title: residual primary mammary tumor, post-treatment, Patient83

tag: tissue

tag: timing biopsies

value: yes

value: extensive residual disease

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

value: Femara


title: ATAC_iXist-ChrX-Dom_SmA3_NPC_d7

status: Public on Feb 28 2024

type: SRA

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Paired-end fastq files from ATAC-seq were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Aligned reads were assigned to separate files corresponding to either the CAST (“genome1”) or 129/Sv (“genome2”) genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “--paired” parameter and a strain-specific SNP file compiled from UCSC annotations.
Bigwig files were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
For quantitative allelic analysis of RE accessibility over the timecourse of XCI, consensus chrX REs identified from our initial analysis of WT iXist-ChrX time-courses (GSE240677) were labelled and parsed into gtf file format by awk commands. These were used as input for featureCounts (Liao et al. 2014) to count sequencing fragments overlapping REs in both the total and allele-specific alignment files for each time point. Counts matrices were loaded into RStudio for further analysis. Alllelic filters were performed separately for the two paired time-courses (ie. iXist-ChrX-Dom WT vs SmA3 was treated as one dataset) as follows: only peaks containing at least 10 allelically-assigned fragments in >80% of samples and showing biallelic signal in uninduced mESCs (0.15 < allelic ratio < 0.85) were retained. Allelic ratios (Xi/(Xi + Xa)) were then calculated for all sample time points and used for further analysis.
Assembly: mm10
Supplementary files format and content: Bigwig files of ATAC-seq tracks (unspit and allelic) for all samples
Supplementary files format and content: Tables of allelic ratios for WT vs SmHD1mut for iXist-ChrX-Cast and iXist-ChrX-Dom time-courses (.txt)

molecule: genomic DNA

organism: Mus musculus

source_name: iXist-ChrX-Dom

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) with 10% foetal calf serum (FCS; ThermoFisher), 2 mM L-glutamine, 0.1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 100 U/mL penicillin/ 100 μg/mL streptomycin (all from Life Technologies) and 1000 U/mL LIF made in-house. Cells were grown on gelatin-coated plates under standard cell culture conditions (37oC, 5% CO2, humid) on a ‘feeder’ layer of SNLP mouse fibroblasts mitotically inactivated by Mitomycin-C (Sigma Aldrich). mESCs were routinely passaged at ~80% confluency every 2-3 days using TrypLE Express (ThermoFisher), and were pre-plated off feeders for 30-40 min before experiments. For NPC differentiation, mESCs were first extensively isolated from feeder cells by four rounds of pre-plating, each for 35-40 min. 0.5x106 mESCs were plated to gelatin-coated T25 flasks in N2B27 media (50:50 DMEM/F-12:Neurobasal (Gibco) supplemented with 1X N2 and 1X B27 (ThermoFisher), 1 mM L-glutamine, 100 μM β-mercaptoethanol, 50 U/mL penicillin / 50 μg/mL streptomycin (all from Life Technologies) with 1 μg/ml doxycycline for continuous Xist induction. After 7 days, cells were detached with Accutase (Merck Life Sciences) and 3 x 106 cells were plated to grow in suspension in 90 mm bacterial petri dishes containing N2B27 media supplemented with 1 μg/ml doxycycline and 10 ng/ml EGF and FGF (Peprotech). Embryoid-body-like aggregates were collected by mild centrifugation (100 g for 2 min) on day 10 and re-plated to 90 mm gelatinised cell culture dishes in N2B27 + dox + FGF/EGF media. Upon reaching ~80% confluency, NPC outgrowths were passaged using Accutase at a 1:3 - 1:4 ratio to new cell culture dishes until the establishment of a homogenous cellular population of NPCs from approximately day 17.

extract_protocol:
Chromatin accessibility was assayed by ATAC-seq using a protocol adapted from “Omni-ATAC” (Corces et al. 2017). Briefly, 1-5x106 cells were harvested as pellets, washed with PBS, and nuclei were isolated by incubation for 1 min at room temperature in 600 μl HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H2O, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT). Nuclei were then centrifuged at 1200 g for 5 min at 4oC, followed by three washes with cold RSB buffer (10 mM NaCl, 10 mM Tris pH 7.4, 3 mM MgCl2). After counting, 5x105 nuclei were centrifuged (1500g for 5min at 4oC) and resuspended in 50 μl H2O. 5x104 nuclei (5 μl) were taken for each transposition assay, performed in technical duplicate for each sample in a 50 μl transposition mix of: 1X Tn5 reaction buffer (10 mM TAPS, 5 mM MgCl2, 10% dimethyl- formamide), 0.1% Tween-20 (Sigma), 0.01% Digitonin (Promega), 2.5 μl Tagment DNA TDE1 enzyme (Illumina), 16.5 μl PBS and 5 μl H2O. As controls for transposition and mapping bias, tn5-digested ‘input’ controls were made by performing tagmentation for 50 ng iXist-ChrX genomic DNA by a basic 50 μl transposition mix of 1X TDE buffer and 2.5 μl TDE1 Enzyme (Illumina) in H2O. Both sample and input mixes were incubated at 37oC for 35 minutes in a thermomixer at 1000 rpm, then cleaned-up with ChIP DNA Clean and Concentrator kit (Zymo) and eluted in 14 μl elution buffer for storage at -20oC.
ATAC-seq libraries were prepared by ∼8 cycles of PCR using NEBNext High Fidelity 2X PCR Master Mix (NEB) and primers containing Illumina barcodes (Buenrostro et al. 2013). Libraries were purified and size selected using Agencourt AMPure XP bead clean-up (Beckman Coulter) to ensure a size distribution containing mono-, di- and tri-nucleosomal fragments between 150-800bp.
2x79bp paired-end

treatment_protocol: Xist expression from the TetOn promoter was induced by addition of 1  µg/ml doxycycline (Sigma, D9891) to the culture medium.

tag: xist (dox)_induction

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

value: mESC to NPC intermediate

tag: strain

value: Dom/129S x Cast

tag: Sex

value: Female


title: ATAC_iXist-ChrX-Dom_SmA3_NPC_d15

value: Neural progenitor cell (NPC)


title: residual primary mammary tumor, post-treatment, Patient44

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

country: Belgium

institute: CHU Liege

library_source: transcriptomic

data_processing:
The CLC Genomics v22 software (Qiagen) is used to remove low-quality reads from raw NGS sequences, perform trimming and mapping to the Homo sapiens genome hg38 and the RNA database v91
Supplementary files format and content: the processed datafile is containing the raw counts of reads. The colums are Gene Names, Chromosomes, coordinates, ensembl identifiers, and raw counts for each of the 122 libraries

molecule: total RNA

organism: Homo sapiens

source_name: mammary tumor

extract_protocol:
deparaffinization and extraction steps were carried out using the AllPrep DNA/RNA FFPE kit (#80234, Qiagen), according to manufacturer’s recommendations and DNA was removed from the samples with the TURBO DNA-free™ kit (#AM1907, Thermo Fisher Scientific), by following manufacturer’s instructions. Total RNA samples were then quantified by using Quant-it™ RiboGreen RNA Assay kit (#R11490, Thermo Fisher Scientific
ribosomal RNA depletion were performed with the NEBNext rRNA Depletion kit (Human/Mouse/Rat) with sample purification beads (#E6350, New England Biolabs). Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep with Beads kit (#E7765, New England Biolabs). Adaptors and primers used for the library preparation were from NEBNext Multiplex Oligos for Illumina (Dual Index Set 1), 96 rxns (#E7760, New England Biolabs). The quality of the libraries was evaluated using High Sensitivity DNA kit (chips and reagents) (#5067 and #4626, Agilent) with a 2100 Bioanalyzer system (Agilent). Sequence reads were generated on the Illumina NovaSeq 6000 sequencer, on an S4 cartridge (300 bp). RNA sequencing was performed in 3 distinct batches
bulk stranded total RNA sequencing after depletion of rRNA. Paired-end, 2 x 150bp.

treatment_protocol: Formalin-fixed paraffin-embedded slides from diagnostic biopsies were cut with a depth of 4 µm. Delimitation of the tumoral zone was done by the pathologist after HE staining on one slide, and reported on the other slides. On average, the tumoral zones of 15-20 slides were scratched.

value: mammary tumor

value: post-surgery

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

tag: rcb category

tag: unifocal

value: no

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Right ventricle, no treatment, replicate 3

city: Toronto

first: Michael

middle: Bradley

last: Dewar

state: Ontario

address: 661 University Avenue

department: Physiology

country: Canada

institute: University of Toronto

data_processing:
Merge files from different sequencing lanes using "zcat" function in linux terminal
Trim adapators using the Cutadapt software in paired-end mode
Obtain transcript abundance using Kallisto software. Bootstraps were set to 100
Assembly: mm10
Supplementary files format and content: Abundance.tsv files: Matrix of abundance data in tsv format. Rows are transcript names, columns are transcript length, effective length, estimated counts, and TPM.
Supplementary files format and content: Abundance.h5 files: Matrix of abundance data in HDF5 format. Rows are transcript names, columns are transcript length, effective length, estimated counts, and TPM.

molecule: polyA RNA

source_name: Heart

growth_protocol: Mice were housed in a pathogen-free environment at the University of Toronto’s Division of Comparative Medicine Animal Facility, and had ad libitum access to water and standard rodent chow.

extract_protocol:
Following excision of the mouse heart, the atria and atrioventricular valves were surgically removed. We then dissected the left and right ventricle free walls, and washed the tissue in chilled DPBS. Remaining septal tissue was discarded. LV and RV tissue samples were then minced and digested in a solution of 2 mg/ml Collagenase type II (Worthington Cat#: LS004176) and 2 mg/ml Dispase II (Sigma Cat#: D4693) at 37°C for 45 minutes. Trituration was performed with a 10mL serological pipette at the 15, 30, and with a 1 mL pipette at the 45 minute mark. Samples were then filtered through 70 µm strainers into 30mL of chilled DPBS, split into two 15mL Eppendorf tubes, and centrifuged for 7 min at 500g. . After decanting, pellets were resuspended in 100uL of Hank’s Balanced Salt Solution (HBSS containing 2% FBS, and incubated with CD31 and CD45 magnetic beads for 15 minutes. Endothelial (CD31+) and hematopoietic cells (CD45+) were subsequently removed using the AutoMacs instrument (Miltenyi Biotec). The remaining cells were stained with DAPI, and live CFs (GFP+, DAPINeg) were sorted on the Aria IIu (BD Biosciences) into HBSS containing 2% FBS. RNA was then isolated using the RNeasy Micro Kit (Qiagen, Cat.#: 74004) according to manufacturer's instructions and stored at -80°C until library construction.
RNA samples were assessed on a RNA 6000 Pico chip (Agilent Technologies) to determine sample quality. Seven nanograms of total RNA per sample was used to prepare RNA libraries using the SMARTer Stranded Total RNA-seq Kit V3– Pico Input Mammalian (Takara Bio USA Inc.). Briefly, the samples underwent first-strand synthesis via random priming oligos on the 3’ end. A template switching oligo mix (TSO) is then incorporated to allow the RT reaction to continue replicating the 5’ of the RNA strand. Following this, the samples were PCR amplified to incorporate full-length Illumina adapters and sample barcodes by binding to either the TSO stretch on the 5’ end, or the random priming oligo sequence on the 3’ end. The amplified cDNA is treated with ZapR which specifically targets ribosomal RNA in the presence of mammalian-specific R-Probes. This process leaves non-ribosomal RNA untouched, while ribosomal RNA are cleaved, leaving them non-amplifiable. A final PCR reaction is done to enrich the uncut strands of cDNA to generate the final RNA library. Final RNA library sizing was verified on High sensitivity DNA kit (Agilent Technologies) using the Agilent Bioanalyzer while library concentration was quantified by qPCR using the KAPA SYBR FAST qPCR kit (Roche). All libraries were normalized and pooled together, denatured with 0.2N NaOH and diluted to a final concentration of 250 pM.  Pooled libraries were loaded onto an Illumina Novaseq V1.5 cartridge for cluster generation and sequencing on an Illumina Novaseq 6000 instrument (Illumina) Paired-end 101 bp protocol to achieve  ~ 40 million reads per sample.

