.
DEGs were then subjected to ClusterProfiler R package for GO and KEGG enrichment analysis.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Subcutaneous tumor

growth_protocol: 4T1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Tumors were extracted from Subcutaneous area of mice. RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: Tumor proliferation inhibition was induced by treatment with different drugs.

value: Subcutaneous tumor

value: cancer cell

tag: time

value: Day 14


title: dko_Cntr_ATAC, rep1

description:
Library name: sample 13
Column name in counts_HS_ATAC.txt: dko-CK1
counts_HS_ATAC.txt
dko-CK.merge_RPKM.bw


title: Skin, SDS_Day5, rep1


title: HCT116 RAD21-mAC cells, 120 min 1 uM DMSO, biol rep1

description: Library name: 4C_AIDU1_R1.fastq.gz

value: cell line

value: Human colorectal cancer cell-line HCT116

value: HCT116-RAD21-mAC OsTIR1(F74G)


title: Skin, SDS_Day3, rep1


title: hsfb1_HS_ATAC, rep2

description:
Library name: sample 12
Column name in counts_HS_ATAC.txt: hsfb-HS2
counts_HS_ATAC.txt
hsfb-HS.merge_RPKM.bw

value: hsfb1, ko


title: Lipo-MK1775+NLG-1

description: whole_transcripts_FPKM.txt column name: 5-1


title: K562, untreated, biol replicate 3

description: Library name: 4C_K562_rep3

value: Human leukemia cell line

value: WT

value: untreated


title: Lipo-MK1775-2

description: whole_transcripts_FPKM.txt column name: 4-2


title: Skin, SDS_Day1, rep2


title: hsfb1_HS_ATAC, rep1

description:
Library name: sample 11
Column name in counts_HS_ATAC.txt: hsfb-HS1
counts_HS_ATAC.txt
hsfb-HS.merge_RPKM.bw

value: HS


title: K562, untreated, biol replicate 2

description: Library name: 4C_K562_rep2


title: Skin, SDS_Day1, rep1


title: hsfb1_Cntr_ATAC, rep2

description:
Library name: sample 10
Column name in counts_HS_ATAC.txt: hsfb-CK2
counts_HS_ATAC.txt
hsfb-CK.merge_RPKM.bw


title: K562, untreated, biol replicate 1

description: Library name: 4C_K562_rep1


title: Free-MK1775+NLG919-2

description: whole_transcripts_FPKM.txt column name: 3-2


title: Skin, Day0, rep2

value: Control


title: hsfb1_Cntr_ATAC, rep1

description:
Library name: sample 9
Column name in counts_HS_ATAC.txt: hsfb-CK1
counts_HS_ATAC.txt
hsfb-CK.merge_RPKM.bw


title: HCT116, untreated, biol replicate 3

description: Library name: 4C_HCT116_rep3


title: Free-MK1775+NLG919-1

description: whole_transcripts_FPKM.txt column name: 3-1


title: Skin, Day0, rep1

value: whole skin


title: hsfa1_HS_ATAC, rep2

description:
Library name: sample 8
Column name in counts_HS_ATAC.txt: hsfa-HS2
counts_HS_ATAC.txt
hsfa-HS.merge_RPKM.bw

value: hsfa1, ko


title: HCT116, untreated, biol replicate 2

description: Library name: 4C_HCT116_rep2


title: Free-MK1775-2

description: whole_transcripts_FPKM.txt column name: 2-2


title: HFSC, C18:0, rep2

source_name: Hair follicle

value: Hair follicle


title: hsfa1_HS_ATAC, rep1

description:
Library name: sample 7
Column name in counts_HS_ATAC.txt: hsfa-HS1
counts_HS_ATAC.txt
hsfa-HS.merge_RPKM.bw

value: gemmalings


title: Free-MK1775-1

description: whole_transcripts_FPKM.txt column name: 2-1


title: HCT116, untreated, biol replicate 1

description: Library name: 4C_HCT116_rep1


title: Human Treg stim, Donor 1, Input ChIP, Formaldehyde fixation

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens St.

institute: UCSF Gladstone Institutes

description: Library name: D1_Treg_Input_Stim_ChIP_form

data_processing:
Reads were mapped to the hg38 human genome using Bowtie2 with default parameters. Duplicate reads were removed using SAMtools. Matching input control was used to call peaks. Peak calling was performed using MACS2 (Tregs) or MACS3 (all other samples) with significance set between e-2 to e-8. Bigwig tracks were generated using deepTools bamCoverage with RPKM normalization. Blacklisted regions (downloaded from ENCODE) were excluded from called peaks using bedtools.
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig and MACS2/MACS3 peak bed files.

source_name: Blood

growth_protocol: Primary human T cells subsets were isolated from peripheral blood mononuclear cells (PBMCs) sourced from consented, fresh Human Peripheral Blood Leukopaks (STEMCELL Technologies, catalog no. 70500). Leukopaks were washed twice with 1X volume of EasySep Buffer (DPBS, 2% fetal bovine serum [FBS], 1 mM pH 8.0 EDTA) using centrifugation and resuspended at 50e6-200e6 cells/mL. CD4+CD25highCD127low Tregs and CD4+CD25low Tconv were isolated from washed PBMCs using the EasySep Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, catalog no. 18063) according to manufacturer’s protocol. For enhanced cell purity, Tregs were stained for CD4 (Biolegend, catalog no. 344634 or 344620), CD25 (Tonbo, catalog no. 20-0259-T100), and CD127 (Becton Dickinson, catalog no. 557938) and further sorted into a CD4+CD25highCD127low population via FACS on a BD FACSAria or BD FACSAria Fusion I. Tregs and Tconvs were cultured in X-VIVO15 media (Lonza, catalog no. 02-053Q) supplemented with 5% FBS, 55 µM 2-Mercaptoethanol, and 4 mM N-Acetyl-L-Cysteine. For CRISPRi screening, CRISPRi validation, and CRISPRn screening, recombinant Human IL-2 (R&D Systems, catalog no. 202-GMP or BT-002-GMP) was supplemented at 200 IU/mL, and cells were stimulated for 48 hours with CTS Dynabeads CD3/CD28 beads (Thermo Fisher Scientific, catalog no. 40203D) at a cell to bead ratio of 1:1. After 48 hours, beads were removed using magnetic separation. For all other experiments, cells were cultured using recombinant Human IL-2 (R&D Systems, catalog no. 202-GMP or BT-002-GMP) supplemented at 300 IU/mL and stimulated with 12.5 uL/mL Immunocult Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, catalog no. 10970), to enhance cell recovery, growth, and viability. Cells were cultured at 37C and 5% CO2 and split to 5E5-1.5E6 cells/mL every ~48 hours by topping off media and completely replacing the appropriate dose of IL-2.

