title: B cell_2

description:
Library name: Sample 2
RiboMeth-seq

value: Peripheral blood


title: R32_25_31

status: Public on Jun 25 2026

type: SRA

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

description: Library name: R32_25_31

library_source: transcriptomic

data_processing:
Alignment with STAR 2.7
Read counts with Feature count (SubRead 2.0.6)
Assembly: GRCm39
Supplementary files format and content: Microsoft Excel file with raw counts

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: C57BL/6J mice were transfected with HTVI of plasmids coding for NICD1 (10 µg/mouse), myr-AKT (10 µg/mouse), and the Sleeping Beauty transposase. C57BL/6J mice without HTVI injection were used as healthy controls (C).

extract_protocol:
Automated Maxwell system (Promega)
Illumina Stranded mRNA Prep Ligation kit

treatment_protocol: Mice were sacrificed at 2 and 3 weeks after HTVI. Healthy liver (C) and CCA tumors were excised and stored at -80ºC until the RNA extraction step.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: cell type

value: 2 weeks post-HTVI

tag: strain


title: PIIV-7 dpv

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

department: Molecular Microbiology and Immunology

country: USA

institute: The University of Texas at San Antonio

description: Library name: PIIV7

data_processing:
Raw reads were aligned to the mouse reference genome (GRCm38, Ensembl) using STAR, and sorted with SAMtools. Strand-specificity was verified using RSeQC v2.6.4 in conjunction with the mouse RSeQC reference file (GRCm38_mm10_Ensembl.bed.gz). Gene-level raw counts were normalized using HTSeq with 0.75 quartile normalization and log₂-transformed. Differential gene expression (DEG) between groups was calculated using GFold, and genes exhibiting ≥3-fold change were considered significant
Assembly: GRCm38, Ensembl
Supplementary files format and content: quartile normalization and log₂-transformed count data

source_name: Spleen

growth_protocol: Whole cell vaccines of NMI (PIV) and NMII (PIIV) were prepared by inactivating purified C. burnetii NMI and NMII with 1% formaldehyde

extract_protocol:
After 7 and 28 dpv, mice were euthanized by CO2 exposure followed by cervical dislocation. Spleens were homogenized through a 70 µm cell strainer, red blood cells were lysed using ACK buffer, and cells were centrifuged at 400 × g for 10 minutes. Viable cells were counted using a hemocytometer and Trypan blue, with >98% viability for all assays. Immediately after cell separation, 5 million cells of splenocytes from each group were pooled together and total RNA was isolated using the RNeasy Mini Kit (Qiagen). Contaminating DNA was removed with the TURBO DNA-free Kit (Ambion), and RNA samples were processed for Illumina sequencing.
The integrity of isolated total RNA was assessed by capillary electrophoresis fragment analysis (University of Missouri DNA Core Laboratory), and both the 28S/18S rRNA ratio and RNA integrity number (RIN) were calculated. All samples exhibited RIN scores above 9.5 and were subsequently used for library preparation. Strand-specific RNA-seq libraries were generated using the Illumina TruSeq HT Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. Libraries were normalized, pooled, and sequenced on an Illumina HiSeq 2000 using a 100-nucleotide paired-end protocol.

treatment_protocol: Mice were divided into four groups (PBS, Adjuvant, PIV, PIIV), each with four biological replicates. Vaccination was administered subcutaneously: mice were restrained by scruff, and 10 µg of PIV or PIIV in 50 µL PBS plus 50 µL aluminum hydroxide gel (Alum) adjuvant (Invivogen) was injected into the scruff skin to a depth of 0.5 cm using a sterile 25G needle. The adjuvant group received 50 µL PBS with 50 µL adjuvant, and the PBS group received 100 µL PBS.

value: Spleen

value: Splenocytes

tag: treatment

value: PIIV-vaccinated

tag: time

value: 7 dpv


title: B cell_1

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Library name: Sample 1
RiboMeth-seq

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: rDNA reference sequence from Krogh et al, NAR 2016 (find reference in the paper)
Supplementary files format and content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Tissue and tumor samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: B cell

value: adult

value: normal


title: PIV-7 dpv

description: Library name: PIV7

value: PIV-vaccinated


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, G05

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: CH10_T4_D1_G05

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: liver

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: liver

tag: cell line

value: epithelial cell

value: hepatocellular carcinoma

value: test

tag: batch


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, E08

description: Library name: CH10_T4_D1_E08


title: CHIP057, Input, Triptolide, rep1

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description:
Library name: CHIP057
RAD21_RAD21AID_Trip_FE.100bp.bw
RAD21_RAD21AID_Trip_peaks.narrowPeak

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

molecule: genomic DNA

growth_protocol: Human skin non-treatment control (NTC) fibroblasts and fibroblasts from a Freidrich's Ataxia patient (FRDA) fibroblast cells were cultured in DMEM (Gibco #11965084) supplemented with 10% fetal bovine serum (Cytiva SH30910.03), 1% penicillin/streptomycin (Invitrogen #15140122), and 1% non-essential amino acids (Invitrogen # 11140050) at 37C with 20% O2 and 5% CO2. RAD21-mAID-HCT116 cells were cultured in McCoys (Invitrogen #16600082) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin at 37C with 20% O2 and 5% CO2.

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms

treatment_protocol: Human fibroblasts were grown in complete media (DMEM, 10% FBS, 1% penicillin/streptomycin) and plated at 40% confluency. The next day, dCas9-KRAB-FXN guide or dCas9-KRAB-Scramble guide was introduced into NTC fibroblasts for 2d followed by 2d selection in blasticidin. RAD21-mAID-HCT116 cells were propagated in standard medium (McCoy’s with 10% FBS and 1% penicillin/streptomycin) and plated in 10cm dishes at 40% density and grown overnight. The following morning, a time course was started for three conditions (DMSO control, triptolide-only, and auxin + triptolide). At time 0, DMSO control and triptolide-only cells were incubated in fresh media alone; auxin + triptolide cells were incubated in fresh media + 1μM auxin (5-Ph-IAA, Tocris Bioscience). After 1 hour, 200nM final triptolide (Selleckchem) was added to triptolide-only and auxin + triptolide cells. 12 hours post-triptolide, all cells were harvested for ChIP (see “ChIP and library preparation for sequencing”). DMSO was used as a vehicle control.

value: Human colon cancer

tag: chip antibody

value: Input

value: Triptolide


title: Adjuvant Control-7 dpv

description: Library name: A7

value: Adjuvant-treated


title: E17.5_liver_MO

city: Pullman

first: Min

last: Du

state: WA

address: 1815 Ferdinand's Ln

department: Animal Science

institute: Washington State University

description:
Library name: Sample 6
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and sample aggregation were performed using Cell Ranger software (v8.0.1) from 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Mouse mm10
Supplementary files format and content: Processed data files include gene-cell expression matrices generated by Cell Ranger, provided in Market Exchange Format (.mtx.gz) with accompanying gene annotation (features.tsv.gz) and barcode (barcodes.tsv.gz) files.

growth_protocol: The C57/BL6 female mice were randomly separated into two groups which were fed either a control diet (10% energy from fat) or a high-fat diet (45% energy from fat), respectively. When the difference in body weight between the two groups exceeded 20%, female mice were mated with males fed a regular diet

extract_protocol:
Pregnant mice were euthanized by CO₂ asphyxiation followed by cervical dislocation. Embryonic tissues, including placenta, yolk sac, and fetal liver at embryonic day 13.5 (E13.5), and fetal liver at E17.5, were collected. For each tissue type, nine embryos per treatment group—control (CT) and maternal obesity (MO)—were harvested. Tissues from each group were pooled and placed into 50 mL conical tubes containing DMEM supplemented with 4% fetal bovine serum (FBS), and kept on ice to preserve cell viability.  Tissues were minced into approximately 1 mm fragments using fine scissors under sterile conditions in a biosafety cabinet. The tissue fragments were then digested in 10 volumes of DMEM containing 2.5% FBS, 100 μg/mL Collagenase Type IV, 50 μg/mL DNase I, and 100 μg/mL heparin. To preserve erythroid cells, red blood cell lysis was not performed. Digestion was carried out at 37 °C in a humidified incubator with 5% CO₂ for 30 minutes.  The enzymatic reaction was stopped by adding an equal volume of DMEM containing 2.5% FBS. The cell suspension was centrifuged at 800 rpm for 5 minutes at room temperature. After discarding the supernatant, the cell pellet was resuspended in PBS supplemented with 0.4% FBS and filtered through a 40 μm cell strainer to remove debris and aggregates.  Cell concentration and viability were assessed using trypan blue exclusion and a hemocytometer. Only samples with viability greater than 80% were used for downstream single-cell RNA sequencing. Final cell suspensions were adjusted to a concentration of 1000 cells/μL.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium GEM-X Single Cell 3’ v4 Reagent Kit, following the manufacturer's standard protocol. Libraries were sequenced on an Illumina NextSeq 2000 platform with paired-end reads.

treatment_protocol: High-fat diet feeding

value: Liver

value: MO


title: R32_25_30

description: Library name: R32_25_30

value: WT

value: 2 weeks post-HTVI


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, D11

description: Library name: CH10_T4_D1_D11


title: CHIP056, RAD21, Triptolide, rep2

description:
Library name: CHIP056
RAD21_RAD21AID_Trip_FE.100bp.bw
RAD21_RAD21AID_Trip_peaks.narrowPeak

value: RAD21 (Abcam, #ab992)


title: HepG2, 3-hydroxybenzophenone, CH10, 6h, A03

description: Library name: CH10_T4_D1_A03


title: CHIP055, RAD21, Triptolide, rep1

description:
Library name: CHIP055
RAD21_RAD21AID_Trip_FE.100bp.bw
RAD21_RAD21AID_Trip_peaks.narrowPeak


title: E17.5_liver_CT

description:
Library name: Sample 5
10x Genomics

value: CT


title: Naïve Control-2

description: Library name: C2

value: Spleen

value: Splenocytes

value: PBS-treated

value: 28 dpv


title: E13.5_liver_MO

description:
Library name: Sample 4
10x Genomics


title: Naïve Control-1

description: Library name: C1

value: 7 dpv


title: HepG2, Avobenzone, CH10, 6h, F07

description: Library name: CH10_T1_D3_F07

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: CHIP054, Input, Vehicle, rep2

description:
Library name: CHIP054
RAD21_RAD21AID_Ctrl_FE.100bp.bw
RAD21_RAD21AID_Ctrl_peaks.narrowPeak

value: Human colon cancer

value: Input

value: Vehicle


title: HepG2, Avobenzone, CH10, 6h, G04

description: Library name: CH10_T1_D3_G04

value: test


title: E13.5_liver_CT

description:
Library name: Sample 3
10x Genomics

value: Liver


title: pir2-1 pir1∆ tgs1∆_Biorep2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: pir2-1 pir1∆ tgs1∆_Biorep2
pir2-1 pir1∆ tgs1∆_18C