treatment_protocol: Mice did not receive any treatments before tissue extraction

tag: tissue

value: Heart

tag: tissue region

value: Right ventricle

value: Cardiac fibroblasts

tag: genotype

value: Male


title: Right ventricle, no treatment, replicate 1

tag: cell type


title: ATAC_iXist-ChrX-Dom_SmA3_ES_d0

tag: xist (dox)_induction

value: No dox

tag: cell line

value: Mouse embryonic stem cell (mESC)

tag: strain

tag: Sex


title: Right ventricle, no treatment, replicate 4


title: Right ventricle, no treatment, replicate 2


title: ATAC_iXist-ChrX-Dom_SmA3_NPC_d3

value: iXist-ChrX-Dom


title: Mouse Liver Nuclei (ATAC-seq)

city: Leipzig

first: Volker

last: Soltys

address: Deutscher Platz 6

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

description: easySHARE-seq

data_processing:
*library strategy: easySHARE-seq
All fastq files were demultiplexed using a custom C-script.
Reads were trimmed using cutadapt.
Reads were aligned to mm10 using bwa or STAR
Dupicate reads were removed using Picard Tools
Reads were filtered for MAPQ > 30 or uniquely mapping
Assembly: mm10 or hg38
Supplementary files format and content: Counts Data is indexed by genes (row), cell (column)
Supplementary files format and content: Fragment data contains fragment position (1-3 column), and assigned cell barcode (4th column) and count 95th column)

source_name: liver

growth_protocol: HEK Cells were cultured in media containing DMEM/F-12 with GlutaMAX™ Supplement, 10% FBS and 1% Pen/Strep at 37°C. Cells were harvested on the day of the experiment by simply pipetting them off the plate and were then spun down for 5 min at 250G. OP9-DL4 cells were cultured in alpha-MEM medium containing 5% FBS and 1% PenStrep. On the day of the experiment, the cells were harvested by aspirating the media and adding 5 ml of Trypsin, followed by an incubation at 37°C for 5 min. Then, 5ml of media was added and cells were spun down for 5 min at 25G.

extract_protocol: The Liver was extracted, rinsed in HBSS, cut into smaller pieces, frozen in liquid nitrogen and stored in the freezer at -80°C for a maximum of two weeks. On the day of the experiment, 1 ml of ice cold Lysis Solution (0.1% Triton-X 100, 1mM DTT, 10mMM Tris-HCl pH8, 0.1mM EDTA, 3mM Mg(Ac)2, 3mM CaCl2 and 0.32M Sucrose) was added to the tube. Everything was transferred to a pre-cooled Douncer and dounced 10x using Pestle A and 15x using Pestle B. The solution was added to a thick wall Ultracentrifuge Tube on ice and topped up with 4ml ice cold Lysis Solution. Then 9 ml of Sucrose solution (10mM Tris-HCl pH8.0, 3mM Mg(Ac)2, 3mM DTT, 1.8M Sucrose) was carefully pipetted to the bottom of the tube to create a sucrose cussion. Samples were spun in a pre-cooled Ultracentrifuge with a SW-28 rotor at 24.400rpm for 1.5 hours at 4°C. Afterwards, all supernatant was carefully aspirated so as not to dislodge the pellet at the bottom and 1 ml ice cold DEPC-treated water supplemented with 10µl SUPERase & 15µl Recombinant RNase Inhibitor was added. Without resuspending, the tube was kept on ice for 20 min. The pellet was then resuspended by pipetting ~15 times slowly up and down followed by a 40µm cell straining step.

value: liver


title: Mouse Liver Nuclei (RNA-seq)

description: easySHARE-seq


title: ATAC_iXist-ChrX-Dom_WT_NPC_d15

value: Dom/129S x Cast


title: ATAC_iXist-ChrX-Cast_WT_ES_d0

value: Female


title: residual primary mammary tumor, post-treatment, Patient43

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: extensive residual disease

tag: grade

tag: node invasion

value: yes

tag: nac category

tag: nac herceptin_binary

value: Nolvadex


title: ATAC_iXist-ChrX-Cast_WT_NPC_d15

value: Neural progenitor cell (NPC)


title: residual primary mammary tumor, post-treatment, Patient50

tag: tissue

value: mammary tumor

value: post-surgery

value: female

tag: rcb category

value: moderate residual disease

tag: unifocal

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Left ventricle, no treatment, replicate 5

value: Heart

tag: tissue region

value: Left ventricle

tag: cell type

tag: genotype

tag: Sex


title: ATAC_iXist-ChrX-Cast_SmD5_ES_d0

tag: xist (dox)_induction

tag: cell line

tag: strain


title: primary mammary tumor, pre-treatment, Patient41

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

value: no residual disease

tag: grade

tag: node invasion

value: no

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary


title: ATAC_iXist-ChrX-Dom_WT_NPC_d3

value: iXist-ChrX-Dom

value: mESC to NPC intermediate

value: Dom/129S x Cast


title: ATAC_iXist-ChrX-Dom_WT_NPC_d5

value: Female


title: residual primary mammary tumor, post-treatment, Patient89

tag: tissue

value: yes

tag: rcb category

tag: unifocal

value: others

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: residual primary mammary tumor, post-treatment, Patient39

value: mammary tumor

tag: timing biopsies

tag: patient id

tag: Sex

value: Luminal B

value: Nolvadex


title: Left ventricle, no treatment, replicate 4

tag: tissue region

tag: cell type

value: Cardiac fibroblasts

tag: genotype

value: Male


title: Left ventricle, no treatment, replicate 3

value: Heart

value: Left ventricle


title: ATAC_iXist-ChrX-Dom_WT_ES_d0

tag: xist (dox)_induction

value: No dox

tag: cell line

value: Mouse embryonic stem cell (mESC)

tag: strain


title: ATAC_iXist-ChrX-Dom_SmA3_NPC_d5


title: YY1_ChIP_iXist-ChrX-Cast_ES_d6_Rep2

data_processing:
Paired-end fastq files were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Bigwig files of pileup tracks were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
Peaks were called from the four samples (2 x d0, 2 x d6) individually with MACS2 “-f BAMPE -g mm -q 0.01”, and regions where two or more peaks overlap were retained as the consensus peak set. A consensus from peaks called in the four input samples (by MACS2 “-f BAMPE -g mm --broad --broad-cutoff 0.01”) was also generated and subtracted from the consensus OCT4 peaks.
Assembly: mm10
Supplementary files format and content: Bigwig files of YY1 ChIP-seq (total and allele-specific) and inputs
Supplementary files format and content: Tables of allelic ratios for ChrX YY1 peaks at d0 and d6 Xist expression

source_name: iXist-ChrX-Cast

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) with 10% foetal calf serum (FCS; ThermoFisher), 2 mM L-glutamine, 0.1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 100 U/mL penicillin/ 100 μg/mL streptomycin (all from Life Technologies) and 1000 U/mL LIF made in-house. Cells were grown on gelatin-coated plates under standard cell culture conditions (37oC, 5% CO2, humid) on a ‘feeder’ layer of SNLP mouse fibroblasts mitotically inactivated by Mitomycin-C (Sigma Aldrich). mESCs were routinely passaged at ~80% confluency every 2-3 days using TrypLE Express (ThermoFisher). Before experiments, feeder cells were removed by pre-plating to gelatinised cell culture dishes for 30-40 min, with slower-attaching mESCs taken from suspension and plated to new gelatinised dishes.

extract_protocol:
5x107 mESCs were collected from confluent 150mm dishes, washed once with PBS and pelleted by centrifugation at 400g for 4 min. Cell pellets were resuspended for double-crosslinking in 10 ml 2 mM disuccinimidyl glutarate (DSG) followed by addition of 1% formaldehyde and a further 12 min of incubation with mild rotation (at room temperature). Crosslinking was quenched by addition of glycine to a final concentration of 135 μM and pellets were centrifuged (400g for 4 min at 4oC) and washed once with cold PBS. Nuclei and chromatin extraction was then performed by sequential rounds of pellet resuspension, rotation at 4oC for 10 min, and centrifugation (400g for 4 min at 4oC) with LB1, LB2 and LB3 buffers: LB1 - 50 mM HEPES pH7.9. 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.05% NP40 (IGEPAL CA630), 0.25% Triton X-100; LB2 - 10 mM Tris HCl pH8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; LB3 - 10 mM Tris HCl (pH8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with freshly-added 0.1% sodium deoxycholate (Sigma) and 0.5% N-lauroylsarcosine (Sigma) (all buffers with freshly-added PIC). Crosslinked chromatin resuspended in 1 ml LB3 was then sonicated using a BioRuptor Pico (Diagenode) for 30 cycles of 30 seconds on/off. 110 μl LB3 + 10% Triton X-100 (pre-warmed to 50oC to help Triton dissolve) was added to 1 ml sonicated chromatin and mixed well by inversion. Max centrifugation (16,000g for 10 min at 4oC) cleared debris to leave a chromatin supernatant. For immunoprecipitation, ∼150 μg of chromatin per IP (∼100 μl of 1ml) was diluted to 1.1ml in ChIP-dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl). Protein A agarose beads (ThermoFisher) pre-blocked for 1 hour with 0.2 mg/ml BSA and 50 μg/ml yeast tRNA were added to diluted chromatin (40μl per 1ml) and incubated for 30-60 min with rotation at 4oC. Beads were pelleted by centrifugation (1000g 4 min at 4oC) and pre-cleared supernatant chromatin was taken to new tubes for immunoprecipitation. Chromatin samples were then incubated overnight with anti-OCT4A antibody (C3OA3C1 rabbit mAb, Cell Signaling) rotating at 4oC, before blocked Protein A agarose beads were again added and samples were places on a rotator for 1 hour at 4oC to bind antibody-bound chromatin fragments to beads. Agarose beads were then washed with low salt buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8, 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH8) and two washes with TE buffer (10 mM Tris-HCl pH8, 1 mM EDTA), with each ChIP wash consisting of rotation of beads for 3 minutes at 4oC followed by centrifugation of beads at 1000g for 2 min at 4oC. After the washes, chromatin was eluted from beads for 30 min by rotation at room temperature in 150μl fresh elution buffer (1% SDS, 0.1 M NaHCO3), followed by reverse crosslinking by addition of 1.2 μl 5M NaCl and shaking incubation (1100 rpm) at 65oC for 4 h, followed by treatment with RNaseA (1.2 μl of 1 mg/ml then shaking at 42oC for 1 h) and ProteinaseK (1.2 μl of 20 mg/ml then shaking at 45oC for 1 h) and DNA purification with ChIP DNA Clean and Concentrator kit (Zymo).
1-5ng of ChIP DNA was taken for Illumina sequencing library preparation using the NEBNext Ultra II DNA Library Prep Kit with NEBNext Single indices (E7645) with 14 cycles of PCR amplification with the 65oC elongation step reduced to 30 seconds.
2x81bp paired-end