extract_protocol:
Up to 2.5E7 cells were cross-linked in PBS with 1% methanol-free formaldehyde (Thermo, catalog no. 28908) for 10 min at room temperature followed by quenching in glycine at 125 mM final concentration. Tconv and selected Treg samples were cross-linked in 2 mM disuccinimidyl glutarate (Thermo, catalog no. 20593) in PBS for 30 min at room temperature prior to formaldehyde treatment. Cross-linked cell pellets were snap-frozen in liquid nitrogen and stored at –80ºC. Nuclei were isolated from thawed, cross-linked cells via sequential lysis in LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-360, and 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% sodium deoxycholate [NaDOC], and 0.5% N-laurylsarcosine) supplemented with 0.5 mM phenylmethylsulfonyl fluoride (PMSF, Sigma, catalog no. P7626) and 0.5X protease inhibitor cocktail (PIC, Sigma, catalog no. P8340). Chromatin was sheared on a Covaris E220 focused ultrasonicator using 1 mL milliTubes (Covaris, catalog no. 520128) with 140W peak incident power, 5% duty factor, 200 cycles per burst, 6ºC temperature setpoint (minimum 3ºC, maximum 9ºC), fill level 10, and time 12-14 min to obtain target size 200-700 bp. Triton X-100 was added to final concentration of 1% prior to immunoprecipitation for 16 h at 4ºC with 2-8 µg of indicated antibodies bound to a 1:1 mixture of protein A and protein G magnetic beads (Thermo, catalog nos. 10001D and 10003D). Bead-bound antibody-chromatin complexes were sequentially washed three times with Wash Buffer 1 (20 mM Tris pH 8, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium dodecyl sulfate [SDS], and 0.1% NaDOC), twice with Wash Buffer 2 (20 mM Tris-HCl pH 8, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, and 0.1% NaDOC), twice with Wash Buffer 3 (20 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-360, and 0.5% NaDOC), twice with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween-20), and once with TE0.1 (10 mM Tris-HCl pH 8, 0.1 mM EDTA, 0.5 mM PMSF, and 0.5X PIC) supplemented with 0.5 mM PMSF and 0.5X PIC. Beads were resuspended in TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) prior to on-bead library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB, catalog no. E7370L) as described previously (Texari et al., 2021). ChIP-seq libraries were multiplexed for paired-end sequencing on an Illumina NextSeq 2000 or NovaSeq X instrument.
On-bead library preparation was conducted using the NEBNext Ultra II DNA Library Prep Kit (NEB, catalog no. E7370L) as described previously (Texari et al., 2021). ChIP-seq libraries were multiplexed for paired-end sequencing.

treatment_protocol: Nine days after isolation and initial stimulation, a portion of cells were stimulated with 12.5 µL/mL Immunocult Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, catalog no. 10970). Eleven days post-initial stimulation, rested (Rest) and restimulated (Stim) cells were fixed for ChIP-seq.

value: Blood

value: Treg

tag: condition

value: stim

tag: donor

value: Donor 1

tag: chip target

value: Input

tag: fixation method

value: Formaldehyde

tag: chip antibody


title: HFSC, C18:0, rep1

tag: tissue


title: HFSC, C18:1, rep2


title: hsfa1_Cntr_ATAC, rep2

description:
Library name: sample 6
Column name in counts_HS_ATAC.txt: hsfa-CK2
counts_HS_ATAC.txt
hsfa-CK.merge_RPKM.bw

tag: cell line

value: Cntr


title: negative control 2

description: whole_transcripts_FPKM.txt column name: 1-2

value: Subcutaneous tumor

tag: cell type

value: cancer cell

value: negative control

value: Day 14


title: Lipo-MK1775-1

description: whole_transcripts_FPKM.txt column name: 4-1


title: hsfa1_Cntr_ATAC, rep1

description:
Library name: sample 5
Column name in counts_HS_ATAC.txt: hsfa-CK1
counts_HS_ATAC.txt
hsfa-CK.merge_RPKM.bw

tag: genotype


title: Human Treg stim, Donor 1, H3K27ac ChIP, Formaldehyde fixation

description: Library name: D1_Treg_H3K27ac_Stim_ChIP_form

value: H3K27ac (EpiCypher, 13-0045)


title: 4T1 cells, Wee1 siRNA 3#

description: whole_transcripts_FPKM.txt column name: 3-3

source_name: breast cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: cell proliferation inhibition was induced by treatment with MK1775 and Wee1 siRNA.Cells were then fed with DMEM supplemented with 10% FBS.

value: breast cancer

tag: treatment

value: Wee1 siRNA knockdown

tag: protocol

value: cell proliferation inhibition

value: Day 2


title: negative control 1

description: whole_transcripts_FPKM.txt column name: 1-1


title: HFSC, EtOH, rep2

value: Hair follicle

value: EtOH


title: Human Treg rest, Donor 1, Input ChIP, Formaldehyde fixation

description: Library name: D1_Treg_Input_Rest_ChIP_form

value: Blood

value: Treg

value: rest


title: Tak-1_HS_ATAC, rep1

description:
Library name: sample 3
Column name in counts_HS_ATAC.txt: Tak1-HS1
counts_HS_ATAC.txt
Tak1-HS.merge_RPKM.bw

value: gemmalings

value: Tak-1, wt

value: HS

tag: batch


title: Human Treg rest, Donor 1, H3K27ac ChIP, Formaldehyde fixation

description: Library name: D1_Treg_H3K27ac_Rest_ChIP_form

value: Donor 1

value: Formaldehyde


title: Tak-1_Cntr_ATAC, rep2

description:
Library name: sample 2
Column name in counts_HS_ATAC.txt: Tak1-CK2
counts_HS_ATAC.txt
Tak1-CK.merge_RPKM.bw

value: Cntr


title: 4T1 cells, Wee1 siRNA 2#

description: whole_transcripts_FPKM.txt column name: 3-2

value: cancer cell


title: Human Tconv stim, Donor 2, Input ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_Input_ChIP_dsg