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

organism: Schizosaccharomyces pombe

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction

value: Msmt0 leu1-32 ade6-210 his2 ura4::Tf2-1CI pir2-1-FLAG::KanMX tgs1D::NatMX pir1D::KanMX

tag: growth

value: Growth in YEA 18°C


title: CHIP053, Input, Vehicle, rep1

description:
Library name: CHIP053
RAD21_RAD21AID_Ctrl_FE.100bp.bw
RAD21_RAD21AID_Ctrl_peaks.narrowPeak


title: E13.5_placenta_yolk sac_MO

description:
Library name: Sample 2
10x Genomics

source_name: Placenta, yolk sac

value: Placenta, yolk sac

value: MO


title: HepG2, Avobenzone, CH10, 6h, E10

description: Library name: CH10_T1_D3_E10


title: tgs1∆ ago1∆ pir1∆_Biorep2

description:
Library name: tgs1∆ ago1∆ pir1∆_Biorep2
tgs1∆ ago1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-210/216 ura4DS/e/ura4D18 ago1D::KanMX tgs1D::NatMX pir1D::KanMX otr1R(Sph1)::ura4+


title: CHIP052, RAD21, Vehicle, rep2

description:
Library name: CHIP052
RAD21_RAD21AID_Ctrl_FE.100bp.bw
RAD21_RAD21AID_Ctrl_peaks.narrowPeak

value: RAD21 (Abcam, #ab992)


title: E13.5_placenta_yolk sac_CT

description:
Library name: Sample 1
10x Genomics

value: CT


title: pac1A342T pir1∆_Biorep3

description:
Library name: pac1A342T pir1∆_Biorep3
pac1A342Tpir1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI pac1A342T pir1D::KanMX


title: HepG2, Avobenzone, CH10, 6h, A02

description: Library name: CH10_T1_D3_A02


title: COLXIV_WT_ZT_0 biol rep 4

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

description: Library name: W_Z_5

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: GRCm38.102
Supplementary files format and content: Count matrix in excel format

molecule: polyA RNA

source_name: epidermis

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the NZY Total RNA Isolation Kit (NZY Tech)
Libraries were prepared using the TruSeq stranded mRNA Library Prep (20020595, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing. Briefly, 500 ng of total RNA were used for polyA‐mRNA selection using Oligo‐dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, which was performed using reverse transcriptase (SuperScript II; 18064‐014, Invitrogen). Then, second strand cDNA was synthesised, incorporating dUTP in place of dTTP and generating blunt‐ended ds cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments (A‐tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (A63882, Beckman Coulter). Final libraries were analysed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (5067‐1504 or DNF‐473, Agilent) to estimate the quantity and validate the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche).

treatment_protocol: Epidermal cells suspensions were obtained from the skin of 47 weeks old ColXIV KO and WT mice that were sacrificed at different times of the day (ZT0, 4, 8, 12, 16, 20).

value: epidermis

value: ColXIV WT


title: CHIP051, RAD21, Vehicle, rep1

description:
Library name: CHIP051
RAD21_RAD21AID_Ctrl_FE.100bp.bw
RAD21_RAD21AID_Ctrl_peaks.narrowPeak


title: pac1A342T_Biorep3

description:
Library name: pac1A342T_Biorep3
pac1A342T_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI pac1A342T


title: HepG2, Avobenzone, CH10, 6h, H01

description: Library name: CH10_T1_D2_H01

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: CHIP050, Input, Triptolide + Auxin, rep2

description:
Library name: CHIP050
LB1_HCT_AuxTrip.bw
LAD_HCT_AuxTrip.bed

value: Human colon cancer

value: Input

value: Triptolide + Auxin


title: CHIP049, Input, Triptolide + Auxin, rep1

description:
Library name: CHIP049
LB1_HCT_AuxTrip.bw
LAD_HCT_AuxTrip.bed


title: pac1A342T pir1∆_Biorep2

description:
Library name: pac1A342T pir1∆_Biorep2
pac1A342Tpir1∆_18C


title: COLXIV_WT_ZT_0 biol rep 3

description: Library name: W_Z_4


title: HepG2, Avobenzone, CH10, 6h, F04

description: Library name: CH10_T1_D2_F04

value: test


title: COLXIV_WT_ZT_0 biol rep 2

description: Library name: W_Z_3


title: HepG2, Avobenzone, CH10, 6h, E07

description: Library name: CH10_T1_D2_E07


title: pac1A342T_Biorep2

description:
Library name: pac1A342T_Biorep2
pac1A342T_18C

value: Growth in YEA 18°C


title: CHIP048, LMNB1, Triptolide + Auxin, rep2

description:
Library name: CHIP048
LB1_HCT_AuxTrip.bw
LAD_HCT_AuxTrip.bed

value: LMNB1 (abcam, #ab16048)


title: pir1∆_Biorep8

description:
Library name: pir1∆_Biorep8
pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(Sph1)::ura4+


title: HepG2, Avobenzone, CH10, 6h, D10

description: Library name: CH10_T1_D2_D10


title: COLXIV_WT_ZT_0 biol rep 1

description: Library name: W_Z_2


title: WT_Biorep7

description:
Library name: WT_Biorep7
WT_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI


title: HepG2, Avobenzone, CH10, 6h, G01

description: Library name: CH10_T1_D1_G01


title: CHIP046, Input, Triptolide, rep3

description:
Library name: CHIP046
LB1_HCT_Trip.bw
LAD_HCT_Trip.bed

value: Triptolide


title: CHIP047, LMNB1, Triptolide + Auxin, rep1

description:
Library name: CHIP047
LB1_HCT_AuxTrip.bw
LAD_HCT_AuxTrip.bed


title: COLXIV_WT_ZT_20 biol rep 4

description: Library name: W_V_4


title: COLXIV_WT_ZT_20 biol rep 3

description: Library name: W_V_3


title: COLXIV_WT_ZT_20 biol rep 2

description: Library name: W_V_2


title: HepG2, Avobenzone, CH10, 6h, E04

description: Library name: CH10_T1_D1_E04


title: pac1A342T_36C

description: Library name: RNAseq_5d

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

growth_protocol: For RNA Seq, cells were grown in YEA at 30°C, 18°C or  36°C for 5 hours for temperature-sensitive strains  as mentioned

value: Yeast Whole Cells

value: Growth in YEA at 26°C then shifted to  36°C for 5hrs


title: HepG2, Avobenzone, CH10, 6h, D07

description: Library name: CH10_T1_D1_D07


title: WT_Biorep6

description:
Library name: WT_Biorep6
WT_18C


title: CHIP045, Input, Triptolide, rep2

description:
Library name: CHIP045
LB1_HCT_Trip.bw
LAD_HCT_Trip.bed


title: COLXIV_WT_ZT_20 biol rep 1

description: Library name: W_V_1

value: epidermis


title: CHIP044, Input, Triptolide, rep1

description:
Library name: CHIP044
LB1_HCT_Trip.bw
RAD21_RAD21AID_Trip_FE.100bp.bw
LAD_HCT_Trip.bed
RAD21_RAD21AID_Trip_peaks.narrowPeak


title: HepG2, Avobenzone, CH10, 6h, B10

description: Library name: CH10_T1_D1_B10


title: CHIP043, LMNB1, Triptolide, rep3

description:
Library name: CHIP043
LB1_HCT_Trip.bw
LAD_HCT_Trip.bed


title: WT_36C_c

description: Library name: RNAseq_4d


title: COLXIV_WT_ZT_8 biol rep 4

description: Library name: W_8_6

value: ColXIV WT


title: HepG2, DMSO, CH10, 6h, G08

description: Library name: CH10_DMSO_G08

value: vehicle


title: pac1A342T pir1∆

description: Library name: RNAseq_3d

source_name: pac1A342T pir1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI pac1A342T pir1D::KanMX


title: COLXIV_WT_ZT_8 biol rep 3

description: Library name: W_8_4


title: CHIP042, LMNB1, Triptolide, rep2

description:
Library name: CHIP042
LB1_HCT_Trip.bw
LAD_HCT_Trip.bed


title: pac1A342T

description: Library name: RNAseq_2d

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI pac1A342T


title: HepG2, DMSO, CH10, 6h, F05

description: Library name: CH10_DMSO_F05

value: liver

value: epithelial cell

value: hepatocellular carcinoma


title: CHIP041, LMNB1, Triptolide, rep1

description:
Library name: CHIP041
LB1_HCT_Trip.bw
LAD_HCT_Trip.bed

value: Human colon cancer


title: COLXIV_WT_ZT_8 biol rep 2

description: Library name: W_8_2


title: HepG2, DMSO, CH10, 6h, D02

description: Library name: CH10_DMSO_D02


title: COLXIV_WT_ZT_8 biol rep 1

description: Library name: W_8_1


title: tgs1∆ mmi1∆

description:
Library name: RNAseq_10b
tgs1∆ mmi1∆_18C

source_name: Yeast Whole Cells

value: Msmt0 leu1-32 ade6-210 his2 ura4-D18 tgs1D::KanMX mei4DC<NAT mmi1D::HYG


title: pir1∆_Biorep7

description: Library name: RNAseq_1d

value: Growth in YEA 18°C


title: HepG2, DMSO, CH10, 6h, C10

description: Library name: CH10_DMSO_C10


title: CHIP039, Input, Vehicle, rep2

description:
Library name: CHIP039
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed

value: Input

value: Vehicle


title: mmi1∆

description:
Library name: RNAseq_9b
mmi1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4-D18 mei4DC<NAT mmi1D::HYG


title: CHIP040, Input, Vehicle, rep3

description:
Library name: CHIP040
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed


title: HepG2, DMSO, CH10, 6h, B12

description: Library name: CH10_DMSO_B12


title: COLXIV_WT_ZT_4 biol rep 4

description: Library name: W_4_4


title: CHIP038, Input, Vehicle, rep1

description:
Library name: CHIP038
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed


title: A549, Myricetin, CA11, 6h, G04

description: Library name: CA11_T8_D3_G04

source_name: lung

value: lung

value: Adenocarcinoma

value: test


title: COLXIV_WT_ZT_4 biol rep 3

description: Library name: W_4_3

value: epidermis


title: tgs1∆ ago1∆ pir1∆

description:
Library name: RNAseq_8b
ago1∆ tgs1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-210/216 ura4DS/e/ura4D18 ago1D::KanMX tgs1D::NatMX pir1D::KanMX otr1R(Sph1)::ura4+

value: Yeast Whole Cells


title: CHIP037, LMNB1, Vehicle, rep3

description:
Library name: CHIP037
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed

value: LMNB1 (abcam, #ab16048)


title: COLXIV_WT_ZT_4 biol rep 2

description: Library name: W_4_2

value: ColXIV WT


title: ago1∆ pir1∆_Biorep3

description:
Library name: RNAseq_7b
ago1∆ pir1∆_18C

value: Msmt0  leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX ago1D::KanMX otr1R(SphI)::ura4+


title: A549, Myricetin, CA11, 6h, F07

description: Library name: CA11_T8_D3_F07

value: epithelial cell


title: CHIP036, LMNB1, Vehicle, rep2

description:
Library name: CHIP036
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed


title: COLXIV_WT_ZT_4 biol rep 1

description: Library name: W_4_1


title: CHIP035, LMNB1, Vehicle, rep1

description:
Library name: CHIP035
LB1_HCT_Ctrl.bw
LAD_HCT_Ctrl.bed


title: A549, Myricetin, CA11, 6h, E10

description: Library name: CA11_T8_D3_E10


title: COLXIV_WT_ZT_16 biol rep 4

description: Library name: W_16_4


title: A549, Myricetin, CA11, 6h, A02

description: Library name: CA11_T8_D3_A02


title: CHIP034, Input, CRISPRi_Scr, rep2

description:
Library name: CHIP034
RAD21_SCR_FE.100bp.bw
RAD21_SCR_peaks.narrowPeak

source_name: WT fibroblast

value: WT fibroblast

value: Human fibroblast


title: pir2-1 pir1∆ tgs1∆

description:
Library name: RNAseq_5b
pir2-1 tgs1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4::Tf2-1CI pir2-1-FLAG::KanMX tgs1D::NatMX pir1D::KanMX


title: COLXIV_WT_ZT_16 biol rep 3

description: Library name: W_16_3


title: pir2-1 pir1∆_BioRep3

description:
Library name: RNAseq_4b
pir2-1 pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4::tf2-1CI pir2-1-flag::kanMX6 pir1D::KanMX

value: Growth in YEA 18°C


title: CHIP033, Input, CRISPRi_Scr, rep1

description:
Library name: CHIP033
RAD21_SCR_FE.100bp.bw
RAD21_SCR_peaks.narrowPeak

value: Input


title: A549, Myricetin, CA11, 6h, H01

description: Library name: CA11_T8_D2_H01


title: COLXIV_WT_ZT_16 biol rep 2

description: Library name: W_16_2


title: tgs1∆pir1∆_Biorep3

description:
Library name: RNAseq_3b
tgs1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-216 his2 pir1D::KanMX6 tgs1D::KanMX otr1R(SphI)::ura4+


title: A549, Myricetin, CA11, 6h, F04

description: Library name: CA11_T8_D2_F04

value: lung


title: CHIP032, RAD21, CRISPRi_Scr, rep2

description:
Library name: CHIP032
RAD21_SCR_FE.100bp.bw
RAD21_SCR_peaks.narrowPeak

value: RAD21 (Abcam, #ab992)


title: COLXIV_WT_ZT_16 biol rep 1

description: Library name: W_16_1


title: pir1∆_Biorep5

description:
Library name: RNAseq_2b
pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(Sph1)::ura4+


title: A549, Myricetin, CA11, 6h, E07

description: Library name: CA11_T8_D2_E07

value: Adenocarcinoma

value: test


title: COLXIV_WT_ZT_12 biol rep 4

description: Library name: W_12_6

value: epidermis


title: WT_BioRep5

description:
Library name: RNAseq_1b
WT_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI

value: Yeast Whole Cells


title: COLXIV_WT_ZT_12 biol rep 3

description: Library name: W_12_4

value: ColXIV WT


title: A549, Myricetin, CA11, 6h, G01

description: Library name: CA11_T8_D1_G01

value: epithelial cell


title: COLXIV_WT_ZT_12 biol rep 2

description: Library name: W_12_3


title: A549, Myricetin, CA11, 6h, E04

description: Library name: CA11_T8_D1_E04


title: ccr4∆_BioRep3

description:
Library name: 251002n
ccr4∆_18C

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT); HG19 human genome reference; T2T.CHM13v2.0 human telomere-to-telomere human reference.
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent). Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction.

value: Msmt0 leu1-32 ade6-216/210 his2 ura4::tf2-1CI ccr4D::kan


title: A549, Myricetin, CA11, 6h, D07

description: Library name: CA11_T8_D1_D07


title: CHIP028, LMNB1, CRISPRi_Scr, rep2

description:
Library name: CHIP028
LB1_SCR.CPM_1kb.woTNR.e120.S10Kb.bw
LB1_SCR.b5s15_5_wBlklst_domains.final.bed

value: WT fibroblast

value: Human fibroblast

value: LMNB1 (abcam, #ab16048)


title: COLXIV_WT_ZT_12 biol rep 1

description: Library name: W_12_2


title: CHIP027, LMNB1, CRISPRi_Scr, rep1

description:
Library name: CHIP027
LB1_SCR.CPM_1kb.woTNR.e120.S10Kb.bw
LB1_SCR.b5s15_5_wBlklst_domains.final.bed


title: COLXIV_KO_ZT_0 biol rep 4

description: Library name: K_Z_5

value: ColXIV KO


title: pir2-1 pir1∆_BioRep2

description:
Library name: 251012m
pir2-1 pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4::tf2-1CI pir2-1-flag::kanMX6 pir1D::KanMX

value: Growth in YEA 18°C


title: pir2-1_BioRep2

description:
Library name: 251012l
pir2-1_18C

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI pir2-1-FLAG<<KanMX


title: A549, Myricetin, CA11, 6h, B10

description: Library name: CA11_T8_D1_B10

value: lung


title: gene expression

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

country: Italy

institute: University of Torino

data_processing:
cellranger multi
cellrancer aggr with aggr_all_config.csv configuration file
Assembly: custom genome with Fucciplex gene
Supplementary files format and content: H5
Supplementary files format and content: aggr_all_config.csv

source_name: Fucciplex

extract_protocol:
10x genomics 3' v3.1 and cell multiplexing
10x genomics 3' v3.1 and cell multiplexing with feature barcode

value: Fucciplex

value: hPSC differentiated


title: ago1∆ tgs1∆_BioRep2

description:
Library name: 251012k
ago1∆ tgs1∆_18C

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI ago1D::kan  tgs1D::Nat


title: CALIPERS expression

data_processing:
cellranger multi
cellrancer aggr with aggr_all_config.csv configuration file
Assembly: custom genome with CALIPERS gene
Supplementary files format and content: H5
Supplementary files format and content: aggr_all_config.csv

source_name: CALIPERS

value: CALIPERS


title: COLXIV_KO_ZT_0 biol rep 2

description: Library name: K_Z_3

value: epidermis


title: A549, DMSO, CA11, 6h, F05

description: Library name: CA11_DMSO_F05

value: Adenocarcinoma

value: vehicle


title: ago1∆ pir1∆_Biorep2

description:
Library name: 251002j
ago1∆ pir1∆_18C

value: Msmt0  leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX ago1D::KanMX otr1R(SphI)::ura4+


title: cell multiplexing oligos

library_source: other

data_processing:
cellranger multi
cellrancer aggr with aggr_all_config.csv configuration file
Assembly: custom genome with Fucciplex gene
Supplementary files format and content: H5
Supplementary files format and content: aggr_all_config.csv
Library strategy: cell multiplexing oligos

molecule: other


title: COLXIV_KO_ZT_0 biol rep 1

description: Library name: K_Z_2


title: ago1∆_BioRep2

description:
Library name: 251012i
ago1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4DS/E ago1D::KanMX otr1R(SphI)::ura4+


title: tgs1∆ pir1∆_BioRep2

description:
Library name: 251012h
tgs1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-216 his2 pir1D::KanMX6 tgs1D::KanMX otr1R(SphI)::ura4+


title: A549, DMSO, CA11, 6h, C10

description: Library name: CA11_DMSO_C10

value: epithelial cell


title: COLXIV_KO_ZT_20 biol rep 4

description: Library name: K_V_4


title: CHIP026, Input, FRDA, rep2

description:
RAD21_PT_FE.100bp.bw
RAD21_PT_peaks.narrowPeak

source_name: FRDA fibroblast

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms
Libraries were quantified and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run.

value: FRDA fibroblast

value: Input

value: FRDA


title: A549, DMSO, CA11, 6h, B12

description: Library name: CA11_DMSO_B12


title: COLXIV_KO_ZT_20 biol rep 3

description: Library name: K_V_3

value: ColXIV KO


title: Adrenaline_P04_D02

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P04-20230908-012_S204

data_processing:
Sequence reads were aligned using STAR (version 2.7.9a)
Counts matrix was generated using RSEM (version 1.3.1)
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: RSEM_Counts_Cardiopedia-Ligand.xlsx file includes raw counts for each sample

extract_protocol:
Total RNA was isolated using the NuceloMag RNA kit (Macherey-Nagel) on the EpMotion 5075t
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (polyA RNA selection) on the EpMotion 5075t

treatment_protocol: hCO were stimulated with a library of 90 ligands (n = 2-5 hCO per ligand in final RNA-seq dataset after passing all quality control). After 24 hours, media was aspirated and hCO were washed with ice cold PBS- and lysed for RNAseq.