value: iXist-ChrX-Cast

tag: chip antibody

value: anti-YY1 D5D9Z (CST rabbit mAb)


title: YY1_ChIP_iXist-ChrX-Cast_ES_d0_Rep2


title: residual primary mammary tumor, post-treatment, Patient37

tag: tissue

value: post-surgery

value: female

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal A

tag: rcb category

value: extensive residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: no

value: Nolvadex then arimidex


title: Left ventricle, no treatment, replicate 2

tag: tissue region

tag: Sex


title: YY1_ChIP_iXist-ChrX-Cast_ES_d0_Rep1

tag: cell type

value: Dom/129S x Cast

value: Female


title: ATAC_iXist-ChrX-Dom_WT_NPC_d7

tag: xist (dox)_induction

value: iXist-ChrX-Dom

value: mESC to NPC intermediate


title: YY1_ChIP_iXist-ChrX-Cast_ES_d6_Rep1

tag: cell line


title: Sorted_tdTomato_positive_tumor_cells_replicate4 [tdT.d9639]

city: Cambridge

first: Norihiro

last: Goto

state: MA

address: 500 Main Street, Building 76

department: Department of Biology

country: USA

institute: Massachusetts Institute of Technology

data_processing:
Paired-end RNA-seq data were mapped to the UCSC mm10 mouse genome build using Salmon
Assembly: mm10
Supplementary files format and content: ngoto_230707Yil_intCt.txt.gz is a tab delimited text of count data

source_name: Colon cancer

extract_protocol:
Ambion PureLink RNA Mini Kit
NEBNext Ultra II Directional RNA preparation with poly(A) selection

value: Colon cancer

tag: mice with_tumors

tag: genotype

value: AKP


title: Left ventricle, no treatment, replicate 1

tag: tissue

value: Heart

value: Left ventricle

value: Cardiac fibroblasts

value: Male


title: residual primary mammary tumor, post-treatment, Patient31

value: mammary tumor

tag: timing biopsies

value: post-surgery

tag: patient id

tag: age diagnostic

value: yes

value: Luminal B

value: moderate residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Sorted_tdTomato_positive_tumor_cells_replicate3 [tdT.d9638]


title: residual primary mammary tumor, post-treatment, Patient30

value: female

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: Nolvadex


title: Sorted_tdTomato_positive_tumor_cells_replicate1 [tdT.d9636]

tag: cell type

tag: mice with_tumors

tag: genotype


title: Succinate 4h LPS treated monocyte rep2

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

country: China

institute: xiamen university

data_processing:
Sequence reads trimmed for adaptor sequence/low-quality using trim_galore
Mapping genome by  mm10
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each samples

source_name: Bone marrow monocyte

extract_protocol:
Total RNA was extracted by Trizol method
RNA libraries for RNA-seq were prepared using protocols of Novogene company

treatment_protocol: Mice were treated with or without 300 mM succinate for 7 days, and CD11b+Ly6Chi monocytes from bone marrow were sorted, then stimulated in presence or absence of LPS in vitro.

value: Bone marrow monocyte

tag: treatment

value: Succinate LPS


title: Autochthonous_AKPVT_tumor_replicate7 [AKPVT5.d9635]

value: Colon cancer

value: AKPVT


title: Succinate 4h LPS treated monocyte rep3


title: residual primary mammary tumor, post-treatment, Patient29

tag: tissue

tag: timing biopsies

tag: patient id

tag: Sex

tag: age diagnostic

value: TNBC

tag: breast conservative_surgery

tag: sentinel lymph_node


title: Autochthonous_AKPVT_tumor_replicate6 [AKPVT5.d9634]

value: AKP


title: Succinate 4h LPS treated monocyte rep1


title: residual primary mammary tumor, post-treatment, Patient28

tag: statut menopausal

tag: molecular category

tag: rcb category

value: extensive residual disease

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Autochthonous_AKPVT_tumor_replicate5 [AKPVT5.d9633]

tag: cell type

tag: mice with_tumors


title: Control 4h LPS treated monocyte rep3

tag: treatment

value: Control LPS


title: residual primary mammary tumor, post-treatment, Patient27

tag: tissue

value: mammary tumor

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary


title: Autochthonous_AKPVT_tumor_replicate3 [AKPVT3.d9631]

tag: genotype


title: Autochthonous_AKPVT_tumor_replicate2 [AKPVT3.d9630]


title: Control 4h LPS treated monocyte rep2


title: residual primary mammary tumor, post-treatment, Patient38

tag: timing biopsies

value: post-surgery

tag: patient id

tag: Sex

tag: age diagnostic

tag: statut menopausal

tag: breast conservative_surgery

tag: sentinel lymph_node

value: Nolvadex then arimidex


title: residual primary mammary tumor, post-treatment, Patient23

value: yes

tag: molecular category

value: Luminal B

tag: rcb category

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Femara

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Autochthonous_AKPVT_tumor_replicate1 [AKPVT3.d9629]

tag: cell type

tag: mice with_tumors


title: Normal_colonic_crypt_replicate4 [Crypt.d9628]

source_name: Normal colonic epithelia

value: Normal colonic epithelia

value: WT


title: Sorted_tdTomato_positive_tumor_cells_replicate2 [tdT.d9637]


title: Normal_colonic_crypt_replicate3 [Crypt.d9627]


title: Control 4h LPS treated monocyte rep1

tag: treatment


title: residual primary mammary tumor, post-treatment, Patient22

tag: tissue

value: female

value: no

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: Nolvadex


title: Normal_colonic_crypt_replicate2 [Crypt.d9626]

tag: genotype


title: Succinate unstimulated monocyte rep3

value: Bone marrow monocyte

value: Succinate


title: residual primary mammary tumor, post-treatment, Patient20

tag: timing biopsies

tag: patient id

tag: Sex

tag: age diagnostic

tag: statut menopausal

value: moderate residual disease

value: taxanes alone

tag: breast conservative_surgery

tag: sentinel lymph_node


title: Bulk_AKP_tumor_replicate6 [AKPtumor.d9624]

tag: cell type

value: Colon cancer

value: AKP


title: Succinate unstimulated monocyte rep2


title: Bulk_AKP_tumor_replicate5 [AKPtumor.d9623]

tag: mice with_tumors


title: Succinate unstimulated monocyte rep1

tag: treatment


title: Bulk_AKP_tumor_replicate3 [AKPtumor.d9621]


title: Autochthonous_AKPVT_tumor_replicate4 [AKPVT3.d9632]

value: AKPVT


title: Bulk_AKP_tumor_replicate2 [AKPtumor.d9620]


title: residual primary mammary tumor, post-treatment, Patient13

tag: tissue

value: mammary tumor

value: post-surgery

tag: molecular category

value: TNBC

tag: rcb category

value: minimal residual disease

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: residual primary mammary tumor, post-treatment, Patient14

tag: timing biopsies

value: yes

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

value: Femara


title: Bulk_AKP_tumor_replicate4 [AKPtumor.d9622]

tag: genotype


title: Naïve_AKP_organoid_replicate2 [Naive.d9617]

source_name: Colon cancer organoids

tag: cell type

value: Colon cancer organoids


title: residual primary mammary tumor, post-treatment, Patient11

tag: patient id

tag: Sex

value: female

tag: age diagnostic

tag: statut menopausal

value: no

value: extensive residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node


title: Naïve_AKP_organoid_replicate3 [Naive.d9618]

tag: mice with_tumors


title: Control unstimulated monocyte rep3

value: Bone marrow monocyte

tag: treatment

value: Control


title: residual primary mammary tumor, post-treatment, Patient12

tag: tissue

tag: molecular category

value: Luminal A

tag: rcb category

value: moderate residual disease

value: anthracyclines and taxanes

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Naïve_AKP_organoid_replicate1 [Naive.d9616]

tag: genotype

value: AKP


title: Control unstimulated monocyte rep2

tag: cell type


title: 2wk_SOX17KO

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger version 6.0.1
Assembly: mm10

source_name: colon

extract_protocol:
Colon tumours were collected under the fluorescent microscope, minced using surgical scissors, and digested in a digestion buffer containing 500 U/ml Collagenase Type 1 and 20 μg/ml DNase at 37 °C for 40 min with gentle agitation. Tumours were then further dissociated with a gentleMACS Octo Dissociator on the tumour_imp1.1 setting, filtered through a 100-μM filter, and centrifuged for 5 min at 2000 rpm. 7-AAD-negative EpCAM-negative CD45-positive cells were sorted using FACS Aria II.
10x Genomics Single Cell 3' v3

value: colon

value: CD45+ cells


title: Normal_colonic_crypt_replicate1 [Crypt.d9625]

value: Normal colonic epithelia

value: WT


title: 2wk_Control

description: 10x Genomics


title: residual primary mammary tumor, post-treatment, Patient6

value: mammary tumor

tag: timing biopsies

value: post-surgery

tag: patient id

value: yes

value: minimal residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary


title: Right ventricle, female, sham PAB surgery, 14dpi

data_processing:
Merge files from different sequencing lanes using "zcat" function in linux terminal
Paired-end samples were alligned using Cellranger v6.0 (10X-Genomics) with default parameters
Assembly: mm10
Supplementary files format and content: Matrix file: A data matrix containing the number of UMIs associated with each feature (row) and barcode (column).
Supplementary files format and content: Features file: List of features making up the row names for the matrix file
Supplementary files format and content: Barcodes file: List of barcodes making up the column names for the matrix file