growth_protocol: Primary human T cells subsets were isolated from peripheral blood mononuclear cells (PBMCs) sourced from consented, fresh Human Peripheral Blood Leukopaks (STEMCELL Technologies, catalog no. 70500). Leukopaks were washed twice with 1X volume of EasySep Buffer (DPBS, 2% fetal bovine serum [FBS], 1 mM pH 8.0 EDTA) using centrifugation and resuspended at 50e6-200e6 cells/mL. CD4+CD25highCD127low Tregs and CD4+CD25low Tconv were isolated from washed PBMCs using the EasySep Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, catalog no. 18063) according to manufacturer’s protocol. For enhanced cell purity, Tregs were stained for CD4 (Biolegend, catalog no. 344634 or 344620), CD25 (Tonbo, catalog no. 20-0259-T100), and CD127 (Becton Dickinson, catalog no. 557938) and further sorted into a CD4+CD25highCD127low population via FACS on a BD FACSAria or BD FACSAria Fusion I. Tregs and Tconvs were cultured in X-VIVO15 media (Lonza, catalog no. 02-053Q) supplemented with 5% FBS, 55 µM 2-Mercaptoethanol, and 4 mM N-Acetyl-L-Cysteine. For CRISPRi screening, CRISPRi validation, and CRISPRn screening, recombinant Human IL-2 (R&D Systems, catalog no. 202-GMP or BT-002-GMP) was supplemented at 200 IU/mL, and cells were stimulated for 48 hours with CTS Dynabeads CD3/CD28 beads (Thermo Fisher Scientific, catalog no. 40203D) at a cell to bead ratio of 1:1. After 48 hours, beads were removed using magnetic separation. For all other experiments, cells were cultured using recombinant Human IL-2 (R&D Systems, catalog no. 202-GMP or BT-002-GMP) supplemented at 300 IU/mL and stimulated with 12.5 uL/mL Immunocult Human CD3/CD28/CD2 T Cell Activator (STEMCELL Technologies, catalog no. 10970), to enhance cell recovery, growth, and viability. Cells were cultured at 37C and 5% CO2 and split to 5E5-1.5E6 cells/mL every ~48 hours by topping off media and completely replacing the appropriate dose of IL-2.

value: Tconv

value: stim

value: Donor 2

value: Input

value: DSG/formaldehyde


title: HFSC, EtOH, rep1

value: Hair follicle


title: 4T1 cells, Wee1 siRNA 1#

description: whole_transcripts_FPKM.txt column name: 3-1

value: breast cancer

value: Wee1 siRNA knockdown

value: cell proliferation inhibition

value: Day 2


title: Tak-1_Cntr_ATAC, rep1

description:
Library name: sample 1
Column name in counts_HS_ATAC.txt: Tak1-CK1
counts_HS_ATAC.txt
Tak1-CK.merge_RPKM.bw

value: gemmalings


title: Human Tconv rest, Donor 2, Input ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_Input_ChIP_dsg

value: Blood

value: rest


title: 4T1 cells, MK1775 treatment 3

description: whole_transcripts_FPKM.txt column name: 2-3


title: Dot1l_KO_rep2

city: Montréal

first: Javier

middle: M

last: Di Noia

state: QC

address: 110 Pine Avenue West

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

data_processing:
Sequencing adapters were trimmed with fastp (0.23.1) with (parameter- --detect_adapter_for_pe).
Trimmed means were mapped to custom CH12F3 genome (modified mm10) and dm6 genomes with STAR (2.7.9a) following manual instructions for multi-sample 2-pass mapping.
Gene expression counts were determined with featureCounts (Rsubread 2.12.2). Drosophila reads were used to scale DESeq2 (1.38.2) for differential gene expression.
Mapped reads to mouse genome were filtered for mapping quality (MAPQ>=1) with using samtools (1.16.1) to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 1bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and dm6
Supplementary files format and content: bigwig (forward and reverse strands)

molecule: polyA RNA

growth_protocol: CH12F3-G (a subclone with higher CSR activity derived by limiting dilution from CH12F3) were cultured in RPMI 1640 media (Wisent) supplemented with 10% fetal bovine serum (Wisent), 1% penicillin/streptomycin (Wisent) and 0.1 mM 2-mercaptoethanol (Bioshop).

extract_protocol:
Briefly, 0.5million CH12F3 WT or Dot1l-/- cells and 0.1million Kc167 Drosophila cells (as spike-in) were mixed. RNA was extracted using Qiagen RNeasy Micro kit.
mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and library was prepared using KAPA RNA HyperPrep kit (Roche Diagnostics) as per manufacturer's instructions.

value: unstimulated


title: 4T1 cells, MK1775 treatment 2

description: whole_transcripts_FPKM.txt column name: 2-2


title: Dot1l_KO_rep1


title: Human Tconv stim, Donor 1, Input ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_Input_ChIP_dsg

value: Donor 1


title: dko_HS, rep3

description:
Library name: sample 36
Column name in counts_HS.txt: dko_hs_3
counts_HS.txt

data_processing:
Raw sequences from Marchantia were first processed to remove adaptors using fastp (v0.24.0). The cleaned reads were then mapped to the reference genome (Marchantia genome v6.1r1) using STAR (v2.7.9a) with default settings. Read count matrix were generated by featureCounts function from subread (v2.0.6).
Assembly: Marchantia genome MpTak_v6.1r1
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
Plant samples were frozen in liquid nitrogen, and total RNA was extracted from gemmalings using the RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing following standard NovaSeq protocols.

value: hsfa1/hsfb1, ko

value: HS


title: HFSC, C18:1, rep1


title: WT_rep3

value: WT


title: dko_HS, rep1

description:
Library name: sample 34
Column name in counts_HS.txt: dko_hs_1
counts_HS.txt


title: Human Tconv rest, Donor 1, Input ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_Input_ChIP_dsg

value: Tconv


title: Tak-1_HS_ATAC, rep2

description:
Library name: sample 4
Column name in counts_HS_ATAC.txt: Tak1-HS2
counts_HS_ATAC.txt
Tak1-HS.merge_RPKM.bw

value: Tak-1, wt


title: dko_HS, rep2

description:
Library name: sample 35
Column name in counts_HS.txt: dko_hs_2
counts_HS.txt


title: 4T1 cells, negative control 3

description: whole_transcripts_FPKM.txt column name: 1-3

value: cancer cell

value: NC


title: WT_rep2


title: 4T1 cells, MK1775 treatment 1

description: whole_transcripts_FPKM.txt column name: 2-1


title: Human Tconv stim, Donor 2, H3K27ac ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_H3K27ac_ChIP_dsg

value: stim

value: Donor 2

value: DSG/formaldehyde

value: H3K27ac (Active Motif, 39133)


title: Human Tconv stim, Donor 2, FOXP3 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_FOXP3_ChIP_dsg

value: FOXP3 (Novus, NB600-242)