title: CHIP025, Input, FRDA, rep1

description:
RAD21_PT_FE.100bp.bw
H3K9me2_PT_1_AK132_AK134.inpLg2_1kb.woTNR.e100.S10Kb.bw
RAD21_PT_peaks.narrowPeak


title: COLXIV_KO_ZT_20 biol rep 2

description: Library name: K_V_2


title: cwf10-1_BioRep2

description:
Library name: 251012f
cwf10-1_36C

value: Growth in YEA at 26°C then shifted to  36°C for 5hrs


title: A549, Kaempferol, CA10, 6h, H12

description: Library name: CA10_T7_D3_H12

value: lung

value: test


title: CHIP024, RAD21, FRDA, rep2

value: RAD21 (Abcam, #ab992)


title: eas1∆ mug174-1_BioRep2

description:
Library name: 251012e
eas1∆ mug174-1_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI eas1D::NatMX mug174-1-3HA::KanMX

value: Growth in YEA 18°C


title: A549, Kaempferol, CA10, 6h, D04

description: Library name: CA10_T7_D3_D04


title: COLXIV_KO_ZT_20 biol rep 1

description: Library name: K_V_1

value: epidermis


title: CHIP023, RAD21, FRDA, rep1


title: B7T

city: 广东省

first: LI

last: ShuJun

address: 广州市番禺区新造镇新造路1号

department: 附属第五医院

country: China

institute: 广州医科大学

data_processing:
The sequencing data is subjected to filtration using SOAPnuke (V2.1.0). This involves purging reads that contain adapter sequences, reads with more than 20% low-quality bases, and reads with more than 5% unknown bases.
Ultimately obtaining clean data and storing them in FASTQ format. The subsequent analysis and data mining were performed
Assembly: GCF_0000014053.9_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor tissues

extract_protocol:
Extract tissue total RNA using miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen). The concentration and RNA integrity were then determined by using Equalbit RNA BR Assay Kit (vazyme) and Qubit Fluorometer (Invitrogen). The samples that meet quality control requirements can be used for library preparation.
Sequencing libraries were generated using MGIEasy RNA Library preparation kit (MGI) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Eventually, circularized DNA were sequenced with MGISEQ-2000 system.

value: tumor tissues


title: COLXIV_KO_ZT_8 biol rep 4

description: Library name: K_8_5


title: mug174-1_BioRep2

description:
Library name: 251012d
mug174-1_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI mug174-1-3HA::KanMX


title: A549, Kaempferol, CA10, 6h, C07

description: Library name: CA10_T7_D3_C07

value: Adenocarcinoma


title: CHIP018, RAD21, NTC, rep2

description:
RAD21_WT_FE.100bp.bw
RAD21_WT_peaks.narrowPeak

value: WT fibroblast

value: Human fibroblast

value: NTC


title: A549, Myricetin, CA11, 6h, D10

description: Library name: CA11_T8_D2_D10

value: epithelial cell


title: ccr4∆ pir1∆_BioRep2

description:
Library name: 251002o
ccr4∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-216 ura4D18 or ura4::tf2-1CI ccr4D::kanMX4  tgs1D::KanMX


title: COLXIV_KO_ZT_8 biol rep 3

description: Library name: K_8_4


title: A549, Kaempferol, CA10, 6h, A10

description: Library name: CA10_T7_D3_A10


title: CHIP017, RAD21, NTC, rep1


title: COLXIV_KO_ZT_8 biol rep 2

description: Library name: K_8_3


title: CHIP004, Input, NTC, rep2

description:
LB1_WT.inpLg2_1kb.woTNR.e100.S10Kb.bw
RAD21_WT_FE.100bp.bw
LB1_WT.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed
RAD21_WT_peaks.narrowPeak

value: Input


title: A549, Kaempferol, CA10, 6h, H09

description: Library name: CA10_T7_D2_H09


title: A549, Kaempferol, CA10, 6h, G12

description: Library name: CA10_T7_D2_G12


title: CHIP003, Input, NTC, rep1


title: WT_BioRep4

description:
Library name: 251012a
WT_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI


title: COLXIV_KO_ZT_4 biol rep 4

description: Library name: K_4_4

value: ColXIV KO


title: CHIP030, Input, CRISPRi_Scr, rep2

description:
Library name: CHIP030
LB1_SCR.CPM_1kb.woTNR.e120.S10Kb.bw
LB1_SCR.b5s15_5_wBlklst_domains.final.bed


title: COLXIV_KO_ZT_8 biol rep 1

description: Library name: K_8_2


title: GFP-RIP_untagged_pir1∆tgs1∆

description:
Library name: RIPseq_30
untagged control_pir1∆tgs1∆

data_processing:
Normalization done to reads per million for each sample. Normalized samples were subtracted from untagged controls
Samples 1, 7, 12 , 23, 24 uses sample 2 as untagged; Samples 3, 25 and 26 uses sample 5 as untagged; Sample 4 uses sample 6 as untagged; Sample 8 uses sample 9 as untagged; Sample 10 uses sample 11 as untagged; Sample 13 uses sample 14 as untagged; Sample 15, 17 and 20 uses sample 16 as untagged; Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 27 uses sample 29 as untagged; Sample 28 uses sample 30 as untagged; Sample 31 uses sample 33 as untagged; Sample 32 uses sample 34 as untagged
Sample 18 uses sample 19 as untagged; Sample 21 uses sample 22 as untagged; Sample 29 uses sample 31 as untagged; Sample 30 uses sample 32 as untagged
Sample 33 uses sample 35 as untagged; Sample 34 uses sample 36 as untagged

Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM) (untagged controls) or RPM-normalized counts for the IP minus RPM counts of an untagged control (IPs).
Supplementary files format and content: Figure 3a,3b: Samples 3,4 for Tf2-3, Samples 7,8,9 for other genes
Supplementary files format and content: Figure 4j: Samples 23,24
Supplementary files format and content: Figure 5e: Samples 17,18
Supplementary files format and content: Figure 7a: Samples 27,28

growth_protocol: Cells were grown on YEA rich media at 30°C  for all cases except for experiments performed to check meiotic targets. For meiotic targets, cells grown to 0.1 OD600 at 30°C in YEA was shifted to 18°C for 24 hrs

extract_protocol:
Immunoprecipitation of epitope tagged protein, Proteinase treatment to remove protein; DNAse treatment to remove DNA and acid phenol-chloroform extraction to isolate associated RNA followed by ethanol precipitation
For RIP Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
RNA coimmunoprecipitated with epitope tagged proteins were used for library preparation.

value: Msmt0 leu1-32 ade6-216 his2 ura4DS/E pir1D::KanMX tgs1D::KanMX otr1R(Sph1)::ura4+

value: Yeast Whole Cells

tag: rip antibody

value: Anti-GFP Ab290

value: Growth in YEA 30°C, shifted to 18°C for 24 hrs


title: Y12_1

description: Library name: Y12_1

extract_protocol:
RNA was extracted from epidermal cell pellets frozen in Trizol using the RNeasy Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Kit (RS-122-2201/2202, Illumina) according to the manufacturer's protocol, using 150 to 300 ng of total RNA; ribosomal RNA depletion, RNA was then fragmented for 4.5 min at 94ºC. The remaining steps were followed according to the manufacturer’s instructions. Final libraries were analysed on an Agilent Technologies 2100 Bioanalyzer system using the Agilent DNA 1000 chip to estimate the quantity and validate the size distribution; libraries were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (07960204001, Roche) before amplification with Illumina’s cBot.

treatment_protocol: Epidermal cells suspensions were obtained from the skin of adult (18-25 weeks old) and aged (80-90 weeks old) that were sacrificed at different times of the day (ZT0, 4, 8, 12, 16, 20).

tag: age

value: Y

tag: replicate


title: A549, Kaempferol, CA10, 6h, C04

description: Library name: CA10_T7_D2_C04

value: lung

value: test


title: CHIP002, LMNB1, NTC, rep2

description:
LB1_WT.inpLg2_1kb.woTNR.e100.S10Kb.bw
LB1_WT.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed

value: LMNB1 (abcam, #ab16048)


title: GFP-RIP_untagged

description:
Library name: RIPseq_29
untagged control_WT

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 CI


title: CHIP001, LMNB1, NTC, rep1

value: WT fibroblast


title: 7a,25-OHC_P04_G01

description: Library name: LigandScreen-P04-20230908-007_S199


title: GFP-RIP_Pir2_GFP_pir1∆_tgs1∆

description:
Library name: RIPseq_28
Tgs1-GFP_pir1∆_tgs1∆

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 /ura4DS/E  Pir2-GFP<<KanMX pir1D::KanMX tgs1D::KanMX