extract_protocol:
Following excision of the mouse heart, the atria and atrioventricular valves were surgically removed. We then dissected the left and right ventricle free walls, and washed the tissue in chilled DPBS. Remaining septal tissue was discarded. LV and RV tissue samples were then minced and digested in a solution of 2 mg/ml Collagenase type II (Worthington Cat#: LS004176) and 2 mg/ml Dispase II (Sigma Cat#: D4693) at 37°C for 45 minutes. Trituration was performed with a 10mL serological pipette at the 15, 30, and with a 1 mL pipette at the 45 minute mark. Samples were then filtered through 70 µm strainers into 30mL of chilled DPBS, split into two 15mL Eppendorf tubes, and centrifuged for 7 min at 500g. . After decanting, pellets were resuspended in 100uL of Hank’s Balanced Salt Solution (HBSS containing 2% FBS, and incubated with CD31 and CD45 magnetic beads for 15 minutes. Endothelial (CD31+) and hematopoietic cells (CD45+) were subsequently removed using the AutoMacs instrument (Miltenyi Biotec). The remaining cells were stained with DAPI, and live CFs (GFP+, DAPINeg) were sorted on the Aria IIu (BD Biosciences) into HBSS containing 2% FBS for preparation for scRNA-seq.
FACS-isolated CFs were manually counted using a hemocytometer before single-cell library preparation using the 10x Genomics Chromium system. Library preparation and sequencing were performed at The Centre for Applied Genomics at the Peter Gilgan Centre for Research and Learning. Approximately 10,000 cells were loaded on the 10X Genomics Chromium Controller instrument to generate single-cell GEMs (gel beads in emulsion) using the Chromium Single Cell 3ʹ Reagent Kits v3 kit (part -1000092, 10X Genomics, Pleasanton, CA) following the manufacturer’s instructions.  Briefly, barcoded full-length cDNA is first produced from poly-adenylated mRNA.  cDNA is then fragmented and made into Illumina-ready libraries.  The final libraries contain a 10X barcode, UMI, sample index and Illumina P5 and P7 sequences.  Size, quality and concentration of the cDNA and corresponding 10X library were evaluated by the Agilent 2100 Bioanalyzer system and quantified using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).   Libraries were sequenced on the Illumina NovaSeq6000 instrument on the S4 flowcell using 29+8+101 sequencing configuration to generate 500M reads of data per sample.

value: Heart

tag: tissue region

value: Right ventricle

value: Cardiac fibroblasts

tag: treatment

value: Sham PAB surgery

tag: time

value: 14 days post-surgery

tag: Sex

value: Female


title: Bulk_AKP_tumor_replicate1 [AKPtumor.d9619]

value: Colon cancer

tag: mice with_tumors


title: 1wk_SOX17KO

description: 10x Genomics

tag: tissue


title: Right ventricle, female, PAB surgery, 14dpi

value: PAB surgery


title: residual primary mammary tumor, post-treatment, Patient3

value: female

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

value: Luminal B

tag: rcb category

value: moderate residual disease

value: anthracyclin alone

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Arimidex

tag: sequencing batch


title: OCT4_ChIP_iXist-ChrX-Cast_ES_d6_Rep2

data_processing:
2x81bp paired-end
Paired-end fastq files were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Bigwig files of pileup tracks were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
Peaks were called from the four samples (2 x d0, 2 x d6) individually with MACS2 “-f BAMPE -g mm -q 0.01”, and regions where two or more peaks overlap were retained as the consensus peak set. A consensus from peaks called in the four input samples (by MACS2 “-f BAMPE -g mm --broad --broad-cutoff 0.01”) was also generated and subtracted from the consensus OCT4 peaks.
mm10
Supplementary files format and content: Consensus OCT4 peaks and input peaks (likely mapping artifacts) in iXist-ChrX-Cast mESCs (bed)
Supplementary files format and content: Bigwig files of OCT4 ChIP-seq (total and allele-specific) and inputs
Supplementary files format and content: Tables of allelic ratios for ChrX OCT4 peaks at d0 and d6 Xist expression

extract_protocol:
5x107 mESCs were collected from confluent 150mm dishes, washed once with PBS and pelleted by centrifugation at 400g for 4 min. Cell pellets were resuspended for double-crosslinking in 10 ml 2 mM disuccinimidyl glutarate (DSG) followed by addition of 1% formaldehyde and a further 12 min of incubation with mild rotation (at room temperature). Crosslinking was quenched by addition of glycine to a final concentration of 135 μM and pellets were centrifuged (400g for 4 min at 4oC) and washed once with cold PBS. Nuclei and chromatin extraction was then performed by sequential rounds of pellet resuspension, rotation at 4oC for 10 min, and centrifugation (400g for 4 min at 4oC) with LB1, LB2 and LB3 buffers: LB1 - 50 mM HEPES pH7.9. 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.05% NP40 (IGEPAL CA630), 0.25% Triton X-100; LB2 - 10 mM Tris HCl pH8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA; LB3 - 10 mM Tris HCl (pH8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with freshly-added 0.1% sodium deoxycholate (Sigma) and 0.5% N-lauroylsarcosine (Sigma) (all buffers with freshly-added PIC). Crosslinked chromatin resuspended in 1 ml LB3 was then sonicated using a BioRuptor Pico (Diagenode) for 30 cycles of 30 seconds on/off. 110 μl LB3 + 10% Triton X-100 (pre-warmed to 50oC to help Triton dissolve) was added to 1 ml sonicated chromatin and mixed well by inversion. Max centrifugation (16,000g for 10 min at 4oC) cleared debris to leave a chromatin supernatant. For immunoprecipitation, ∼150 μg of chromatin per IP (∼100 μl of 1ml) was diluted to 1.1ml in ChIP-dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl). Protein A agarose beads (ThermoFisher) pre-blocked for 1 hour with 0.2 mg/ml BSA and 50 μg/ml yeast tRNA were added to diluted chromatin (40μl per 1ml) and incubated for 30-60 min with rotation at 4oC. Beads were pelleted by centrifugation (1000g 4 min at 4oC) and pre-cleared supernatant chromatin was taken to new tubes for immunoprecipitation. Chromatin samples were then incubated overnight with anti-OCT4A antibody (C3OA3C1 rabbit mAb, Cell Signaling) rotating at 4oC, before blocked Protein A agarose beads were again added and samples were places on a rotator for 1 hour at 4oC to bind antibody-bound chromatin fragments to beads. Agarose beads were then washed with low salt buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8, 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH8) and two washes with TE buffer (10 mM Tris-HCl pH8, 1 mM EDTA), with each ChIP wash consisting of rotation of beads for 3 minutes at 4oC followed by centrifugation of beads at 1000g for 2 min at 4oC. After the washes, chromatin was eluted from beads for 30 min by rotation at room temperature in 150μl fresh elution buffer (1% SDS, 0.1 M NaHCO3), followed by reverse crosslinking by addition of 1.2 μl 5M NaCl and shaking incubation (1100 rpm) at 65oC for 4 h, followed by treatment with RNaseA (1.2 μl of 1 mg/ml then shaking at 42oC for 1 h) and ProteinaseK (1.2 μl of 20 mg/ml then shaking at 45oC for 1 h) and DNA purification with ChIP DNA Clean and Concentrator kit (Zymo).
1-5ng of ChIP DNA was taken for Illumina sequencing library preparation using the NEBNext Ultra II DNA Library Prep Kit with NEBNext Single indices (E7645) with 14 cycles of PCR amplification with the 65oC elongation step reduced to 30 seconds.

tag: xist (dox)_induction

tag: cell line

value: iXist-ChrX-Cast

tag: cell type

value: Mouse embryonic stem cell (mESC)

tag: strain

value: Dom/129S x Cast

tag: chip antibody

value: anti-OCT4A C3OA3C1 (CST rabbit mAb)


title: ChIPinput_iXist-ChrX-Cast_ES_d0_Rep2

value: No dox

tag: Sex


title: residual primary mammary tumor, post-treatment, Patient1

value: mammary tumor

tag: timing biopsies

value: post-surgery

tag: patient id

value: yes

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: Femara

tag: mapped to_intergenic_(%_reads)


title: OCT4_ChIP_iXist-ChrX-Cast_ES_d6_Rep1

value: Female


title: Control unstimulated monocyte rep1

value: Bone marrow monocyte

tag: treatment

value: Control


title: ChIPinput_iXist-ChrX-Cast_ES_d0_Rep1


title: OCT4_ChIP_iXist-ChrX-Cast_ES_d0_Rep1


title: residual primary mammary tumor, post-treatment, Patient2

tag: tissue

value: female

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

value: TNBC

tag: rcb category

value: extensive residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category


title: primary mammary tumor, pre-treatment, Patient40

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: Sex

value: Luminal B

value: moderate residual disease

tag: sequencing batch


title: primary mammary tumor, pre-treatment, Patient39

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: Nolvadex


title: Left ventricle, female, TAC surgery, 14dpi

tag: tissue

value: Heart

tag: tissue region

value: Left ventricle

tag: cell type

value: Cardiac fibroblasts

tag: genotype

tag: treatment

value: TAC surgery

tag: time

value: 14 days post-surgery


title: Right ventricle, male, PAB surgery, 14dpi

value: Right ventricle

value: PAB surgery

value: Male


title: Right ventricle, male, sham PAB surgery, 14dpi

value: Sham PAB surgery


title: HSCs_Dis3KO, replicate1

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

country: Japan

institute: Kumamoto University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim galore version: 0.6.6.
Trimmed sequence reads were mapped to mm10 using STAR 2.7.8a.
Read count extraction and normalization were performed using RSEM v1.3.3.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Hematopoietic stem cells

extract_protocol:
RamDA-seq was performed using 100 cells. Briefly, hematopoietic stem cells (100 cells) were directly sorted into the cell lysis buffer (10 U RNasein plus, 10% Roche Cell Lysis Buffer, 0.3% NP40, and RNase-free water) in a 96-well PCR plate.The cell lysates were then denatured and treated with genomic DNA digestion mix containing DNaseI. Firrst strand  cDNA was then synthesized with first not-so randam primers using PrimeScript RT reagent kit (Takara Bio), followed by second strand dDNA synthesis with second not-so random primers using Klenow Fragment (New England Biolabs).
Sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Total bone marrow cells (5×10^6 cells) isolated from Dis3fl/fl or Dis3fl/fl;Mx-Cre mice were transplanted into lethally irradiated CD45.1 recipient mice. Four weeks after transplantation, Cre recombinase was induced by intraperitoneal injections of 300 μg of pIpC on days 0 and 2. On day 4, hematopoietic stem cells were isolated from the bone marrow from these mice using the L-ESLAM (Lineage-EPCR+CD150+CD48-) definition.