title: 4T1 cells, negative control 2

description: whole_transcripts_FPKM.txt column name: 1-2

value: breast cancer

value: cell proliferation inhibition

value: Day 2


title: Tak-1_HS, rep2

description:
Library name: sample 32
Column name in counts_HS.txt: tak_hs_2
counts_HS.txt

value: gemmalings


title: WT_rep1

value: unstimulated


title: Human Tconv stim, Donor 2, SATB1 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_SATB1_ChIP_dsg

value: Blood

value: SATB1 (Abcam, ab109122)


title: Tak-1_HS, rep3

description:
Library name: sample 33
Column name in counts_HS.txt: tak_hs_3
counts_HS.txt

value: HS


title: Dot1l_KO_rep3


title: IgG_Dot1l_KO

data_processing:
Sequencing adapters and first 10bp were trimmed with fastp 0.23.1.
Trimmed means were mapped to before alignment with bowtie2 (2.4.4) to the spiked-in E. coli (k12) and custom CH12F3 genome (modified mm10).
Duplicates reads were removed with MarkDuplicatesSpark from Picard tools through gatk (4.2.4.0) and were filtered for mapping quality (MAPQ>=1) using samtools (1.16.1).
Normalization using spike-in reads was performed using DiffBind package (3.8.3), specifically by using DESeq2 (1.38.2) to calculate scaling factors on “background bin” signals for spike-in reads estimated by the csaw package (1.32.0).
These scaling factors were then used to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 20bp.
Assembly: custom reference genome reflecting the recombined V(D)J loci in CH12, produced by modifying mouse (mm10) reference genome based on the IgH and Igκ cDNA sequences from CH12F3 cells using Reform; and k12
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed following a protocol described previously (Hogan AK, et al. 2021 EMBO J.), with the following modifications: 5 million CH12-F3 of viable cells were employed per condition. CH12-F3 cells were permeabilized with 0.001% digitonin as determined by optimization. Following incubation with Calcium Incubation Buffer for 30min at 0C, reaction was stopped with STOP buffer containing 1ng of E.coli Spike-in DNA (Epicypher, 15-1016). The released chromatin fragments were purified with Nucleotide Purification Kit (Qiagen) and eluted in 25µL of Tris-HCl (pH 8).
Libraries were prepared using the KAPA HyperPrep library kit (Roche Diagnostics) as per manufacturer's instructions. Normalization of the samples quantities was done after quantification of the ligation products by qPCR and library size distribution was assessed on a 2100 bioanalyzer.

tag: antibody

value: IgG


title: 4T1 cells, negative control 1

description: whole_transcripts_FPKM.txt column name: 1-1


title: Human Tconv stim, Donor 2, EGR2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_EGR2_ChIP_dsg

value: Tconv

value: EGR2 (Abcam, ab43020)


title: Human Treg stim, Donor 2, SRF ChIP, Formaldehyde fixation

description: Library name: D2_Treg_Stim_SRF_ChIP_form

value: Treg

value: SRF

value: Formaldehyde

value: SRF (ActiveMotif, 61385)


title: IgG_WT

value: WT


title: Human Tconv stim, Donor 2, MBD2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_MBD2_ChIP_dsg

value: stim

value: Donor 2

value: DSG/formaldehyde

value: MBD2 (Active Motif, 39547)


title: H3K27me3_WT


title: dko_Cntr, rep3

description:
Library name: sample 30
Column name in counts_HS.txt: dko_cntr_3
counts_HS.txt

value: gemmalings

value: hsfa1/hsfb1, ko

value: Cntr


title: Human Treg stim, Donor 2, SATB1 ChIP, Formaldehyde fixation

description: Library name: D2_Treg_Stim_SATB1_ChIP_form

value: Blood

value: SATB1 (Abcam, Ab109122)


title: Human Tconv stim, Donor 2, CTCF ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_CTCF_ChIP_dsg

value: CTCF

value: CTCF (Abcam, ab128873)


title: Human Tconv stim, Donor 2, YY1-active-motif ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_YY1-active-motif_ChIP_dsg

value: Tconv

value: YY1 (Active Motif, 61779)


title: dko_Cntr, rep1

description:
Library name: sample 28
Column name in counts_HS.txt: dko_cntr_1
counts_HS.txt


title: Tak-1_Cntr, rep3

description:
Library name: sample 27
Column name in counts_HS.txt: tak_cntr_3
counts_HS.txt

value: Tak-1, wt


title: Human Treg stim, Donor 2, Input ChIP, Formaldehyde fixation

description: Library name: D2_Treg_Stim_Input_ChIP_form

value: Treg

value: Input

value: Formaldehyde


title: Human Treg stim, Donor 2, FOXP3 ChIP, Formaldehyde fixation

description: Library name: D2_Treg_Stim_FOXP3_ChIP_form

value: stim

value: FOXP3 (Novus, NB600-242)


title: CTCF_Dot1l_KO_1

value: unstimulated


title: CTCF_Dot1l_KO_2


title: CTCF_WT_2

value: WT


title: Human Tconv stim, Donor 2, YY1-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_YY1-abcam_ChIP_dsg

value: Donor 2

value: DSG/formaldehyde


title: Human Tconv stim, Donor 2, GATA3-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_stim_GATA3-abcam_ChIP_dsg

value: GATA3 (Abcam, ab199428)


title: CTCF_WT_1


title: Gonadotroph adenomas, replicate 5, scRNAseq

city: Lyon

first: Philippe

last: BERTOLINO

address: 28 rue Laennec

institute: INSERM

description: 10x Genomics

data_processing:
First, Fastq files are processed and trimmed by using Fastp v0.20.1 (https://github.com/OpenGene/fastp) . Reads with phred quality at least equal to 30 (-q 30) are qualified for the quantification step. Length filtering is disabled (-L) while adapter sequence auto-detection is enabled (--detect_adapter_for_pe).
Association of reads with their cells of origin, collapsing of reads according to unique molecular identifiers (UMIs), and generation of gene or feature counts from the reads to generate a cell x gene matrix were made using kallisto and bustools Python wrapper's : kb-python v0.26.0 (https://www.kallistobus.tools/)
Assembly: Hg38
Supplementary files format and content: kb-python output files
Supplementary files format and content: barcodes.txt : list of barcodes
Supplementary files format and content: genes.txt : list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format

source_name: Pituitary

extract_protocol:
Single-cell suspension of the resected pituitary adenoma fragment was obtained through mechanical enzymatic dissociation (Collagenase P) then passedthrough a 100 μmmesh-strainer. Red blood cells were lysed. The whole processwas achieved within the 2 hours following the surgical resection, cell viability was evaluated to reach at least 70 percent prior encapsulation.
Library was performedas recommended by the manufacturer's for the Chromium Next GEM Single Cell 3' GEM Kit.