title: COLXIV_KO_ZT_4 biol rep 1

description: Library name: K_4_1

value: epidermis


title: A549, Kaempferol, CA10, 6h, G09

description: Library name: CA10_T7_D1_G09

value: epithelial cell

value: Adenocarcinoma


title: cy1021, M1M3, heart

city: Madison

first: David

middle: H

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

description: Library name: cy1021-2023c116-5_S385234

data_processing:
Raw FASTQ files were aligned to a custom GRCh38 reference genome supplemented with macaque MAFA sequences using Space Ranger  v3.0.1 with per-sample custom probe sets (provided). Manual tissue alignment was performed for 12 of 16 samples using CytAssist-derived alignment JSONs (provided); remaining samples used automatic alignment. This produced per-sample 2µm binned count matrices (filtered_feature_bc_matrix.h5) and spatial coordinates (tissue_positions.parquet).
Cell segmentation was performed on 2µm bins using bin2cell v0.3.3 with StarDist v0.9.1 nuclear segmentation models applied to the CytAssist fluorescence channel and H&E images. Segmented cell-level count matrices were normalized (total count normalization, target sum 10,000), log1p-transformed, and filtered (min 10 counts, max 2,000 counts per cell; min 10 cells per gene). Highly variable genes were identified and PCA, neighbor graph, and Leiden clustering (resolution 0.5) were computed using scanpy v1.11.5. Samples with non-zero lateral image shift were processed with corrected spatial offsets prior to bin aggregation.
Cell types were annotated using CellTypist v1.7.1 with tissue-specific Human Cell Atlas models and majority voting with overclustering. Annotated cell-level AnnData objects are provided as _annotated.h5ad files.
Assembly: GRCh38 (custom build, supplemented with Macaca fascicularis MAFA sequences)
Supplementary files format and content: filtered_feature_bc_matrix.h5 — 10x Genomics HDF5 feature-barcode matrix from Space Ranger v3.0.1; UMI counts for Visium HD 2µm bins under tissue. Genes (Visium Human Transcriptome v2 panel + custom MHC probes) × 2µm bin barcodes.
Supplementary files format and content: tissue_positions.parquet — Apache Parquet table mapping each 2µm bin barcode to its array row/column index, full-resolution pixel coordinates, and in/out-of-tissue flag (Space Ranger v3.0.1 spatial output).
Supplementary files format and content: _annotated.h5ad — AnnData/HDF5 cell-level object from bin2cell v0.3.3 segmentation; total-count-normalized log1p counts in .X, raw counts in a layer, CellTypist v1.7.1 cell-type labels and Leiden clusters in .obs, spatial coordinates in .obsm (scanpy v1.11.5).
Supplementary files format and content: _cytassist.tif — CytAssist instrument capture image (TIFF) used for tissue detection and spatial/fiducial registration in Space Ranger.
Supplementary files format and content: _*.svs — Aperio whole-slide H&E brightfield image (SVS/TIFF) of the tissue section, used for histological reference and image registration.
Supplementary files format and content: _alignment.json — manual tissue/fiducial alignment file (JSON) from 10x Loupe Browser, used as Space Ranger input for the 12 of 16 samples requiring manual CytAssist–histology alignment.
Supplementary files format and content: *_hg38_v2_probeset.csv — 10x Genomics probe set reference (CSV): Visium Human Transcriptome v2 probes plus 219 custom MHC (M1/M3) probe pairs. Per-genotype panels (m1_m1, m1_m3, m3_m3) provided as supplementary files; used as the Space Ranger probe-set input.
Library strategy: Spatial Transcriptomics

organism: Macaca fascicularis

source_name: heart

extract_protocol:
10µm sections from formalin-fixed paraffin-embedded tissues were cut with a cyrostat
Spatial transcriptome sequencing libraries were prepared with 10X Genomics VisiumHD Spatial Gene Expression slides and reagent kit according to manufacturer's instructions

value: heart

value: normal control


title: A549, Kaempferol, CA10, 6h, F12

description: Library name: CA10_T7_D1_F12


title: COLXIV_KO_ZT_16 biol rep 4

description: Library name: K_16_4

value: ColXIV KO


title: GFP-RIP_Tgs1-GFP_pir1∆_mmi1∆_BioRep2

description:
Library name: RIPseq_26
Tgs1-GFP_pir1∆_mmi1∆

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E  Tgs1-GFP pir1D::KanMX mmi1D::hphMX mei4DC<<Nat otr1R(Sph1)::ura4+


title: cy1021, M1M3, lung

description: Library name: cy1021-2023c116-2_S385232


title: COLXIV_KO_ZT_16 biol rep 3

description: Library name: K_16_3


title: A549, Kaempferol, CA10, 6h, A07

description: Library name: CA10_T7_D1_A07


title: B4T

address: 广州市番禺区新造镇新造路1号

value: tumor tissues


title: COLXIV_KO_ZT_16  biol rep 2

description: Library name: K_16_2


title: cy1021, M1M3, liver

description: Library name: cy1021-2023c116-1_S385231

value: liver


title: A549, 4-hydroxybenzophenone, CA10, 6h, H06

description: Library name: CA10_T6_D3_H06


title: GFP-RIP_Tgs1-GFP_pir1∆_mmi1∆_BioRep1

description:
Library name: RIPseq_24
Tgs1-GFP_pir1∆_mmi1∆

value: Yeast Whole Cells

value: Anti-GFP Ab290

value: Growth in YEA 30°C


title: cy1008, M1M3, heart

description: Library name: cy1008-2023c069-5_S385230


title: COLXIV_KO_ZT_16 biol rep 1

description: Library name: K_16_1


title: GFP-RIP_Tgs1-GFP_pir1∆_BioRep1

description:
Library name: RIPseq_23
Tgs1-GFP_pir1∆

value: Msmt0 leu1-32 ade6-210 his2 ura4 DS/E Tgs1-GFP::KanMX6 pir1D otr1R(Sph1)::ura4 +


title: A549, 4-hydroxybenzophenone, CA10, 6h, F09

description: Library name: CA10_T6_D3_F09

value: lung

value: test


title: cy1008, M1M3, kidney

description: Library name: cy1008-2023c069-3_S385229

source_name: kidney

value: kidney


title: GFP-RIP_untagged_abp1DDE_eas1∆mug174-1_BioRep2

description:
Library name: RIPseq_14
untagged control_abp1DDE_eas1∆mug174-1

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX


title: A549, 4-hydroxybenzophenone, CA10, 6h, E12

description: Library name: CA10_T6_D3_E12


title: cy1008, M1M3, lung

description: Library name: cy1008-2023c069-2_S385228


title: COLXIV_KO_ZT_12 biol rep 3

description: Library name: K_12_4

value: epidermis


title: GFP-RIP_Tgs1-GFP_abp1DDE_eas1∆mug174-1_BioRep2

description:
Library name: RIPseq_13
Tgs1-GFP_abp1DDE_eas1∆mug174-1

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) Tgs1-GFP::KanMX6 abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX


title: A549, Kaempferol, CA10, 6h, B07

description: Library name: CA10_T7_D2_B07

value: epithelial cell

value: Adenocarcinoma


title: A549, 4-hydroxybenzophenone, CA10, 6h, A04

description: Library name: CA10_T6_D3_A04


title: cy1008, M1M3, liver

description: Library name: cy1008-2023c069-1_S385227

value: normal control


title: GFP-RIP_Tgs1-GFP_abp1DDE_BioRep2a

description:
Library name: RIPseq_12
Tgs1-GFP_abp1DDE

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  Tgs1-GFP::KanMX abp1DDE-FLAG::Nat otr1R(sph1)::ura4+


title: COLXIV_KO_ZT_12 biol rep 2

description: Library name: K_12_3

value: ColXIV KO


title: COLXIV_KO_ZT_12 biol rep 1

description: Library name: K_12_2


title: cy0993, M3M3, heart

description: Library name: cy0993-2024c108-5_S385226

value: heart


title: GFP-RIP_untagged_abp1DDE_cwf10-1_BioRep1

description:
Library name: RIPseq_11
untagged control_cwf10-1

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E cwf10-1 abp1-DDE-FLAG::Nat otr1R(Sph1)::ura4+


title: pir1∆_Biorep6

description:
Library name: RNAseq_6b
pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(Sph1)::ura4+

value: Yeast Whole Cells

value: Growth in YEA 18°C


title: cy1021, M1M3, kidney

description: Library name: cy1021-2023c116-3_S385233


title: cy0993, M3M3, kidney

description: Library name: cy0993-2024c108-3_S385225


title: L. interrogans serogroup Pomona 202100004 in EMJH medium replicate #3

city: Paris

first: Rania

last: Ouazahrou

address: 28 rue docteur Roux

country: France

institute: Institut Pasteur Paris

description:
Library name: PO4_EMJH_3_S28
PO4_raw_counts.txt

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.19.2)
FeatureCounts 2.0.1 was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: L. interrogans serogroup Icterohaemorrhagiae (G4) : isolate 202101402 (IC1) ; 202102576 (IC2) ; 202102995 (IC3) ; 202100001 (IC4) ; 202102907 (IC5). L. interrogans serogroup Pomona (G13) :  201801210 (PO1) ; 201700303 (PO2) ; 201902969 (PO3) ; 202100004 (PO4).
Supplementary files format and content: Tabulated files containing raw counts for each sample

organism: Leptospira interrogans

source_name: serogroup Pomona isolate 202100004

growth_protocol: Leptospira strains were cultivated aerobically in Ellighausen-McCullough-Johnson-Harris liquid medium (EMJH) at 30°C with shaking at 100 rpm.

extract_protocol:
Total RNAs were extracted using RNeasy Mini Kit (Qiagen), with a DNAse digestion (Qiagen) incorporated in the protocol.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit with the addition of custom primer that target L. interrogans rRNA following manufacturer's protocol.

treatment_protocol: Exponential phase cultures of the five G4 strains and the four G13 strains used (each strain, at least, in duplicate) in EMJH and EMEM medium at 3 days post-incubation.