value: Hematopoietic stem cells

tag: strain


title: HSCs_Dis3KO, replicate2


title: 1wk_Control

description: 10x Genomics

value: colon

value: CD45+ cells


title: HSCs_WT, replicate2

value: wild type


title: primary mammary tumor, pre-treatment, Patient38

value: mammary tumor

value: pre-surgery

value: female

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

value: extensive residual disease

value: no

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Nolvadex then arimidex

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient37

tag: timing biopsies

tag: patient id

tag: Sex

value: Luminal A

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: hormonotherapy type_category

tag: sequencing batch


title: Left ventricle, female, sham TAC surgery, 14dpi

tag: tissue

value: Heart

tag: tissue region

value: Left ventricle

tag: cell type

value: Cardiac fibroblasts

tag: genotype

tag: treatment

value: Sham TAC surgery

tag: time

value: 14 days post-surgery

value: Female


title: HSCs_WT, replicate1

value: Hematopoietic stem cells

tag: strain


title: Left ventricle, male, TAC surgery, 14dpi

value: TAC surgery

value: Male


title: YY1ab_ChIP_iXist-ChrX-Cast_ES_d0_Rep2

data_processing:
Paired-end fastq files were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Bigwig files of pileup tracks were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
Peaks were called from the four samples (2 x iXist-ChrX-Dom, 2 x iXist-ChrX-Cast) individually with MACS2 “-f BAMPE -g mm -q 0.01”, and regions where two or more peaks overlap were retained as the consensus peak set. A consensus from peaks called in the four input samples (by MACS2 “-f BAMPE -g mm --broad --broad-cutoff 0.01”) was also generated and subtracted from the consensus YY1 peaks.
Peaks were also annotated with a YY1 “enrichment score” in mESCs using all four samples as replicates for the “cov” command from the BAMscale tool (Ponger et al., 2020).
Assembly: mm10
Supplementary files format and content: Consensus YY1 peaks and input peaks (likely mapping artifacts) in iXist-ChrX mESCs (bed)
Supplementary files format and content: Bigwig files of YY1 ChIP-seq and inputs

extract_protocol:
2-3x107 cells were collected and immediately processed for fixation using reagents provided in the truChIP Chromatin Shearing Kit with Formaldehyde (Covaris). After one wash with PBS, cells were resuspended in Fixing Buffer A and fixed with fresh 1% formaldehyde for exactly 10 min on a rotator at room temperature. After quenching and two washes with cold PBS, pellets of 1x107 were processed immediately or snap-frozen and stored at -80oC. Nuclear and Chromatin extraction for sonication was performed according to the recommended protocol for “High Cell” numbers (1x107 cells) in the Covaris truChIP Chromatin Shearing Kit manual (PN 010179). Chromatin was then sheared using a Covaris S220 Focused-ultrasonicator in AFA milliTUBEs with 1 ml of cells in Shearing Buffer D3. Typically 20 min of sonication was required to achieve chromatin fragments of the desired target size (200 to 700bp), and it was necessary to check chromatin shearing efficiency for each sample individually by agarose gel electrophoresis before proceeding with immunoprecipitation. After achieving satisfactory shearing, sonicated chromatin was adjusted to a final concentration of 150 mM NaCl and 1% Triton and pre-cleared by centrifugation at 10,000g for 5 min at 4oC.  ProteinA magnetic Dynabeads (40 μl per sample) were blocked in Chromatin IP buffer (Shearing Buffer D3 diluted with 2X Covaris truChIP IP Buffer and supplemented with 1X Protease Inhibitor Cocktail) with 1 mg/ml BSA and 1 mg/ml yeast tRNA for 1 h rotating at 4oC. After 2 washes with IP buffer, blocked beads were added to chromatin extract for  rotation for 1 h at 4oC and then placed on a magnet. Supernatant chromatin was taken to a new Protein LoBind eppendorf tube (total volume 1100 μl) and beads were discarded. At this step, 100 μl was taken to a new tube as a 10% input sample. 5 μl anti-YY1 antibody (Cell Signaling D5D9Z) was added to the remaining 1 ml extract and incubated on a rotator at 4oC overnight. The following day, blocked ProteinA magnetic Dynabeads were added to each tube of chromatin and rotated for 1 h at 4oC to allow for binding of Ab-conjugated chromatin fragments to beads. Beads were washed in buffers of increasing salt as follows: 2 x Low Salt (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8.1, 150 mM NaCl), 2 x High Salt (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8.1, 500 mM NaCl), 2 x LiCl (0.25 M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH8.1), 2 x TE buffer. Each wash was performed by rotating the beads for 3 min at 4oC before placing samples back on a magnetic rack and discarding the supernatant. After washes, chromatin fragments were extracted by two rounds of elution from beads (each of 15 min at room temperature) in a total of 120 μl fresh elution buffer (1 % SDS, 0.1 M NaHCO3). Reverse crosslinking of both eluted ChIP samples and inputs was performed by addition of 1.2 μl 5M NaCl and shaking incubation (1100 rpm) at 65oC for 4 h, followed by treatment with RNaseA (1.2 μl of 1 mg/ml then shaking at 42oC for 1 h) and ProteinaseK (1.2 μl of 20 mg/ml then shaking at 45oC for 1 h). ChIP DNA was purified with the Zymo ChIP DNA Clean & Concentrator kit (Zymo Research).
Roughly 1 ng of ChIP DNA was taken for Illumina sequencing library preparation using the NEBNext Ultra II DNA Library Prep Kit with NEBNext Single indices (E7645) with 12 cycles of PCR amplification.

treatment_protocol: untreated

tag: agent

value: No dox

tag: cell line

value: iXist-ChrX-Dom

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast

tag: chip antibody

value: Cell Signaling D5D9Z (rabbit mAb)


title: YY1ab_ChIP_iXist-ChrX-Cast_ES_d0_Rep1

tag: Sex


title: Right ventricle, no treatment

value: Right ventricle

value: pooled male and female


title: ChIP_input_iXist-ChrX-Cast_ES_d0_Rep2


title: primary mammary tumor, pre-treatment, Patient36

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

value: no residual disease

tag: unifocal

value: yes

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: mapped to_intergenic_(%_reads)


title: ChIP_input_iXist-ChrX-Cast_ES_d0_Rep1

tag: cell type

tag: strain

value: Female


title: YY1ab_ChIP_iXist-ChrX-Dom_ES_d0_Rep2

tag: agent

tag: cell line


title: primary mammary tumor, pre-treatment, Patient35

tag: tissue

tag: Sex

value: minimal residual disease

tag: grade

tag: node invasion

tag: nac category

tag: hormonotherapy type_category

value: Femara

tag: sequencing batch


title: Left ventricle, male, sham TAC surgery, 14dpi

value: Heart

tag: tissue region

value: Left ventricle

value: Cardiac fibroblasts

tag: genotype

tag: treatment

value: Sham TAC surgery

tag: time

value: 14 days post-surgery

value: Male


title: YY1ab_ChIP_iXist-ChrX-Dom_ES_d0_Rep1

value: No dox

value: iXist-ChrX-Dom

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast

tag: chip antibody

value: Cell Signaling D5D9Z (rabbit mAb)


title: ChIP_input_iXist-ChrX-Dom_ES_d0_Rep2


title: primary mammary tumor, pre-treatment, Patient34

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

value: no residual disease

tag: unifocal

tag: nac herceptin_binary

value: no

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: mapped to_intergenic_(%_reads)


title: ChIP_input_iXist-ChrX-Dom_ES_d0_Rep1

tag: agent

tag: cell line

tag: cell type

tag: strain

tag: Sex

value: Female


title: primary mammary tumor, pre-treatment, Patient33

tag: tissue

tag: timing biopsies

value: Luminal B

value: minimal residual disease

tag: grade

tag: node invasion

value: yes

tag: nac category

value: anthracyclines and taxanes

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d6_dTag52h

description:
cC3_chRNA_AR_table.txt
cC3_chrRNA_AllelicFoldChange.txt

data_processing:
Mapping and processing of ChrRNA-seq data from iXist-ChrX YY1-FKBP12-3xT7 mESCs was performed by a similar pipeline to our previous studies (Nesterova et al., 2019; Bowness et al., 2022). Raw fastq files were first mapped to rRNA by bowtie2 (v2.3.5.1; Langmead and Salzberg.,  2012) and rRNA-mapping reads were discarded. Remaining reads were aligned to the N-masked genome using STAR (v2.5.2b; Dobin et al., 2013) using parameters “-outFilterMultimapNmax 1 -outFilterMismatchNmax 4 -alignEndsType EndToEnd”.
Aligned reads were assigned to separate files corresponding to either the CAST (“genome1”) or 129/Sv (“genome2”) genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “--paired” parameter and a strain-specific SNP file compiled from UCSC annotations.
For both “unsplit” and “allelic” files of each sample, read fragments overlapping genes were counted by featureCounts (Liao et al., 2014) “-t transcript -g gene id -s 2” using a non-redundant annotation file of all transcripts and lncRNAs from NCBI RefSeq.
Allelic analysis of gene silencing in aF1 and cC3 iXist-ChrX YY1-FKBP12-3xT7 mESCs was performed using R and RStudio on allelic count matrices produced by featureCounts. Genes which passed allelic filters in our previous analyses of wild-type gene silencing (Bowness et al., 2022; Supplemental File 1) were retained for Allelic Ratio analysis (Xi/(Xi + Xa)). Slightly fewer genes were amenable to Allelic Fold Change analysis (aF1 - 219/246; cC3 - 329/399) because fold changes cannot be calculated in situations where there are 0 counts for one allele of a gene (e.g. where the gene is completely silent on day 6).
Assembly: mm10
Supplementary files format and content: tables of counts for individual samples
Supplementary files format and content: tables of allelic ratios and allelic fold change for all samples (.txt)
Library strategy: ChrRNA-seq

molecule: nuclear RNA

source_name: iXist-ChrX-Cast YY1-FKBP-T7 (cC3)

extract_protocol:
2 x 107 mESCs were collected from confluent 90mm dishes, washed once with PBS, then snap-frozen and stored at -80oC. Chromatin extraction was performed as follows: Cell pellets were lysed on ice for 5 min in RLB (10 mM Tris pH7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40). Nuclei were then purified by centrifugation through 24% sucrose/RLB (2800 g for 10 min at 4oC), resuspended in NUN1 (20 mM Tris pH7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.1 mM DTT), and then lysed by gradual addition of an equal volume NUN2 (20 mM HEPES pH 7.9, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea, 0.1 mM DTT). After 15 min incubation on ice with occasional vortexing, the chromatin fraction was isolated as the insoluble pellet after centrifugation (2800 g for 10 min at 4oC). Chromatin pellets were resuspended in 1mL TRIzol (Invitrogen) and fully homogenenised and solubilised by eventually being passed through a 23-gauge needle 10 times. This was followed by isolation of chromatin-associated RNA by TRIzol/chloroform extraction with isopropanol precipitation. Precipitated RNA pellets were washed twice with 70% ethanol and air-dried. Final ChrRNA samples were then resuspended in H2O, treated with TurboDNAse and measured by Nanodrop (both ThermoFisher).
500 ng – 1 µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit (RS-122-2301).