value: Pituitary

tag: disease state

value: Gonadotroph adenoma

tag: Sex

value: female


title: Gonadotroph adenomas, replicate 4, scRNAseq

description: 10x Genomics


title: Tak-1_HS, rep1

description:
Library name: sample 31
Column name in counts_HS.txt: tak_hs_1
counts_HS.txt

source_name: gemmalings

value: gemmalings

value: HS


title: Human Tconv rest, Donor 2, H3K27ac ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_H3K27ac_ChIP_dsg

value: Blood

value: Tconv

value: rest

value: H3K27ac (Active Motif, 39133)


title: Tak-1_Cntr, rep2

description:
Library name: sample 26
Column name in counts_HS.txt: tak_cntr_2
counts_HS.txt

value: Tak-1, wt

value: Cntr


title: Rpb1_Dot1l_KO


title: Tak-1_Mock, rep3

description:
Library name: sample 24
Column name in counts_ABA.txt: Tak1-CK3
counts_ABA.txt

value: Mock


title: Tak-1_Cntr, rep1

description:
Library name: sample 25
Column name in counts_HS.txt: tak_cntr_1
counts_HS.txt


title: Rpb1_WT

value: unstimulated


title: Gonadotroph adenomas, replicate 3, scRNAseq

description: 10x Genomics

value: male


title: Human Tconv rest, Donor 2, SATB1 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_SATB1_ChIP_dsg

value: Donor 2

value: SATB1 (Abcam, ab109122)


title: Gonadotroph adenomas, replicate 6, scRNAseq

description: 10x Genomics


title: Tak-1_Mock, rep2

description:
Library name: sample 23
Column name in counts_ABA.txt: Tak1-CK2
counts_ABA.txt


title: Human Tconv rest, Donor 2, EGR2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_EGR2_ChIP_dsg

value: DSG/formaldehyde

value: EGR2 (Abcam, ab43020)


title: dko_Cntr, rep2

description:
Library name: sample 29
Column name in counts_HS.txt: dko_cntr_2
counts_HS.txt

value: hsfa1/hsfb1, ko


title: Gonadotroph adenomas, replicate 2, scRNAseq

description: 10x Genomics

value: Pituitary

value: Gonadotroph adenoma


title: ire1DX, serum, rep 3

city: London

first: Patrick

last: Lajoie

state: Ontario

address: Medical Sciences Building, Elgin Road

department: Anatomy and Cell Biology

institute: Western University

description:
Library name: Sample 18
ire1DX cells treated with fetal bovine serum

data_processing:
FASTQ files were delivered by Azenta Life Sciences. All data processing was performed in R studio.
Quality control and trimming was performed using Trim Galore default settings (v0.6.6.). Reads with lengths <50 bp were removed.
Reads were aligned to Candida albicans SC5314 Assembly 22 genome (NCBI RefSeq assembly GCF_000182965.3) using STAR (Spliced Transcripts Alignment to a Reference; v2.7.9a).
featureCounts was used to count mapped reads using default settings (Rsubread package, v2.0.3.)
Assembly: Candida albicans SC5314 Assembly 22, NCBI RefSeq assembly GCF_000182965.3
Supplementary files format and content: .xlsx file with raw gene counts (all genes and conditions in one file)

organism: Candida albicans

source_name: ire1DX (Woolford et al., 2016)

growth_protocol: Overnight yeast cultures were prepared by inoculating a colony of cells from a refrigerated agar stock plate into YPD media (1% yeast extract, 2% peptone, 2% dextrose) and grown overnight in a 30°C rotating incubator.

extract_protocol:
Total RNA was extracted using a MasterPure Yeast RNA Purification kit from LGC Biosearch Technologies. The quality of purified RNA samples was assessed by Bioanalyzer RNA analysis (Agilent; performed by the London Regional Genomics Centre) to ensure an RNA Integrity Number (RIN) of 8 or higher. Final concentration of RNA used for library preparation ranged from 37.3-98.5 ng/µL (1.12-2.96 µg).
Library preparation was performed by Azenta Life Sciences. Total RNA was purified using polyA selection and RNA samples were converted to Illumina TruSeq cDNA libraries.

treatment_protocol: Overnight cultures were diluted to an OD600 of 0.1 and grown to log phase for 90 minutes. They were then either a) grown an additional two hours with no treatment at 30°C (untreated condition), b) grown an additional two hours with 1.5 µg/mL tunicamycin at 30°C (tunicamycin condition), or c) grown an additional 4 hours with 10% fetal bovine serum at 37°C (serum condition).

value: ire1DX (Woolford et al., 2016)

value: Yeast cells

value: Diminished expression of IRE1

value: 10% fetal bovine serum

tag: treatment temperature

tag: treatment duration

value: 4 hours


title: Tak-1_Mock, rep1

description:
Library name: sample 22
Column name in counts_ABA.txt: Tak1-CK1
counts_ABA.txt

value: gemmalings

value: Tak-1, wt


title: Gonadotroph adenomas, replicate 1, scRNAseq

description: 10x Genomics


title: Tak-1_ABA, rep3

description:
Library name: sample 21
Column name in counts_ABA.txt: Tak1-ABA3
counts_ABA.txt

value: ABA


title: TNFalpha treated Human skeletal muscle cells from healthy subject#8

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description: Library name: HM8_TNF_count

data_processing:
Reads were mapped with GEMtools v1.6.2  onto the human genome GRCh37 and the gene annotation GENCODE 19. Reads having a proper orientation and a GEM mapping quality score of 150 or above were kept for the gene quantification step (read count per gene). These counts were used to generate read per kilobase per million reads (RPKM)
Assembly: GRCHh37
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Human skeletal muscle cells

extract_protocol:
RNA extraction was performed following standard RNeasy protocol (RNeasy, Qiagen)
RNA-seq libraries were prepared with the Illumina TruSeq protocol following manufacturer’s instructions

value: Human skeletal muscle cells

value: TNFalpha


title: ire1DX, serum, rep 2

description:
Library name: Sample 17
ire1DX cells treated with fetal bovine serum


title: Human Tconv rest, Donor 2, CTCF ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_CTCF_ChIP_dsg

value: Blood

value: Tconv

tag: condition

value: rest

value: Donor 2

value: CTCF

value: CTCF (Abcam, ab128873)


title: Tak-1_ABA, rep2

description:
Library name: sample 20
Column name in counts_ABA.txt: Tak1-ABA2
counts_ABA.txt