tag: serogroup

value: Pomona

value: Bacterial cell

value: EMJH medium


title: A549, 4-hydroxybenzophenone, CA10, 6h, E09

description: Library name: CA10_T6_D2_E09

value: lung

value: test


title: cy0993, M3M3, lung

description: Library name: cy0993-2024c108-2_S385224


title: L. interrogans serogroup Pomona 202100004 in EMJH medium replicate #2

description:
Library name: PO4_EMJH_2_S27
PO4_raw_counts.txt


title: A549, 4-hydroxybenzophenone, CA10, 6h, D12

description: Library name: CA10_T6_D2_D12


title: cy0993, M3M3, liver

description: Library name: cy0993-2024c108-1_S385223

value: liver


title: L. interrogans serogroup Pomona 202100004 in EMJH medium replicate #1

description:
Library name: PO4_EMJH_1_S26
PO4_raw_counts.txt


title: A549, 4-hydroxybenzophenone, CA10, 6h, G03

description: Library name: CA10_T6_D1_G03


title: L. interrogans serogroup Pomona 201902969 in EMJH medium replicate #3

description:
Library name: PO3_EMJH_3_S25
PO3_raw_counts.txt

source_name: serogroup Pomona isolate 201902969


title: GFP-RIP_Tgs1-GFP_abp1DDE_BioRep1a

description:
Library name: RIPseq_7
Tgs1-GFP_abp1DDE

value: Anti-GFP Ab290

value: Growth in YEA 30°C


title: cy0861, M1M1, kidney

description: Library name: cy0861-2017c171-3_S385221

value: kidney


title: L. interrogans serogroup Pomona 201902969 in EMJH medium replicate #2

description:
Library name: PO3_EMJH_2_S24
PO3_raw_counts.txt


title: GFP-RIP_untagged_abp1DDE_eas1∆mug174-1_BioRep1

description:
Library name: RIPseq_6
untagged control_abp1DDE_eas1∆mug174-1

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX


title: A549, 4-hydroxybenzophenone, CA10, 6h, D09

description: Library name: CA10_T6_D1_D09

value: epithelial cell

value: Adenocarcinoma


title: cy0861, M1M1, lung

description: Library name: cy0861-2017c171-2_S385220

value: normal control


title: L. interrogans serogroup Pomona 201902969 in EMJH medium replicate #1

description:
Library name: PO3_EMJH_1_S23
PO3_raw_counts.txt


title: GFP-RIP_untagged_BioRep2

description:
Library name: RIPseq_5
untagged control_WT

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 CI


title: COLXIV_KO_ZT_12 biol rep 4

description: Library name: K_12_5

value: epidermis

value: ColXIV KO


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, H06

description: Library name: Ci10_T6_D3_H06

source_name: heart muscle cells

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: Val-1k, TPO/FL/SCF/IL3/IL6, 3d, donor2, batch3

city: Edogawa-ku

first: Kyungtaek

last: Lim

state: Tokyo

address: 1-16-13, Kitakasai

country: Japan

institute: Daiichi Sankyo Co., Ltd.

description: 10X Genomics

library_source: genomic single cell

data_processing:
The cell ranger ATAC pipeline (v2.0) was used for demultiplexing, barcode processing, read mapping against GRCh38, generation of a fragment file (a file contains coordinates of tagmented fragments), peak calling, and peak-cell count matrix construction.
ArchR (v1.0.1) was applied to the resulting fragment files to collect per-cell quality control metrics in addition to those provided from the cell ranger ATAC pipeline.
Assembly: GRCh38
Supplementary files format and content: h5. Barcode-peak count matrix
Supplementary files format and content: TSV, Fragments
Supplementary files format and content: CSV, cellranger-atac per-barcode stats
Supplementary files format and content: CSV, ArchR per-barcode stats

source_name: bone marrow

growth_protocol: Primary human bone marrow CD34+ cells were cultured in StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (TPO, 50 ng/mL), TPO (50 ng/mL)/FLT3 ligand (FL, 100 ng/mL)/SCF (100 ng/mL), interleukin 3 (IL3, 20 ng/mL)/ interleukin 6 (IL6, 100 ng/mL), TPO (50 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL), or TPO (50 ng/mL)/FL (100 ng/mL)/SCF (100 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL) at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Cell nuclei were isolated following the standard protocol provided by 10x Genomics (Protocol number CG000169). In brief, 10,000 to 20,000 cells were lysed using 100 µL of lysis buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%, IGEPAL 0.1%, and Digitonin 0.01%) on ice for 5 minutes. Subsequent to lysis, cells were washed with chilled wash buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%). The cell suspension was centrifuged to pellet the nuclei, which were then resuspended in Nuclei Buffer (Chromium Single Cell ATAC Reagent Kits, 10x Genomics). The concentration of isolated nuclei was determined using a TC20 Automated Cell Counter (Bio-Rad).
Library preparation for scATAC-seq was performed by Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics) with manufacturer’s protocol.

treatment_protocol: Valemetostat or dimethyl sulfoxide was treated during the cell culture.

value: bone marrow

value: bone marrow CD34+ cells

value: valemetostat 1uM

tag: stimulation

tag: donor id

tag: experimental batch


title: A549, 4-hydroxybenzophenone, CA10, 6h, C12

description: Library name: CA10_T6_D1_C12

tag: tissue

value: lung

value: test


title: cy0861, M1M1, liver

description: Library name: cy0861-2017c171-1_S385219

source_name: liver

value: liver

tag: genotype


title: L. interrogans serogroup Pomona 201700303 in EMJH medium replicate #3

description:
Library name: PO2_EMJH_3_S22
PO2_raw_counts.txt

source_name: serogroup Pomona isolate 201700303

value: Pomona

tag: cell type

value: Bacterial cell

value: EMJH medium


title: GFP-RIP_Tgs1-GFP_abp1DDE_eas1∆mug174-1_BioRep1

description:
Library name: RIPseq_4
Tgs1-GFP_abp1DDE_eas1∆mug174-1

tag: strain

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) Tgs1-GFP::KanMX6 abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX

value: Yeast Whole Cells

value: Anti-GFP Ab290

value: Growth in YEA 30°C


title: A549, 2-hydroxybenzophenone, CA10, 6h, F03

description: Library name: CA10_T5_D3_F03

value: epithelial cell

value: Adenocarcinoma

tag: treatment


title: A549, 4-hydroxybenzophenone, CA10, 6h, H03

description: Library name: CA10_T6_D2_H03


title: M91_protein_D7 Muscle

type: RNA

city: Gold Coast

first: Laurelle

last: Jackson

address: 1 Parklands Dr, Southport

department: Pharmacy and Medical Sciences

institute: Griffith University

description:
Muliplexed sample slide, annotations in experimental metadata
MuscleX38_experimental_gridded_metadata.tsv.gz
MuscleX38_gridded_counts.RDS
X38_exprMat_file.csv.gz
X38_fov_positions_file.csv.gz
X38_metadata_file.csv.gz
X38-polygons.csv.gz
X38_tx_file.csv.gz
X38_morphology2D.tar.gz

hyb_protocol: Spatial transcriptomics libraries were  using the CosMx SMI buffers, reagents and imaginig tray, where in situ barcoded hydridisation and imaging-based detection was done.

scan_protocol: Sections were hybridized overnight at 37 °C with the   CosMx™ SMI Mouse Universal Cell Characterization   1K RNA panel

data_processing: Atomx CosMx SMI pipeline was run to generate expMat, metadata, FOV positions, polygon and tx files. For segmentation, Cyto2 (using default AtoMX settings) was used for Lymph samples and default parameters for the muscle samples. Muscle transcripts were subsequently grouped by grid squares by rounding transcript coordinates after conversion from pixel to um with scale factor 0.18 (Resulting grid ID coordinates are at centre of grid square).

label: Xenium probe set

source_name: Muscle

label_protocol: Xenium probe set

growth_protocol: Female BALB/c mice were maintained under specific pathogen-free conditions with ad libitum access to food and water. Animals were housed and handled in accordance with institutional animal ethics and biosafety guidelines. No in vitro cell culture growth conditions applied to this study, as tissues were collected directly from vaccinated animals for downstream spatial transcriptomic analyses.

extract_protocol: tissue preparation protocol: Injection site muscle and draining lymph nodes were   harvested, formalin-fixed, paraffin-embedded (FFPE),   and sectioned for spatial transcriptomic analysis.   For CosMx SMI profiling, FFPE sections were deparaffinised, subjected to antigen retrieval and proteinase K digestion according to the manufacturer’s protocol for the CosMx SMI

treatment_protocol: Groups of three female BALB/c mice per treatment group were immunised intramuscularly in the quadriceps with either AF03-adjuvanted recombinant haemagglutinin (rHA) protein vaccine or phosphate-buffered saline (PBS) control on Days 0 and 21. Blood was collected longitudinally on Days 0, 14, and 35 for serum-based immunogenicity analyses. For spatial transcriptomic profiling, injection site muscle and draining lymph nodes were collected on Days 1 and 7 following vaccination.

value: Muscle

tag: tissue preservation method

value: FFPE

tag: mouse

tag: slide

value: protein

tag: timepoint

value: healthy BALB/c mice


title: GFP-RIP_Tgs1-GFP_abp1DDE_BioRep2

description:
Library name: RIPseq_3
Tgs1-GFP_abp1DDE

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  Tgs1-GFP::KanMX abp1DDE-FLAG::Nat otr1R(sph1)::ura4+

tag: growth


title: L. interrogans serogroup Pomona 201700303 in EMJH medium replicate #2

description:
Library name: PO2_EMJH_2_S21
PO2_raw_counts.txt


title: YT19

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: mm10
Supplementary files format and content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: hippocampus

extract_protocol:
RNA extracted using Qiagen Rneasy extraction
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: For CD8 depletion, Aged (22-24 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a (2.43, BioXCell, BE0061) or InVivoMAb rat IgG2b isotype control (LTF-2, BioXCell, BE0090) in 200 μL PBS every 4 days until time of sacrifice. For adoptive transfer, B6.SJL-Ptprca Pepcb/BoyJ (4 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a in 200 μL PBS day -11 and -7 to deplete resident CD8+ T cells. CD8+ T cells were isolated from single cell suspensions of spleenocytes and PBMCs from young (3-4 months) or aged (22-28 months) C57BL/6J mice using the CD8a+ T cell Isolation Kit (Miltenyi Biotech, 130-104-075) according to manufacturer instructions. For adoptive transfer of young or aged CD8+ T cells, cells were immediately resuspended at concentrations of 3e5 (first injection) or 3e6 (second injection) in 100 μL saline and injected via tail vein. Mice were anesthetized with 87.5 mg per kg ketamine and 12.5 mg per kg xylazine and transcardially perfused with ice-cold phosphate-buffered saline. To process the brains, the whole brain was sectioned in half along the sagittal plane. The hippocampus from one hemisphere was subdissected and flash frozen.

value: hippocampus

tag: Sex

value: male

value: WT

value: Young

value: Young CD8+ T Cell transfer


title: D3_corneal_DMSO_1

first: Paul

last: Khavari

address: 269 Campus Dr

department: Dermatology

description: Library name: D3_corneal_DMSO_1

data_processing:
UMI extraction with UMI tools
read alignment to reference genome using STAR
featureCount generation
DESeq2 with apeGLM shrinkage,
Assembly: GRCh38
Supplementary files format and content: feature counts

source_name: cornea

growth_protocol: Cells were aquired from ATCC (PCS-480-011, grown in ATCC PCS-480-032 and PCS-480-042) (PCS-700-010, grown in ATCC PCS-700-040 and ATCC PCS-700-030)

extract_protocol:
Cells previously transfected with siRNA or treated with pharmacologic compounds were collected in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen).
Libraries were prepared with 10-500ng input to the QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer’s protocol. Libraries were quantified with KAPA Library Quantification Kit Illumina® Platforms (Roche) and sequenced on NovaSeq X+ with ~30 M paired-end, 150 bp reads per sample.