treatment_protocol: Xist expression from the TetOn promoter was induced by addition of 1  µg/ml doxycycline (Sigma, D9891) to the culture medium. dTAG-13 (Tocris, #6605) was applied to FKBP-fusion cell lines at 100 nM to induce protein degradation for 52 hours prior to harvesting cells.

tag: time point

value: Dox

value: iXist-ChrX-Cast YY1-FKBP-T7 (cC3)


title: WT_NORMAL_cage1702300_genderM_mouse2988

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

data_processing:
Samples were trimmed with fastp (version 0.20.0) using default parameters. Quantification was performed using Salmon (version 1.4.0) against a decoy transcriptome (Mus musculus Gencode version 21). Further analysis was performed in R (version 4.1.2) in R studio (version 2021.09.2+382). For differential expression analysis, limma (version 3.50.3) was used on log-CPM transformed counts with prior count set to 3 or DESEq2 (version 1.34.0) was used on non-normalized counts.
Assembly: Mus musculus Gencode version 21
Supplementary files format and content: Countsraw.xlsx: counts acquired with Salmon.
Supplementary files format and content: limma_comparison_1.xlsx: ko tumor versus ko normal
Supplementary files format and content: limma_comparison_2.xlsx: wt tumor versus wt normal
Supplementary files format and content: limma_comparison_3.xlsx: tumor (wt and ko) versus normal (wt and ko)

source_name: tumor-adjacent colon

extract_protocol:
Extraction of RNA from whole tissue or organoids was performed on tissue stored in RNA-later (Sigma-Aldrich) until homogenization using a Tissue-Tearor (Dremel, Racine, WI), followed by phenol/chloroform extraction as described (Genzel L, Rossato JI, Jacobse J, Grieves RM, Spooner PA, Battaglia FP, et al. The Yin and Yang of Memory Consolidation: Hippocampal and Neocortical. PLoS Biol. 2017;15:1–26) and clean-up with the Rneasy Mini Kit with on-column DNAse digestion according to manufacturers’ instructions.
stranded mRNA (polyA-selected) library preparation kit.

value: tumor-adjacent colon

tag: genotype

tag: treatment

value: AOM/DSS


title: KO_NORMAL_cage1698567_genderM_mouse2901


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d6_un

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast


title: primary mammary tumor, pre-treatment, Patient32

value: mammary tumor

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal A

tag: rcb category

value: extensive residual disease

tag: unifocal

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Nolvadex then arimidex


title: KO_NORMAL_cage1706108_genderM_mouse3883

tag: tissue


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d2_un

tag: agent

tag: cell line

tag: cell type

tag: strain

tag: Sex

value: Female


title: KO_NORMAL_cage1698567_genderM_mouse2903

tag: genotype

tag: treatment


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d2_dTag52h

tag: time point


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d0_un

value: No dox


title: primary mammary tumor, pre-treatment, Patient31

tag: timing biopsies

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

value: Luminal B

value: moderate residual disease

tag: grade

tag: node invasion

tag: nac category

value: no

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d6_un

description:
aF1_chrRNA_AR_table.txt
aF1_chrRNA_AllelicFoldChange.txt

source_name: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)

tag: agent

value: Dox

tag: cell line

value: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)


title: WT_NORMAL_cage1702300_genderM_mouse2990

tag: tissue

value: tumor-adjacent colon


title: primary mammary tumor, pre-treatment, Patient30

tag: Sex

tag: molecular category

tag: rcb category

tag: unifocal

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: yes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Nolvadex


title: Left ventricle, no treatment

value: Heart

tag: tissue region

value: Left ventricle

tag: cell type

value: Cardiac fibroblasts

tag: genotype

tag: treatment

tag: time

value: pooled male and female


title: ChIPinput_iXist-ChrX-Cast_ES_d6_Rep1

tag: xist (dox)_induction

value: iXist-ChrX-Cast

value: Mouse embryonic stem cell (mESC)

tag: strain

value: Dom/129S x Cast

tag: chip antibody


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d6_dTag52h

tag: time point

tag: agent

tag: cell line

value: Female


title: primary mammary tumor, pre-treatment, Patient29

tag: tissue

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: Sex

value: female

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

tag: grade

tag: node invasion

tag: nac category

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: residual primary mammary tumor, post-treatment, Patient8

value: post-surgery

value: no

value: Luminal B

value: moderate residual disease

tag: unifocal

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Arimidex


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d2_dTag52h

tag: time point

tag: agent

value: Dox

tag: cell line

value: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)

tag: cell type

tag: strain


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d0_un

value: No dox

tag: Sex


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d2_un


title: primary mammary tumor, pre-treatment, Patient27

tag: tissue

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

tag: grade

value: anthracyclines and taxanes


title: KO_NORMAL_cage1698567_genderM_mouse2902

value: tumor-adjacent colon

tag: genotype

tag: treatment

value: AOM/DSS


title: chrRNA_iXist-ChrX-Dom_aF1_ES_d0_dTag52h

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast

value: Female


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_ES_d6

description:
YY1-T7_ConsensusPeaks.rmInput.bed
YY1_T7ChIP_cC3_AR_table.txt

data_processing:
Paired-end fastq files were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Aligned reads were assigned to separate files corresponding to either the CAST (“genome1”) or 129/Sv (“genome2”) genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “--paired” parameter and a strain-specific SNP file compiled from UCSC annotations.
Bigwig files were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
Peaks were called for all samples individually with MACS2 “-f BAMPE -g mm -q 0.01”, and regions where two or more peaks overlap were retained as the consensus peak set. A consensus from peaks called in the four input samples (by MACS2 “-f BAMPE -g mm --broad --broad-cutoff 0.01”) was also generated and subtracted from the consensus YY1-T7 peaks.
Allelic ratios were calculated for the consensus YY1 pea set generated from endogenous YY1 Ab data, not the peak set supplied here from the T7 Ab (see methods for justification). Consensus YY1 peaks were labelled, parsed into gtf file format, and used as input for featureCounts (Liao et al. 2014) to count sequencing fragments overlapping YY1 peaks in both the total and allele-specific alignment files for each time point. Counts matrices for YY1 timecourses in both aF1 and cC3 lines were loaded to RStudio, whereupon allelic filters of >10 allelically-assigned fragments in >80% of samples and biallelic signal in uninduced mESCs (0.2 < allelic ratio < 0.8) were applied to cC3 and aF1 data sets to result in n = 237 and n = 195 peaks respectively. Allelic ratios (Xi/(Xi + Xa)) were then calculated for all sample time points and used for further analysis.
Assembly: mm10
Supplementary files format and content: Bigwig files of YY-T7 ChIP-seq (both unsplit and allelic) and inputs
Supplementary files format and content: Bed files of consensus YY1-T7 peaks and input peaks (likely mapping artifacts) in iXist-ChrX YY1-FKBP12-3xT7 (includes all peaks across mESC to NPC differentiation)
Supplementary files format and content: Tables of allelic ratios for cC3 and aF1 samples

extract_protocol:
2-3x107 cells were collected and immediately processed for fixation using reagents provided in the truChIP Chromatin Shearing Kit with Formaldehyde (Covaris). After one wash with PBS, cells were resuspended in Fixing Buffer A and fixed with fresh 1% formaldehyde for exactly 10 min on a rotator at room temperature. After quenching and two washes with cold PBS, pellets of 1x107 were processed immediately or snap-frozen and stored at -80oC. Nuclear and Chromatin extraction for sonication was performed according to the recommended protocol for “High Cell” numbers (1x107 cells) in the Covaris truChIP Chromatin Shearing Kit manual (PN 010179). Chromatin was then sheared using a Covaris S220 Focused-ultrasonicator in AFA milliTUBEs with 1 ml of cells in Shearing Buffer D3. Typically 20 min of sonication was required to achieve chromatin fragments of the desired target size (200 to 700bp), and it was necessary to check chromatin shearing efficiency for each sample individually by agarose gel electrophoresis before proceeding with immunoprecipitation. After achieving satisfactory shearing, sonicated chromatin was adjusted to a final concentration of 150 mM NaCl and 1% Triton and pre-cleared by centrifugation at 10,000g for 5 min at 4oC.  ProteinA magnetic Dynabeads (40 μl per sample) were blocked in Chromatin IP buffer (Shearing Buffer D3 diluted with 2X Covaris truChIP IP Buffer and supplemented with 1X Protease Inhibitor Cocktail) with 1 mg/ml BSA and 1 mg/ml yeast tRNA for 1 h rotating at 4oC. After 2 washes with IP buffer, blocked beads were added to chromatin extract for  rotation for 1 h at 4oC and then placed on a magnet. Supernatant chromatin was taken to a new Protein LoBind eppendorf tube (total volume 1100 μl) and beads were discarded. At this step, 100 μl was taken to a new tube as a 10% input sample. 5 μl anti-T7 antibody (rabbit mAb, Cell Signaling D9E1X) was added to the remaining 1 ml extract and incubated on a rotator at 4oC overnight. The following day, blocked ProteinA magnetic Dynabeads were added to each tube of chromatin and rotated for 1 h at 4oC to allow for binding of Ab-conjugated chromatin fragments to beads. Beads were washed in buffers of increasing salt as follows: 2 x Low Salt (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8.1, 150 mM NaCl), 2 x High Salt (0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl pH8.1, 500 mM NaCl), 2 x LiCl (0.25 M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH8.1), 2 x TE buffer. Each wash was performed by rotating the beads for 3 min at 4oC before placing samples back on a magnetic rack and discarding the supernatant. After washes, chromatin fragments were extracted by two rounds of elution from beads (each of 15 min at room temperature) in a total of 120 μl fresh elution buffer (1 % SDS, 0.1 M NaHCO3). Reverse crosslinking of both eluted ChIP samples and inputs was performed by addition of 1.2 μl 5M NaCl and shaking incubation (1100 rpm) at 65oC for 4 h, followed by treatment with RNaseA (1.2 μl of 1 mg/ml then shaking at 42oC for 1 h) and ProteinaseK (1.2 μl of 20 mg/ml then shaking at 45oC for 1 h). ChIP DNA was purified with the Zymo ChIP DNA Clean & Concentrator kit (Zymo Research).
Roughly 1 ng of ChIP DNA was taken for library preparation using the NEBNext Ultra II DNA Library Prep Kit with NEBNext Single indices (E7645) with 12 cycles of PCR amplification.