title: Human Tconv rest, Donor 2, YY1-active-motif ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_YY1-active-motif_ChIP_dsg

tag: donor

value: DSG/formaldehyde

value: YY1 (Active Motif, 61779)


title: ire1DX, tunicamycin, rep 3

description:
Library name: Sample 15
ire1DX cells treated with tunicamycin

value: ire1DX (Woolford et al., 2016)

value: Yeast cells

value: 1.5 µg/mL tunicamycin

value: 2 hours


title: ire1DX, tunicamycin, rep 2

description:
Library name: Sample 14
ire1DX cells treated with tunicamycin

value: Diminished expression of IRE1


title: Human skeletal muscle cells from healthy subject#8

description: Library name: HM8_CTRL_count

value: Control


title: TNFalpha treated Human skeletal muscle cells from healthy subject#6

description: Library name: HM6_TNF_count


title: hsfb1_Mock, rep2

description:
Library name: sample 17
Column name in counts_ABA.txt: Hsfb-CK2
counts_ABA.txt

value: gemmalings

value: hsfb1, ko

value: Mock


title: Human Tconv rest, Donor 2, YY1-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_YY1-abcam_ChIP_dsg

value: Blood

tag: chip target


title: Human Tconv rest, Donor 2, GATA3-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_GATA3-abcam_ChIP_dsg

value: Tconv

tag: fixation method

value: GATA3 (Abcam, ab199428)


title: ire1DX, tunicamycin, rep 1

description:
Library name: Sample 13
ire1DX cells treated with tunicamycin


title: TNFalpha treated Human skeletal muscle cells from healthy subject#5

description: Library name: HM5_TNF_count

value: Human skeletal muscle cells

value: TNFalpha


title: Human Tconv stim, Donor 1, H3K27ac ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_H3K27ac_ChIP_dsg

value: stim

value: Donor 1

tag: chip antibody

value: H3K27ac (Active Motif, 39133)


title: hsfb1_Mock, rep1

description:
Library name: sample 16
Column name in counts_ABA.txt: Hsfb-CK1
counts_ABA.txt

tag: tissue


title: Human skeletal muscle cells from healthy subject#6

description: Library name: HM6_CTRL_count


title: Human Tconv stim, Donor 1, FOXP3 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_FOXP3_ChIP_dsg

value: DSG/formaldehyde

value: FOXP3 (Novus, NB600-242)


title: ire1DX, untreated, rep 2

description:
Library name: Sample 11
ire1DX cells untreated

tag: cell line

value: ire1DX (Woolford et al., 2016)

value: Yeast cells

value: Untreated


title: Human Tconv rest, Donor 2, MBD2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor2_human_Tconv_rest_MBD2_ChIP_dsg

tag: cell type

value: rest

value: Donor 2

value: MBD2 (Active Motif, 39547)


title: hsfb1_ABA, rep3

description:
Library name: sample 15
Column name in counts_ABA.txt: Hsfb-ABA3
counts_ABA.txt

value: gemmalings

tag: genotype

value: hsfb1, ko

value: ABA


title: Human Tconv stim, Donor 1, SATB1 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_SATB1_ChIP_dsg

value: Blood

value: Tconv

value: SATB1 (Abcam, ab109122)


title: TNFalpha treated Human skeletal muscle cells from healthy subject#4

description: Library name: HM4_TNF_count

value: Human skeletal muscle cells

tag: treatment

value: TNFalpha


title: Human skeletal muscle cells from healthy subject#5

description: Library name: HM5_CTRL_count

value: Control


title: ire1DX, serum, rep 1

description:
Library name: Sample 16
ire1DX cells treated with fetal bovine serum

value: Diminished expression of IRE1

value: 10% fetal bovine serum

value: 4 hours


title: hsfb1_ABA, rep2

description:
Library name: sample 14
Column name in counts_ABA.txt: Hsfb-ABA2
counts_ABA.txt


title: Human Tconv stim, Donor 1, EGR2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_EGR2_ChIP_dsg

value: stim

value: Donor 1

value: DSG/formaldehyde

value: EGR2 (Abcam, ab43020)


title: Human skeletal muscle cells from healthy subject#4

description: Library name: HM4_CTRL_count


title: DAY286, serum, rep 3

description:
Library name: Sample 9
Control cells treated with fetal bovine serum

source_name: DAY286 (Davis et al., 2002)

value: DAY286 (Davis et al., 2002)

value: Yeast cells

value: WT


title: hsfb1_Mock, rep3

description:
Library name: sample 18
Column name in counts_ABA.txt: Hsfb-CK3
counts_ABA.txt

value: gemmalings

value: hsfb1, ko

value: Mock


title: Tak-1_ABA, rep1

description:
Library name: sample 19
Column name in counts_ABA.txt: Tak1-ABA1
counts_ABA.txt

value: Tak-1, wt

value: ABA


title: hsfb1_ABA, rep1

description:
Library name: sample 13
Column name in counts_ABA.txt: Hsfb-ABA1
counts_ABA.txt


title: TNFalpha treated Human skeletal muscle cells from healthy subject#3

description: Library name: HM3_TNF_count

value: Human skeletal muscle cells

value: TNFalpha


title: DAY286, serum, rep 2

description:
Library name: Sample 8
Control cells treated with fetal bovine serum


title: hsfa1_Mock, rep3

description:
Library name: sample 12
Column name in counts_ABA.txt: Hsfa-CK3
counts_ABA.txt

value: hsfa1, ko


title: ire1DX, untreated, rep 3

description:
Library name: Sample 12
ire1DX cells untreated

value: ire1DX (Woolford et al., 2016)

value: Diminished expression of IRE1

value: Untreated

value: 2 hours


title: Human skeletal muscle cells from healthy subject#3

description: Library name: HM3_CTRL_count

value: Control


title: hsfa1_Mock, rep2

description:
Library name: sample 11
Column name in counts_ABA.txt: Hsfa-CK2
counts_ABA.txt


title: DAY286, tunicamycin, rep 3

description:
Library name: Sample 6
Control cells treated with tunicamycin

value: 1.5 µg/mL tunicamycin


title: Human Tconv stim, Donor 1, YY1-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_YY1-abcam_ChIP_dsg

value: Blood

value: Tconv

value: stim

value: Donor 1

value: DSG/formaldehyde


title: COTC030 0701 tumor sample

city: Bethesda

first: Anjali

last: Garg

state: Maryland

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

description:
Library name: COTC030_0701_T
Column name in all_sample_raw_count.txt: COTC030_0701_T

data_processing:
The HiSeq Real Time Analysis software (RTA v.3.4.4) was used for processing raw data files.
The Illumina bcl2fastq2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
The trimmed reads were mapped to the CanFam4 reference genome (GSD_1.0 from NCBI) using STAR aligner (version 2.7.0f) with two-pass alignment option.
RSEM (version 1.3.1) was used for gene and transcript quantification based on the CanFam4 GTF file.
Library complexity was measured regarding unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
Assembly: Canis lupus familiaris
Supplementary files format and content: txt file include FPKM values for each sample

organism: Canis lupus familiaris

source_name: Untreated bone primary osteosarcoma

extract_protocol:
RNA for mRNAseq was isolated from canine frozen tumor tissue in RNAlater using Qiagen Allprep DNA/RNA Mini Kit (Cat#80204).
RNA libraries were pooled and sequenced on NovaSeq S1 using a 2x150 cycle kit.