treatment_protocol: cells were treated with DMSO or NEDD8i for 16hrs then harvested

value: cornea

value: corneal epithelial cells


title: A549, 2-hydroxybenzophenone, CA10, 6h, E06

description: Library name: CA10_T5_D3_E06

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: lung

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: lung

tag: cell line

value: test

tag: batch


title: IG8

tag: age

value: Aged

value: IgG2b isotype control


title: A549, 4-hydroxybenzophenone, CA10, 6h, G06

description: Library name: CA10_T6_D2_G06

value: epithelial cell

value: Adenocarcinoma


title: M78_protein_D1 Muscle

value: Muscle

value: FFPE


title: L. interrogans serogroup Pomona 201700303 in EMJH medium replicate #1

description:
Library name: PO2_EMJH_1_S2
PO2_raw_counts.txt

tag: serogroup

value: Pomona

value: Bacterial cell

value: EMJH medium


title: A549, 2-hydroxybenzophenone, CA10, 6h, C09

description: Library name: CA10_T5_D3_C09


title: GFP-RIP_untagged_BioRep1

description:
Library name: RIPseq_2
untagged control_WT

source_name: Yeast Whole Cells

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1 CI

value: Yeast Whole Cells

tag: rip antibody

value: Anti-GFP Ab290

value: Growth in YEA 30°C


title: GFP-RIP_Tgs1-GFP_abp1DDE_cwf10-1_BioRep1

description:
Library name: RIPseq_10
Tgs1-GFP cwf10-1

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E cwf10-1 Tgs1-GFP<<KanMX abp1-DDE-FLAG::Nat otr1R(Sph1)::ura4+


title: M37_PBS_D42 Muscle

value: PBS

value: healthy BALB/c mice


title: GFP-RIP_Tgs1-GFP_abp1DDE_BioRep1

description:
Library name: RIPseq_1
Tgs1-GFP_abp1DDE

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E Tgs1-GFP::KanMX abp1DDE-FLAG::Nat otr1R(sph1)::ura4+


title: GFP-RIP_untagged_abp1DDE_eas1∆mug174-1_BioRep1a

description:
Library name: RIPseq_9
untagged control_abp1DDE_eas1∆mug174-1

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX


title: L. interrogans serogroup Pomona 201801210 in EMJH medium replicate #3

description:
Library name: PO1_EMJH_3_S20
PO1_raw_counts.txt

source_name: serogroup Pomona isolate 201801210


title: M90_protein_D7 Muscle

description:
Muliplexed sample slide, annotations in experimental metadata
MuscleX19_experimental_gridded_metadata.tsv.gz
MuscleX19_gridded_counts.RDS
X19_exprMat_file.csv.gz
X19_fov_positions_file.csv.gz
X19_metadata_file.csv.gz
X19-polygons.csv.gz
X19_tx_file.csv.gz
X19_morphology2D.tar.gz

value: protein


title: A549, 2-hydroxybenzophenone, CA10, 6h, A12

description: Library name: CA10_T5_D3_A12

value: lung

value: epithelial cell

value: test


title: pir2-1_36C

description:
Library name: RNAseq_29
pir2-1_36C_5hrs

data_processing:
Single ended short reads from RNAseq experiments were quality trimmed using fastp (Chen et al. 2018) and aligned to the reference genome using the STAR aligner (Dobin, A. et al., 2013). Wig files, normalized to counts per million mapped reads, were generated by STAR.
Assembly: S. pombe V2 reference with the sequence of the full 40 kb mat region provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI pir2-1-FLAG<<KanMX

value: Growth in YEA at 26°C then shifted to  36°C for 5hrs


title: L. interrogans serogroup Pomona 201801210 in EMJH medium replicate #2

description:
Library name: PO1_EMJH_2_S1
PO1_raw_counts.txt

value: Pomona

value: Bacterial cell


title: A549, 2-hydroxybenzophenone, CA10, 6h, H11

description: Library name: CA10_T5_D2_H11

value: Adenocarcinoma


title: M77_protein_D1 Muscle

value: Muscle

value: FFPE


title: L. interrogans serogroup Pomona 201801210 in EMJH medium replicate #1

description:
Library name: PO1_EMJH_1_S19
PO1_raw_counts.txt

value: EMJH medium


title: A549, 2-hydroxybenzophenone, CA10, 6h, E03

description: Library name: CA10_T5_D2_E03


title: M23_PBS_D7 Muscle


title: WT_36C_b

description:
Library name: RNAseq_28
WT_36C_5hrs

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI

value: Yeast Whole Cells


title: L. interrogans serogroup Pomona 202100004 in cell medium replicate #3

description:
Library name: PO4_cell-med_3_S43
PO4_raw_counts.txt

value: cell medium


title: GFP-RIP_Tgs1-GFP_abp1DDE_eas1∆mug174-1_BioRep1a

description:
Library name: RIPseq_8
Tgs1-GFP_abp1DDE_eas1∆mug174-1

value: Msmt0 leu1-32 ade6-210/216 his2 ura4DS/E  or ura4::tf2-1CI otr1R(sph1)::ura4(?) Tgs1-GFP::KanMX6 abp1DDE-FLAG::Nat eas1D::NatMX mug174-1-3HA::KanMX

value: Anti-GFP Ab290

value: Growth in YEA 30°C


title: pir2-1pir1∆_18C

description:
Library name: RNAseq_27
pir2-1 pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4::tf2-1CI pir2-1-flag::kanMX6 pir1D::KanMX

value: Growth in YEA 18°C


title: A549, 2-hydroxybenzophenone, CA10, 6h, C06

description: Library name: CA10_T5_D2_C06

value: lung

value: epithelial cell

value: test


title: L. interrogans serogroup Pomona 202100004 in cell medium replicate #2

description:
Library name: PO4_cell-med_2_S42
PO4_raw_counts.txt

value: Pomona


title: M11_PBS_D1 Muscle

value: PBS

value: healthy BALB/c mice


title: A549, 2-hydroxybenzophenone, CA10, 6h, B09

description: Library name: CA10_T5_D2_B09

value: Adenocarcinoma


title: M9_PBS_D1 Muscle

value: Muscle

value: FFPE


title: pir2-1_18C

description:
Library name: RNAseq_26
pir2-1_18C

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI pir2-1-FLAG<<KanMX


title: cy0861, M1M1, heart

description: Library name: cy0861-2017c171-5_S385222

value: heart

value: normal control


title: L. interrogans serogroup Pomona 202100004 in cell medium replicate #1

description:
Library name: PO4_cell-med_1_S41
PO4_raw_counts.txt

value: Bacterial cell

value: cell medium


title: A549, 2-hydroxybenzophenone, CA10, 6h, G11

description: Library name: CA10_T5_D1_G11


title: L. interrogans serogroup Pomona 201902969 in cell medium replicate #3

description:
Library name: PO3_cell-med_3_S40
PO3_raw_counts.txt


title: WT_18C_BioRep3

description:
Library name: RNAseq_25
WT_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI

value: Yeast Whole Cells


title: M10_PBS_D1 Muscle


title: ssu72∆ tgs1∆_18C

description:
Library name: RNAseq_24
ssu72∆_tgs1∆_18C

value: Msmt0 leu1-32 ade6-216/210 D18 or DS/E or ura4::tf2-1CI ssu72D::Nat tgs1D::KanMX

value: Growth in YEA 18°C


title: A549, 2-hydroxybenzophenone, CA10, 6h, D03

description: Library name: CA10_T5_D1_D03

value: lung

value: epithelial cell


title: M92_protein_D7 Muscle

description:
Muliplexed sample slide, annotations in experimental metadata
MuscleW38_experimental_gridded_metadata.tsv.gz
MuscleW38_gridded_counts.RDS
W38_exprMat_file.csv.gz
W38_fov_positions_file.csv.gz
W38_metadata_file.csv.gz
W38-polygons.csv.gz
W38_tx_file.csv.gz
W38_morphology2D.tar.gz

value: protein


title: L. interrogans serogroup Pomona 201902969 in cell medium replicate #2

description:
Library name: PO3_cell-med_2_S39
PO3_raw_counts.txt

value: Pomona


title: ssu72∆_18C

description:
Library name: RNAseq_23
ssu72∆_18C

value: Msmt0 leu1-32 ade6-216/210 his2 ura4::tf2-1CI ssu72D::Nat


title: L. interrogans serogroup Pomona 201902969 in cell medium replicate #1

description:
Library name: PO3_cell-med_1_S17
PO3_raw_counts.txt


title: A549, 4-hydroxybenzophenone, CA10, 6h, F06

description: Library name: CA10_T6_D1_F06

value: Adenocarcinoma

value: test


title: A549, 2-hydroxybenzophenone, CA10, 6h, B06

description: Library name: CA10_T5_D1_B06


title: M39_PBS_D42 Muscle

value: Muscle

value: FFPE

value: PBS

value: healthy BALB/c mice


title: A549, 2-hydroxybenzophenone, CA10, 6h, A09

description: Library name: CA10_T5_D1_A09


title: L. interrogans serogroup Pomona 201700303 in cell medium replicate #3

description:
Library name: PO2_cell-med_3_S16
PO2_raw_counts.txt

value: Bacterial cell


title: ccr4∆_pir1∆_18C

description:
Library name: RNAseq_21
ccr4∆_pir1∆_18C

value: Msmt0 leu1-32 ade6-210 ura4DS/E or D18 pir1D::KanMX ccr4D::KanMX otr1R(Sph1)::ura+ (?)