value: dox

value: iXist-ChrX-Cast YY1-FKBP-T7 (cC3)

value: Dom/129S X Cast

tag: chip antibody

value: anti-T7 (rabbit mAb, Cell Signaling D9E1X)


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_NPC_d28

tag: time point

value: Neural progenitor cell (NPC)


title: KO_TUMOR_cage1706108_genderM_mouse3883

source_name: colon tumor

value: colon tumor


title: primary mammary tumor, pre-treatment, Patient26

value: mammary tumor

value: pre-surgery

value: female

value: no residual disease

tag: unifocal

value: no

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: chrRNA_iXist-ChrX-Cast_cC3_ES_d0_dTag52h

tag: agent

value: No dox

tag: cell line

tag: cell type

tag: strain

tag: Sex


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_NPC_d7

value: mESC to NPC intermediate

tag: chip antibody


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_NPC_d5

tag: time point


title: WT_TUMOR_cage1702300_genderM_mouse2989

tag: tissue

tag: genotype

tag: treatment

value: AOM/DSS


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_NPC_d3


title: WT_TUMOR_cage1702300_genderM_mouse2988


title: ChIP_input_iXist-ChrX-Cast_cC3_NPC_d28


title: YY1-T7_ChIP_iXist-ChrX-Cast_cC3_ES_d0

value: Mouse embryonic stem cell (mESC)


title: primary mammary tumor, pre-treatment, Patient24

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

value: Luminal B

tag: rcb category

value: minimal residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: taxanes alone

tag: nac herceptin_binary

value: Arimidex


title: KO_TUMOR_cage1698567_genderM_mouse2902


title: ChIP_input_iXist-ChrX-Cast_cC3_ES_d0

tag: agent

tag: cell line

value: iXist-ChrX-Cast YY1-FKBP-T7 (cC3)

tag: cell type

tag: strain

value: Dom/129S X Cast

tag: Sex

value: Female


title: KO_NORMAL_cage1698567_genderM_mouse2904

tag: tissue

value: tumor-adjacent colon

tag: genotype

tag: treatment


title: primary mammary tumor, pre-treatment, Patient28

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: age diagnostic

value: extensive residual disease

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: WT_NORMAL_cage1702300_genderM_mouse2989


title: primary mammary tumor, pre-treatment, Patient23

value: female

tag: statut menopausal

tag: molecular category

tag: rcb category

tag: unifocal

value: no

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

value: Femara


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_NPC_d7

description:
YY1-T7_ConsensusPeaks.rmInput.bed
YY1_T7ChIP_aF1_AR_table.txt

tag: time point

tag: agent

value: dox

tag: cell line

value: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)

tag: cell type

value: mESC to NPC intermediate

tag: strain

tag: Sex

tag: chip antibody

value: anti-T7 (rabbit mAb, Cell Signaling D9E1X)


title: KO_TUMOR_cage1698567_genderM_mouse2903

tag: tissue

value: colon tumor

tag: genotype

tag: treatment

value: AOM/DSS


title: primary mammary tumor, pre-treatment, Patient22

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

value: yes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_NPC_d3

tag: time point

tag: agent

tag: cell line

tag: cell type

tag: strain

value: Dom/129S X Cast

value: Female


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_NPC_d5

tag: Sex

tag: chip antibody


title: KO_TUMOR_cage1695867_genderM_mouse2901

tag: tissue

tag: genotype

tag: treatment


title: primary mammary tumor, pre-treatment, Patient21

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

value: minimal residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_NPC_d18

tag: time point

tag: agent

tag: cell line

tag: cell type

value: Neural progenitor cell (NPC)

tag: strain


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_ES_d0

value: No dox

value: Mouse embryonic stem cell (mESC)

tag: Sex

tag: chip antibody


title: primary mammary tumor, pre-treatment, Patient20

tag: tissue

tag: timing biopsies

tag: patient id

value: female

value: no

value: moderate residual disease

value: taxanes alone

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Femara

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: KO_TUMOR_cage1698567_genderM_mouse2904

value: colon tumor

tag: genotype

tag: treatment

value: AOM/DSS


title: ChIP_input_iXist-ChrX-Dom_aF1_ES_d0

tag: time point

tag: agent

value: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)


title: WT_TUMOR_cage1702300_genderM_mouse2990


title: primary mammary tumor, pre-treatment, Patient25

tag: age diagnostic

tag: statut menopausal

tag: molecular category

tag: rcb category

value: no residual disease

tag: unifocal

value: yes

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d17_Rep2

data_processing:
Paired-end fastq files from ATAC-seq in iXist-ChrXDom were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Aligned reads were assigned to separate files corresponding to either the CAST (“genome1”) or 129/Sv (“genome2”) genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “--paired” parameter and a strain-specific SNP file compiled from UCSC annotations.
Bigwig files were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
Peak calling was performed on each replicate of ATAC-seq individually by MACS2 (v2.2.7.1; Zhang et al. 2008) using parameters of “-f BAMPE -g mm -q 0.01”. A custom R script using the “GenomicRanges” R package (Lawrence et al., 2013) was used to generate a consensus set of iXist-ChrXDom mESC regulatory elements as regions covered by peaks in at least 2 sample replicates. This script also filters consensus peaks by lower and upper thresholds of 50bp and 10kb respectively. Peaks were also called on tn5-digested gDNA samples by “-f BAMPE -g mm --broad --broad-cutoff 0.01” and these were subtracted from the consensus peak set as likely mapping artifacts.
For quantitative allelic analysis of RE accessibility over the timecourse of XCI, consensus chrX REs were labelled and parsed into gtf file format by awk commands. These were used as input for featureCounts (Liao et al. 2014) to count sequencing fragments overlapping REs in both the total and allele-specific alignment files for each time point. Counts matrices were loaded into RStudio for further analysis. Only peaks containing at least 10 allelically-assigned fragments in >80% of samples and showing biallelic signal in uninduced mESCs (0.15 < allelic ratio < 0.85) were retained (n = 821). Allelic ratios (Xi/(Xi + Xa)) were then calculated for all sample time points and used for further analysis.
Assembly: mm10
Supplementary files format and content: Bigwig files of ATAC-seq tracks (unspit and allelic) and inputs (unsplit)
Supplementary files format and content: Bed files of consensus ATAC peaks in iXist-ChrX (Regulatory elements)
Supplementary files format and content: Table of allelic ratios for ChrX REs over the timecourse (.txt)

extract_protocol:
Chromatin accessibility was assayed by ATAC-seq using a protocol adapted from “Omni-ATAC” (Corces et al. 2017). Briefly, 1-5x106 cells were harvested as pellets, washed with PBS, and nuclei were isolated by incubation for 1 min at room temperature in 600 μl HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H2O, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT). Nuclei were then centrifuged at 1200 g for 5 min at 4oC, followed by three washes with cold RSB buffer (10 mM NaCl, 10 mM Tris pH 7.4, 3 mM MgCl2). After counting, 5x105 nuclei were centrifuged (1500g for 5min at 4oC) and resuspended in 50 μl H2O. 5x104 nuclei (5 μl) were taken for each transposition assay, performed in technical duplicate for each sample in a 50 μl transposition mix of: 1X Tn5 reaction buffer (10 mM TAPS, 5 mM MgCl2, 10% dimethyl- formamide), 0.1% Tween-20 (Sigma), 0.01% Digitonin (Promega), 2.5 μl Tagment DNA TDE1 enzyme (Illumina), 16.5 μl PBS and 5 μl H2O. As controls for transposition and mapping bias, tn5-digested ‘input’ controls were made by performing tagmentation for 50 ng iXist-ChrX genomic DNA by a basic 50 μl transposition mix of 1X TDE buffer and 2.5 μl TDE1 Enzyme (Illumina) in H2O. Both sample and input mixes were incubated at 37oC for 35 minutes in a thermomixer at 1000 rpm, then cleaned-up with ChIP DNA Clean and Concentrator kit (Zymo) and eluted in 14 μl elution buffer for storage at -20oC.
ATAC-seq libraries were prepared by ∼8 cycles of PCR using NEBNext High Fidelity 2X PCR Master Mix (NEB) and primers containing Illumina barcodes (Buenrostro et al. 2013). Libraries were purified and size selected using Agencourt AMPure XP bead clean-up (Beckman Coulter) to ensure a size distribution containing mono-, di- and tri-nucleosomal fragments between 150-800bp.

value: Dox

value: 17 days

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

tag: strain

value: Dom/129S x Cast

tag: Sex

value: Female


title: ChIP_input_iXist-ChrX-Dom_aF1_NPC_d18

value: dox

value: Neural progenitor cell (NPC)

value: Dom/129S X Cast

tag: chip antibody


title: primary mammary tumor, pre-treatment, Patient18

tag: tissue

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

value: female

value: no

value: TNBC

value: moderate residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d6_Rep2

tag: agent

tag: time point

value: 6 days

value: mESC to NPC intermediate


title: primary mammary tumor, pre-treatment, Patient19

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

value: minimal residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

value: Femara then nolvadex


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d17_Rep1

value: Dox

value: 17 days

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

tag: strain

value: Dom/129S x Cast

tag: Sex


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d6_Rep1

value: Female


title: Nr4a1-/- no laser ADT

city: Chicago

first: Jeremy

middle: Arin

last: Lavine

state: Illinois

address: McGaw M343

department: Ophthalmology

institute: Northwestern University

description:
JL-23-1_barcodes.tsv.gz
JL-23-1_features.tsv.gz
JL-23-1_matrix.mtx.gz

library_source: other

data_processing:
Processing of sequencing results to generate combined count matrices (gene expression and ADT) using the 10x genomics Cell Ranger pipeline version 7.0.1
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: retina and choroid

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).  Chromium Single Cell v2 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)

tag: tissue

value: retina and choroid

tag: library type

value: ADT

tag: genotype

tag: treatment

value: sham


title: YY1-T7_ChIP_iXist-ChrX-Dom_aF1_ES_d6

tag: time point

tag: agent

value: dox

value: iXist-ChrX-Dom YY1-FKBP-T7 (aF1)

value: Mouse embryonic stem cell (mESC)

value: Dom/129S X Cast

tag: chip antibody

value: anti-T7 (rabbit mAb, Cell Signaling D9E1X)


title: Wildtype no laser ADT

description:
JL-22-3_barcodes.tsv.gz
JL-22-3_features.tsv.gz
JL-22-3_matrix.mtx.gz


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d3_Rep2

value: 3 days

value: mESC to NPC intermediate


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d1_Rep2

value: 1 day


title: Nr4a1-/- laser ADT

description:
JL-22-2_barcodes.tsv.gz
JL-22-2_features.tsv.gz
JL-22-2_matrix.mtx.gz