value: Untreated bone primary osteosarcoma


title: DAY286, tunicamycin, rep 2

description:
Library name: Sample 5
Control cells treated with tunicamycin

value: DAY286 (Davis et al., 2002)

value: Yeast cells

value: WT


title: hsfa1_ABA, rep3

description:
Library name: sample 9
Column name in counts_ABA.txt: Hsfa-ABA3
counts_ABA.txt

value: gemmalings

value: ABA


title: COTC030 0505 tumor sample

description:
Library name: COTC030_0505_T
Column name in all_sample_raw_count.txt: COTC030_0505_T


title: Human Tconv stim, Donor 1, GATA3-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_GATA3-abcam_ChIP_dsg

value: GATA3 (Abcam, ab199428)


title: hsfa1_ABA, rep2

description:
Library name: sample 8
Column name in counts_ABA.txt: Hsfa-ABA2
counts_ABA.txt

value: hsfa1, ko


title: ire1DX, untreated, rep 1

description:
Library name: Sample 10
ire1DX cells untreated

value: ire1DX (Woolford et al., 2016)

value: Diminished expression of IRE1

value: Untreated


title: COTC030 0504 tumor sample

description:
Library name: COTC030_0504_T
Column name in all_sample_raw_count.txt: COTC030_0504_T


title: Human Tconv rest, Donor 1, H3K27ac ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_H3K27ac_ChIP_dsg

value: rest

value: H3K27ac (Active Motif, 39133)


title: COTC030 0503 tumor sample

description:
Library name: COTC030_0503_T
Column name in all_sample_raw_count.txt: COTC030_0503_T


title: Human Tconv stim, Donor 1, MBD2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_MBD2_ChIP_dsg

value: Blood

value: Tconv

value: MBD2 (Active Motif, 39547)


title: Human Tconv rest, Donor 1, SATB1 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_SATB1_ChIP_dsg

value: Donor 1

value: DSG/formaldehyde

value: SATB1 (Abcam, ab109122)


title: hsfa1_ABA, rep1

description:
Library name: sample 7
Column name in counts_ABA.txt: Hsfa-ABA1
counts_ABA.txt


title: Human Tconv rest, Donor 1, EGR2 ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_EGR2_ChIP_dsg

value: EGR2 (Abcam, ab43020)


title: COTC030 0203 tumor sample

description:
Library name: COTC030_0203_T
Column name in all_sample_raw_count.txt: COTC030_0203_T

value: Untreated bone primary osteosarcoma


title: DAY286, untreated, rep 2

description:
Library name: Sample 2
Control condition. DAY286 is the control strain and an arg+ura+his- derivative of the C. albicans strain BWP17 (isogenic to SC5314).

value: DAY286 (Davis et al., 2002)

value: Yeast cells

value: WT

value: 2 hours


title: Human Tconv stim, Donor 1, YY1-active-motif ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_YY1-active-motif_ChIP_dsg

value: stim

value: YY1 (Active Motif, 61779)


title: dko_Mock, rep3

description:
Library name: sample 6
Column name in counts_ABA.txt: Dko-CK3
counts_ABA.txt

value: gemmalings

value: hsfa1/hsfb1, ko

value: Mock


title: Human Tconv stim, Donor 1, CTCF ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_stim_CTCF_ChIP_dsg

value: Blood

value: CTCF

value: CTCF (Abcam, ab128873)


title: DAY286, serum, rep 1

description:
Library name: Sample 7
Control cells treated with fetal bovine serum

value: 10% fetal bovine serum

value: 4 hours


title: hsfa1_Mock, rep1

description:
Library name: sample 10
Column name in counts_ABA.txt: Hsfa-CK1
counts_ABA.txt

value: hsfa1, ko


title: dko_Mock, rep2

description:
Library name: sample 5
Column name in counts_ABA.txt: Dko-CK2
counts_ABA.txt


title: COTC030 0703 tumor sample

description:
Library name: COTC030_0703_T
Column name in all_sample_raw_count.txt: COTC030_0703_T


title: DAY286, untreated, rep 1

description:
Library name: Sample 1
Control condition. DAY286 is the control strain and an arg+ura+his- derivative of the C. albicans strain BWP17 (isogenic to SC5314).

value: Untreated


title: dko_Mock, rep1

description:
Library name: sample 4
Column name in counts_ABA.txt: Dko-CK1
counts_ABA.txt


title: COTC030 0202 tumor sample

description:
Library name: COTC030_0202_T
Column name in all_sample_raw_count.txt: COTC030_0202_T

value: Untreated bone primary osteosarcoma


title: Human Tconv rest, Donor 1, CTCF ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_CTCF_ChIP_dsg

value: Tconv

value: rest

value: Donor 1

value: DSG/formaldehyde


title: COTC030 1031 tumor sample

description:
Library name: COTC030_1031_T
Column name in all_sample_raw_count.txt: COTC030_1031_T


title: DAY286, tunicamycin, rep 1

description:
Library name: Sample 4
Control cells treated with tunicamycin

value: DAY286 (Davis et al., 2002)

value: Yeast cells

value: WT

value: 1.5 µg/mL tunicamycin

value: 2 hours


title: ClRyeCENH3

city: Seeland OT Gatersleben

first: Anne

last: Fiebig

address: Correnstraße 3

department: BIT

country: Germany

institute: IPK Gatersleben

description:
Library name: ClRyeCENH3
The original chromatin DNA was a mixture of chromatin isolated from flowers of Chamaelirium luteum and leaves of Secale cereale inbred line Lo7 and sonicated to 150-400 bp in length