title: M24_PBS_D7 Muscle


title: pir1∆_18C_BioRep3

description:
Library name: RNAseq_22
pir1∆_18C

value: Msmt0  leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(SphI)::ura4+


title: M79_protein_D1 Muscle

description:
Muliplexed sample slide, annotations in experimental metadata
MuscleW19_experimental_gridded_metadata.tsv.gz
MuscleW19_gridded_counts.RDS
W19_exprMat_file.csv.gz
W19_fov_positions_file.csv.gz
W19_metadata_file.csv.gz
W19-polygons.csv.gz
W19_tx_file.csv.gz
W19_morphology2D.tar.gz


title: A549, 3-hydroxybenzophenone, CA10, 6h, F11

description: Library name: CA10_T4_D3_F11


title: ccr4∆_18C_Rep2

description:
Library name: RNAseq_20
ccr4∆_18C

value: Msmt0 leu1-32 ade6-216/210 his2 ura4::tf2-1CI ccr4D::kan

value: Yeast Whole Cells


title: L. interrogans serogroup Pomona 201700303 in cell medium replicate #2

description:
Library name: PO2_cell-med_2_S15
PO2_raw_counts.txt

value: cell medium


title: L. interrogans serogroup Pomona 201700303 in cell medium replicate #1

description:
Library name: PO2_cell-med_1_S14
PO2_raw_counts.txt


title: ccr4∆ tgs1∆_18C

description:
Library name: RNAseq_19
ccr4∆_tgs1∆_18C

value: Msmt0 leu1-32 ade6-216 ura4D18 or ura4::tf2-1CI ccr4D::kanMX4  tgs1D::KanMX

value: Growth in YEA 18°C


title: M22_PBS_D7 Muscle


title: CHIP031, RAD21, CRISPRi_Scr, rep1

description:
Library name: CHIP031
RAD21_SCR_FE.100bp.bw
RAD21_SCR_peaks.narrowPeak

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

source_name: WT fibroblast

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms

value: WT fibroblast

value: Human fibroblast

tag: chip antibody

value: RAD21 (Abcam, #ab992)


title: L. interrogans serogroup Pomona 201801210 in cell medium replicate #2

description:
Library name: PO1_cell-med_3_S38
PO1_raw_counts.txt

value: Pomona


title: A549, 3-hydroxybenzophenone, CA10, 6h, C03

description: Library name: CA10_T4_D3_C03

tag: tissue

value: lung

value: epithelial cell

value: Adenocarcinoma

value: test


title: M90_protein_D7 Lymph node

description:
Muliplexed sample slide, annotations in experimental metadata
LymphnodeV112_experimental_metadata.tsv.gz
LymphnodeV112_exprMat_file.csv.gz
LymphnodeV112_fov_positions_file.csv.gz
LymphnodeV112_metadata_file.csv.gz
LymphnodeV112-polygons.csv.gz
LymphnodeV112_tx_file.csv.gz
LymphnodeV112_morphology2D.tar.gz

source_name: Lymph node

value: Lymph node

value: FFPE

value: protein

tag: genotype

value: healthy BALB/c mice


title: A549, 3-hydroxybenzophenone, CA10, 6h, A06

description: Library name: CA10_T4_D3_A06

tag: cell type


title: ccr4∆_18C_Rep1

description:
Library name: RNAseq_18
ccr4∆_18C

extract_protocol:
Total RNA isolated using the MasterPure Yeast RNA Purification Kit following the manufacturer's protocol
For RNA Seq-Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).
Total RNA isolated was first ribodepleted using the Ribo-Zero gold plus for humans (Illumina) supplemented with probes against S. pombe ribosomal DNA (IDT) for library construction

tag: strain

value: Msmt0 leu1-32 ade6-216/210 his2 ura4::tf2-1CI ccr4D::kan


title: M92_protein_D7 Lymph node

tag: treatment


title: L. interrogans serogroup Pomona 201801210 in cell medium replicate #1

description:
Library name: PO1_cell-med_1_S37
PO1_raw_counts.txt

value: Bacterial cell


title: ago1∆ tgs1∆_18C

description:
Library name: RNAseq_17
ago1∆ tgs1∆_18C

value: Msmt0 leu1-32 ade6-216 his2 ura4::tf2-1CI ago1D::kan  tgs1D::Nat

value: Yeast Whole Cells


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in EMJH medium replicate #3

description:
Library name: IC5_EMJH_3_S18
IC5_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202102907

value: Icterohaemorrhagiae

value: EMJH medium


title: M91_protein_D7 Lymph node

tag: tissue preservation method


title: A549, 3-hydroxybenzophenone, CA10, 6h, H05

description: Library name: CA10_T4_D2_H05


title: A549, 3-hydroxybenzophenone, CA10, 6h, F08

description: Library name: CA10_T4_D2_F08


title: pir1∆_18C_BioRep2

description:
Library name: RNAseq_16
pir1∆_18C

value: Msmt0  leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(SphI)::ura4+

value: Growth in YEA 18°C


title: A549, 3-hydroxybenzophenone, CA10, 6h, H08

description: Library name: CA10_T4_D3_H08


title: M79_protein_D1 Lymph node

tag: mouse


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in EMJH medium replicate #2

description:
Library name: IC5_EMJH_2_S17
IC5_raw_counts.txt


title: ago1∆ pir1∆_18C

description:
Library name: RNAseq_15
ago1∆ pir1∆_18C

value: Msmt0  leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX ago1D::KanMX otr1R(SphI)::ura4+


title: A549, 3-hydroxybenzophenone, CA10, 6h, E11

description: Library name: CA10_T4_D2_E11

value: lung


title: M77_protein_D1 Lymph node

tag: slide


title: L. interrogans serogroup Icterohaemorrhagiae 202102907 in EMJH medium replicate #1

description:
Library name: IC5_EMJH_1_S16
IC5_raw_counts.txt


title: ago1∆_18C

description:
Library name: RNAseq_14
ago1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4DS/E ago1D::KanMX otr1R(SphI)::ura4+


title: A549, 3-hydroxybenzophenone, CA10, 6h, B03

description: Library name: CA10_T4_D2_B03

value: epithelial cell

value: Adenocarcinoma


title: M78_protein_D1 Lymph node

value: Lymph node

tag: timepoint


title: A549, 3-hydroxybenzophenone, CA10, 6h, G05

description: Library name: CA10_T4_D1_G05

value: test


title: L. interrogans serogroup Icterohaemorrhagiae 202100001 in EMJH medium replicate #3

description:
Library name: IC4_EMJH_3_S15
IC4_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202100001


title: mug174-1-3HA_18C

description:
Library name: RNAseq_13
mug174-1-3HA_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI mug174-1-3HA::KanMX

tag: growth


title: L. interrogans serogroup Icterohaemorrhagiae 202100001 in EMJH medium replicate #2

description:
Library name: IC4_EMJH_2_S14
IC4_raw_counts.txt


title: eas1∆ mug174-1-3HA_18C

description:
Library name: RNAseq_12
eas1∆ mug174-1-3HA

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI eas1D::NatMX mug174-1-3HA::KanMX


title: M22_PBS_D7 Lymph node

value: FFPE

value: PBS

value: healthy BALB/c mice


title: A549, 3-hydroxybenzophenone, CA10, 6h, E08

description: Library name: CA10_T4_D1_E08


title: M23_PBS_D7 Lymph node


title: A549, DMSO, CA11, 6h, G08

description: Library name: CA11_DMSO_G08

value: vehicle


title: L. interrogans serogroup Icterohaemorrhagiae 202100001 in EMJH medium replicate #1

description:
Library name: IC4_EMJH_1_S13
IC4_raw_counts.txt

value: Icterohaemorrhagiae

value: Bacterial cell


title: eas1∆_18C

description:
Library name: RNAseq_11
eas1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI eas1D::NatMX

value: Yeast Whole Cells


title: A549, 3-hydroxybenzophenone, CA10, 6h, D11

description: Library name: CA10_T4_D1_D11


title: M24_PBS_D7 Lymph node


title: L. interrogans serogroup Icterohaemorrhagiae 202102995 in EMJH medium replicate #3

description:
Library name: IC3_EMJH_3_S12
IC3_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202102995

value: EMJH medium


title: WT_18C_BioRep2

description:
Library name: RNAseq_10
WT_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI

value: Growth in YEA 18°C


title: A549, 3-hydroxybenzophenone, CA10, 6h, A03

description: Library name: CA10_T4_D1_A03

value: lung

value: epithelial cell


title: M10_PBS_D1 Lymph node

value: Lymph node


title: L. interrogans serogroup Icterohaemorrhagiae 202102995 in EMJH medium replicate #2

description:
Library name: IC3_EMJH_2_S11
IC3_raw_counts.txt


title: M11_PBS_D1 Lymph node


title: tgs1∆ pir1∆_18C

description:
Library name: RNAseq_9
tgs1∆ pir1∆_18C

value: Msmt0 leu1-32 ade6-216 his2 pir1D::KanMX6 tgs1D::KanMX otr1R(SphI)::ura4+


title: A549, Avobenzone, CA10, 6h, G04

description: Library name: CA10_T1_D3_G04

value: Adenocarcinoma

value: test


title: L. interrogans serogroup Icterohaemorrhagiae 202102995 in EMJH medium replicate #1

description:
Library name: IC3_EMJH_1_S10
IC3_raw_counts.txt


title: A549, Avobenzone, CA10, 6h, F07

description: Library name: CA10_T1_D3_F07


title: pir1∆_18C_BioRep1

description:
Library name: RNAseq_8
pir1∆_18C

value: Msmt0 leu1-32 ade6-210 his2 ura4DS/E pir1D::KanMX otr1R(Sph1)::ura4+


title: M9_PBS_D1 Lymph node

value: FFPE

value: PBS


title: L. interrogans serogroup Icterohaemorrhagiae 202102576 in EMJH medium replicate #3

description:
Library name: IC2_EMJH_3_S9
IC2_raw_counts.txt

source_name: serogroup Icterohaemorrhagiae isolate 202102576


title: tgs1∆_18C

description:
Library name: RNAseq_7
tgs1∆_18C

value: Msmt0  leu1-32 ade6-216 his2 ura4::tf2-1CI  tgs1D::KanMX


title: A549, Avobenzone, CA10, 6h, E10

description: Library name: CA10_T1_D3_E10