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d3_Rep1


title: primary mammary tumor, pre-treatment, Patient16

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

value: no residual disease

value: no

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient17

tag: tissue

tag: Sex

value: extensive residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: anthracyclin alone

tag: nac herceptin_binary

value: Femara


title: tn5_control_gRNA_iXist-ChrX-Dom_NPC_d1_Rep1

tag: agent

value: Dox

tag: time point

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

tag: strain

value: Dom/129S x Cast

value: Female


title: primary mammary tumor, pre-treatment, Patient15

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

tag: rcb category

tag: breast conservative_surgery

tag: sentinel lymph_node

value: Nolvadex


title: tn5_control_gRNA_iXist-ChrX-Dom_ES_d0

value: No dox

value: Mouse embryonic stem cell (mESC)

tag: Sex


title: Wildtype laser ADT

description:
JL-22-1_barcodes.tsv.gz
JL-22-1_features.tsv.gz
JL-22-1_matrix.mtx.gz

tag: tissue

value: retina and choroid

tag: library type

value: ADT

tag: genotype

tag: treatment

value: sham


title: ATAC_iXist-ChrX-Dom_NPC_d17_Rep2

description:
ATAC_ConsensusPeaks.rmtn5.bed
ATAC_NPC_AR_table.txt

tag: agent

tag: time point

value: 17 days

value: Neural progenitor cell (NPC)


title: primary mammary tumor, pre-treatment, Patient14

value: mammary tumor

value: pre-surgery

value: female

value: yes

value: moderate residual disease

tag: unifocal

value: no

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: ATAC_iXist-ChrX-Dom_NPC_d17_Rep1

value: Dox

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

tag: strain

value: Dom/129S x Cast

value: Female


title: Nr4a1-/- no laser mRNA

tag: tissue

tag: library type

value: mRNA


title: ATAC_iXist-ChrX-Dom_NPC_d6_Rep2

value: 6 days

value: mESC to NPC intermediate

tag: Sex


title: primary mammary tumor, pre-treatment, Patient13

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

value: minimal residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node


title: Wildtype no laser mRNA

value: retina and choroid

tag: genotype

value: Wildtype

tag: treatment

value: sham


title: primary mammary tumor, pre-treatment, Patient12

value: mammary tumor

value: pre-surgery

value: female

value: Luminal A

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: ATAC_iXist-ChrX-Dom_NPC_d3_Rep2

tag: agent

value: Dox

tag: time point

value: 3 days

tag: cell line

tag: cell type

tag: strain

tag: Sex


title: ATAC_iXist-ChrX-Dom_NPC_d3_Rep1

value: iXist-ChrX-Dom

value: Dom/129S x Cast


title: Nr4a1-/- laser mRNA

tag: tissue

tag: library type

value: mRNA

tag: genotype

value: laser


title: primary mammary tumor, pre-treatment, Patient11

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

value: extensive residual disease

tag: unifocal

tag: grade

value: yes

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node


title: Wildtype laser mRNA

value: retina and choroid

value: Wildtype

tag: treatment


title: ATAC_iXist-ChrX-Dom_NPC_d1_Rep2

tag: agent

tag: time point

value: 1 day

tag: cell line

tag: cell type

value: mESC to NPC intermediate

value: Female


title: rad50S_CCseq_rep2

city: New York

first: Carolyn

middle: R

last: Milano

email: crmilano@gmail.com, cm5497@nyu.edu

state: NY

address: 15 Washington Place, Apartment 3M

institute: New York University

description: CC-seq

data_processing:
For ChIP-seq, Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. For CC-seq, reads were mapped to SK1 genome (Yue et al., 2017) and Bowtie2, using TermMapper as previously described (Gittens et al, 2019; preprint:Brown et al 2023).
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20
Peaks were identified using MACS broad flag.
Assembly: Genome_build: SK1 (Yue et al., 2017)
Library strategy: CC-seq

organism: Saccharomyces cerevisiae

source_name: meiotic nucleus

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606 which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
For ChIP-seq samples: 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For CC-seq samples: Protein-DNA Covalent-Complex Mapping (CC-seq) in yeast followed a method previously described (Gittens et al, 2019; preprint: Brown et al, 2023). Briefly, meiotic cell samples were chilled and frozen at -20˚C for at least 8 hours, then thawed and spheroplasted (in 1 M sorbitol, 50 mM NaHPO4, 10 mM EDTA, 30 min at 37˚C), fixed in 70% ice-cold ethanol, collected by centrifugation, dried briefly, then lysed in STE (2% SDS, 0.5 M Tris, 10 mM EDTA). Genomic DNA was extracted via Phenol/Chloroform/IAA extraction (25:24:1 ratio) at room temperature, with aqueous material carefully collected, precipitated with ethanol, washed, dried, then resuspended in 1xTE buffer (10 mM Tris/1 mM EDTA). Total genomic DNA was sonicated to <500 bp average length using a Covaris M220 before equilibrating to a final concentration of 0.3 M NaCl, 0.2% Triton X100, 0.1% Sarkosyl. Covalent complexes were enriched on silica columns (Qiagen) via centrifugation, washed with TEN solution (10 mM Tris / 1 mM EDTA / 0.3 M NaCl), before eluted with TES buffer (10 mM Tris / 1 mM EDTA / 0.5% SDS). Samples were treated with Proteinase K at 50˚C, and purified by ethanol precipitation.
For ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For CC-seq, DNA ends were filled and repaired using NEB Ultra II end-repair module, with custom dsDNA adapters ligated sequentially to the sonicated, then blocked, ends with rSAP and then recombinant TDP2 treatment in between these steps to remove the 5-phosphotyrosyl-linked Spo11 peptide. Ampure bead cleanups were used to facilitate sequential reactions. PCR-amplified libraries were quantified on a Bioanalyser and appropriately diluted and multiplexed for deep sequencing (Illumina NextSeq1000 2x51 bp). For further information, a detailed protocol is available (preprint: Brown et al, 2023).

treatment_protocol: No treatment was given prior to sample collection.

tag: tissue

value: meiotic nucleus

tag: timepoint

value: meiosis Hr6


title: hop1-loop2pch2rad50S_CCseq_rep2

description: CC-seq

tag: genotype


title: hop1-loop2rad50S_CCseq_rep2

description: CC-seq


title: FA-TLR-1A treated

city: West Lafayette

first: Philip

middle: S.

last: Low

state: IN

address: 720 Clinic Drive

department: Chemistry

institute: Purdue University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were performed using the Cell Ranger software v6.0.2 (10x Genomics).
All reads were aligned to the ENSEMBL mouse genome version mm10 using the STAR aligner v2.7.2a.
CellRanger was run with the number of expected cells set to 5,000. R version 4.0.1 and Bioconductor version 3.11 were used in all statistical analyses. Cells that had fewer than 200 or greater than 6000 observed genes were discarded. Cells were also removed if greater than 15% of all reads mapped to mitochondrial genes or greater than 50% of all reads mapped to ribosomal genes.
Seurat version 4.0.5  was used for data normalization and cell clustering based on differential gene expressions.
Assembly: mm10
Supplementary files format and content: tab separated values file and matrix file

source_name: Tumor

growth_protocol: 6-8 weeks old Balb/c female mice were subcutaneously injected with 4T1 cells (50,000 cells/mouse)

extract_protocol:
Tumors were dissociated to obtain single cell suspensions. Viable cells were enriched using Dead Cell Removal Microbeads. Cell viability (>95%) was  validated by flow cytometry and were used for scRNA-seq library construction immediately.
Following 10x loading suggestions, ~16,000 cells were loaded into each well of the chip for a targeted cell recovery of 10,000 cells per lane. Chip G from 10x Genomics was utilized for GEM generation and all steps following GEM generation were carried out as described in the 10x Genomics manual.

treatment_protocol: 3nmol/mouse of FA-TLR7-1A was administered intravenously 5 times per week for two weeks

value: Tumor

value: Tumor digestion

value: FA-TLR-1A treated


title: primary mammary tumor, pre-treatment, Patient10

data_processing:
The CLC Genomics v22 software (Qiagen) is used to remove low-quality reads from raw NGS sequences, perform trimming and mapping to the Homo sapiens genome hg38 and the RNA database v91
Supplementary files format and content: the processed datafile is containing the raw counts of reads. The colums are Gene Names, Chromosomes, coordinates, ensembl identifiers, and raw counts for each of the 122 libraries

source_name: mammary tumor

extract_protocol:
deparaffinization and extraction steps were carried out using the AllPrep DNA/RNA FFPE kit (#80234, Qiagen), according to manufacturer’s recommendations and DNA was removed from the samples with the TURBO DNA-free™ kit (#AM1907, Thermo Fisher Scientific), by following manufacturer’s instructions. Total RNA samples were then quantified by using Quant-it™ RiboGreen RNA Assay kit (#R11490, Thermo Fisher Scientific
ribosomal RNA depletion were performed with the NEBNext rRNA Depletion kit (Human/Mouse/Rat) with sample purification beads (#E6350, New England Biolabs). Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep with Beads kit (#E7765, New England Biolabs). Adaptors and primers used for the library preparation were from NEBNext Multiplex Oligos for Illumina (Dual Index Set 1), 96 rxns (#E7760, New England Biolabs). The quality of the libraries was evaluated using High Sensitivity DNA kit (chips and reagents) (#5067 and #4626, Agilent) with a 2100 Bioanalyzer system (Agilent). Sequence reads were generated on the Illumina NovaSeq 6000 sequencer, on an S4 cartridge (300 bp). RNA sequencing was performed in 3 distinct batches
bulk stranded total RNA sequencing after depletion of rRNA. Paired-end, 2 x 150bp.

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: Sex

value: female

value: Luminal B

value: moderate residual disease

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: ATAC_iXist-ChrX-Dom_NPC_d1_Rep1

source_name: iXist-ChrX-Dom

tag: agent

value: Dox

value: iXist-ChrX-Dom

tag: strain

value: Dom/129S x Cast


title: primary mammary tumor, pre-treatment, Patient9

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

tag: unifocal

tag: grade

value: yes

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

value: Femara


title: ATAC_iXist-ChrX-Dom_ES_d0_Rep3

value: No dox

tag: cell line

tag: cell type

value: Mouse embryonic stem cell (mESC)

tag: Sex

value: Female


title: hop1-loop2pch2rad50S_CCseq_rep1

description: CC-seq

tag: tissue

value: meiotic nucleus

tag: timepoint

value: meiosis Hr6

tag: genotype


title: Vehicle treated

description: 10X Genomics

value: Tumor

value: Tumor digestion

tag: treatment

value: Vehicle treated


title: hop1-loop2rad50S_CCseq_rep1

description: CC-seq