data_processing:
ChIP-Seq Mapper (Galaxy version 1.1.1.4) was used to map the ChIP- and input reads on RepeatExplorer-derived contig sequences of repeat clusters.
The paired-end reads of ChIP- and input-seq were quality-filtered by Trimmmomatic (Galaxy Version 0.39) and the resulting reads were mapped to the C. luteum genome assembly using Bowtie2 (Galaxy Version 2.5.3) with default parameters.
The deeptools bamCompare function (Galaxy Version 3.5.4) was used to generate the normalized ChIP-seq signal track of the average of read counts in ChIP over input in a genome-wide 1 kb windows.
Assembly: GCA_964656255
Supplementary files format and content: bigwig

organism: Chamaelirium luteum

source_name: leaf, flower

extract_protocol:
Genomic DNA of C. luteum was extracted from leaf tissue using the DNeasy Plant Mini kit (Qiagen, Germany)
ChIPseq libraries were prepared by NEBNEXT® UltraTM II DNA Library Prep Kit for Illumina (New England Biolabs) and sequenced using NovaSeq 6000 system (Illumina) by Novogene (UK) in the paired-end run (2×150 bp).

treatment_protocol: 0.65 g of C. luteum flower and 1.0 g of Secale cereale (inbred line Lo7) leaf tissue were ground with liquid nitrogen and homogenized separately in 10 ml nuclei isolation buffer (1 M sucrose, 5 mM KCl, 5 mM MgCl2, 60 mM HEPES pH 8.0, 5 mM EDTA, 0.6% Triton X-100, 0.4 mM PMSF, 1 µM pepstatin A, cOmplete protease inhibitor cocktail (Roche)). Nuclei fixation was performed in 1% PFA/ nuclei isolation buffer at RT, 12 rpm for 10 min and terminated by adding glycine to a final concentration of 130 mM. The nuclei suspension was filtrated through Miracloth (Millipore) twice and a 50-µm CellTrics filter (Sysmex) once and centrifuged at 4°C, 3,000 ×g for 10 min. The nuclei pellet was resuspended in 1 ml extraction buffer (0.25 M sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 1 mM EDTA, 5 mM β-mercaptoethanol, 0.1 mM PMSF, 1 µM pepstatin A, cOmplete protease inhibitor cocktail), followed by centrifugation at 4°C, 12,000 ×g for 10 min. After removing the supernatant, nuclei were resuspended in 150 µl of nuclei lysis buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 0.1 mM PMSF, 1 µM pepstatin A, cOmplete protease inhibitor cocktail). Chromatins were sonicated for 14 cycles of 30 s ON, 30 s OFF at high power, in a Bioruptor (Diagenode), followed by an addition of 100 µl ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 1 mM EDTA, cOmplete protease inhibitor cocktail), and continued sonication to a total of 31 cycles under the same setting. The sonicated samples were diluted 10 times with ChIP dilution buffer, centrifuged at 4°C, 13,000 ×g for 5 min, and the supernatant of each samples were transferred to new tubes. To dilute the high proportion of the putative C. luteum centromeric repeat, sonicated chromatin of C. luteum and S. cereale was mixed in a 1:3 ratio. The mixed chromatins were incubated with the ClCENH3 antibody (10 mg/ml) to a final 1:500 dilution at 4°C by shaking at 14 rpm for 12 h. DynabeadsTM Protein A (Invitrogen) in ChIP dilution buffer, corresponding to 0.1× volume of the chromatin solution, was added to the antibody-prebound chromatins and incubated at 4°C by shaking at 14 rpm for 1.5 h. The collected beads were then washed twice in low salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20mM Tris-HCl pH 8.0), followed by three washes in high salt buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), and another two washes in TE buffer at 4°C by shaking at 14 rpm for 5 min. The bead-bound chromatin was purified by using iPure kit v2 (Diagenode) following the manual and quantified using QubitTM dsDNA HS Assay kit (Invitrogen).

value: leaf, flower


title: dko_ABA, rep3

description:
Library name: sample 3
Column name in counts_ABA.txt: Dko-ABA3
counts_ABA.txt

value: gemmalings

value: hsfa1/hsfb1, ko

value: ABA


title: Human Tconv rest, Donor 1, YY1-active-motif ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_YY1-active-motif_ChIP_dsg

value: Blood

value: YY1 (Active Motif, 61779)


title: COTC030 1028 tumor sample

description:
Library name: COTC030_1028_T
Column name in all_sample_raw_count.txt: COTC030_1028_T


title: DAY286, untreated, rep 3

description:
Library name: Sample 3
Control condition. DAY286 is the control strain and an arg+ura+his- derivative of the C. albicans strain BWP17 (isogenic to SC5314).

value: Untreated


title: C. luteum A112 replicate 2

description: Library name: A112_HH2

data_processing:
Sequence reads were adaptor-trimmed using fastp and aligned to the reference genome with BWA-MEM. SAMtools was used to remove duplicate and multi-mapping reads (-q 30), followed by peak calling (-q 0.01) with MACS. For visualization.
Assembly: GCA_964656255
Supplementary files format and content: BAM files containing uniquely mapped reads were converted to BigWig format using deepTools bamCoverage, with Reads Per Kilobase per Million mapped reads (RPKM) normalization.
Supplementary files format and content: narrowPeaks

source_name: leaf

extract_protocol:
Nuclei were isolated from fresh leaf samples of C. luteum, quality and quantity were controlled by flow cytometry, and approximately 75,000 nuclei were used for transposition reaction mix with Tagment DNA Enzyme (TDE1). The resulting transposition product was purified using MinElute PCR Purification Kit (QIAGEN) for library preparation.
Libraries were amplified with NEBNext® High-Fidelity 2x PCR Master Mix (NEB, M0541), followed by sequenced in the paired-end mode (2x 151 cycles) on an Illumina NovaSeq 6000.

value: leaf

value: Tagment DNA Enzyme (TDE1)


title: dko_ABA, rep2

description:
Library name: sample 2
Column name in counts_ABA.txt: Dko-ABA2
counts_ABA.txt


title: dko_ABA, rep1

description:
Library name: sample 1
Column name in counts_ABA.txt: Dko-ABA1
counts_ABA.txt


title: COTC030 1027 tumor sample

description:
Library name: COTC030_1027_T
Column name in all_sample_raw_count.txt: COTC030_1027_T

value: Untreated bone primary osteosarcoma


title: Human Tconv rest, Donor 1, YY1-abcam ChIP, DSG/formaldehyde fixation

description: Library name: Donor1_human_Tconv_rest_YY1-abcam_ChIP_dsg

value: Tconv

value: rest

value: Donor 1


title: C. luteum A112 replicate 1

description: Library name: A112_HH1