title: primary mammary tumor, pre-treatment, Patient8

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

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: Arimidex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Pancreas, CIP injected, 30 days, rep7

status: Public on Feb 28 2024

type: SRA

city: Boston

first: Sahar

last: Nissim

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Brigham and Women's Hospital

description:
TMA2_025
QC_BQC_raw_matrixonly.xlsx

library_source: transcriptomic

data_processing:
*library strategy: spatial transcriptomics
FASTQ read data was then processed through the GeoMx NGS Pipeline software to generate digital count conversion files (.dcc files), which were uploaded back to the GeoMx Digital Spatial Profiler instrument for subsequent processing and analysis.
Initial steps of data processing were performed in the GeoMx Digital Spatial Profiler Analysis Suite (v2.3.3.10). Counts were deduplicated based on UMIs and ROIs and filtered for those containing greater than 5% of genes detected (~1000 gene targets). Negative probes were filtered using the Grubbs outlier test to remove outliers, with 119/120 probes passing filter. Gene probes were filtered for those detected 2% above the limit of quantification (LOQ), with LOQ defined as two standard deviations greater than the geometric mean of the negative probes. Upper quartile (Q3) normalization was performed using all targets. Scaling was not performed.
Downstream analysis was performed in python (v3.10) using rpy2 (v3.5.1) to integrate R tools. The batch effect of slide was regressed out using limma’s (v3.56.1) ‘removeBatchEffect’19 and ‘voom’ normalization was performed prior to PCA visualization. Differentially expressed genes (DEGs) were determined using a linear mixed model with slide as a covariable and Benjamini/Hochberg correction for multiple hypothesis testing.
Assembly: mm10
Supplementary files format and content: segmentSummary_readTypes.xlsx: Tab-delimited spreadsheet containing segment information
Supplementary files format and content: TargetProperties_raw.xlsx: Tab-delimited spreadsheet containing target properties information
Supplementary files format and content: BioProbeInformation.xlsx: Tab-delimited spreadsheet containing bioprobe information
Supplementary files format and content: QC_BQC_raw_matrixonly.xlsx: Tab-delimited spreadsheet containing raw gene-counts matrix post filtering
Supplementary files format and content: QC_BQC_Q3Norm_matrixonly.xlsx: Tab-delimited spreadsheet containing Q3 normalized gene-counts matrix

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
For GeoMx WTA profiling, we generated two 12-core tissue blocks containing each time point. Formalin-fixed paraffin-embedded tissue sections (5 μm) were processed according to the Nanostring Manual Slide Preparation guide (MAN-10150-01). A total of 57 regions of interest (ROIs, 650 μm x 650 μm) were profiled, with 2-4 ROIs selected from each tissue sample.
The GeoMX Digital Spatial Profiler instrument selectively illuminated each ROI with UV light, permitting the photocleavage of a 66 bp-long DNA barcode from each oligonucleotide probe that was hybridized to an mRNA target within the ROI. The DNA barcodes from each ROI were deposited in a collection plate, and PCR was used to uniquely index each ROI’s barcodes with specific Illumina i5/i7 dual indexing primers. Amplified, indexed libraries were then pooled, purified with SPRI beads (Beckman Coulter) and the library quality assessed by capillary electrophoresis using a Fragment Analyzer (Agilent). Paired-end sequencing was performed on a NovaSeq6000 (Illumina), targeting the Nanostring recommended read depth of 2.5 billion read-pairs (calculated using the sum of each ROI’s area).

treatment_protocol: Pancreatitis was induced in C57BL/6 mice at 8-9 weeks of age using intraperitoneal caerulein injections on two consecutive days once every hour for 8 hours. Formalin-fixed paraffin-embedded microarray tissue sections (5 µm) were used for Nanostring's GeoMX Whole Transcriptome Atlas Digital Spatial Profiling.

tag: tissue

value: Pancreas

tag: strain

tag: treatment


title: ATAC_iXist-ChrX-Dom_ES_d0_Rep2

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
ATAC_ConsensusPeaks.rmtn5.bed
ATAC_NPC_AR_table.txt

library_source: genomic

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)

molecule: genomic DNA

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.

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

tag: agent

value: No dox

tag: cell line

value: iXist-ChrX-Dom

tag: cell type

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast

tag: Sex

value: Female


title: ATAC_iXist-ChrX-Dom_NPC_d6_Rep1

value: Dox

tag: time point

value: 6 days

value: mESC to NPC intermediate


title: rad50S_CCseq_rep1

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.

value: meiotic nucleus

tag: timepoint

value: meiosis Hr6

tag: genotype


title: Pancreas, CIP injected, 30 days, rep6

description:
TMA2_024
QC_BQC_raw_matrixonly.xlsx


title: primary mammary tumor, pre-treatment, Patient7

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

country: Belgium

institute: CHU Liege

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

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

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

value: TNBC

tag: rcb category

value: no residual disease

tag: unifocal

value: yes

tag: grade

tag: node invasion

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node


title: ATAC_iXist-ChrX-Dom_ES_d0_Rep1

tag: agent

tag: cell line

tag: strain


title: Wt_Spikein_input_rep2

description:
ChIP-seq
There is no bedgraph file associated with this sample. Spike-in samples were used to ascertain the relative amount of protein binding in the mutant compared to the wild type. txt files with the reads are included for each spike-in sample.

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)

tag: tissue

value: meiosis Hr3


title: Pancreas, CIP injected, 30 days, rep5

description:
TMA2_023
QC_BQC_raw_matrixonly.xlsx

value: Pancreas

tag: treatment


title: Wt_Spikein_Hop1_ChIP_rep2

tag: timepoint

tag: genotype


title: Pancreas, CIP injected, 30 days, rep4

description:
TMA1_029
QC_BQC_raw_matrixonly.xlsx


title: primary mammary tumor, pre-treatment, Patient6

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: Sex

value: female

value: minimal residual disease

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: primary mammary tumor, pre-treatment, Patient5

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

tag: rcb category

tag: unifocal

tag: grade

tag: node invasion

tag: breast conservative_surgery

tag: sentinel lymph_node

value: Femara


title: Pancreas, CIP injected, 30 days, rep3

description:
TMA1_023
QC_BQC_raw_matrixonly.xlsx

tag: tissue

tag: strain

tag: treatment


title: primary mammary tumor, pre-treatment, Patient4

tag: timing biopsies

tag: patient id

tag: Sex

value: Luminal A

value: moderate residual disease

tag: nac category

value: anthracyclin alone

tag: nac herceptin_binary


title: OCT4_ChIP_iXist-ChrX-Cast_ES_d0_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

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.

tag: xist (dox)_induction

value: No dox

tag: cell line

value: iXist-ChrX-Cast

tag: cell type

value: Mouse embryonic stem cell (mESC)

value: Dom/129S x Cast

value: Female

tag: chip antibody

value: anti-OCT4A C3OA3C1 (CST rabbit mAb)


title: Pancreas, CIP injected, 30 days, rep2

description:
TMA1_022
QC_BQC_raw_matrixonly.xlsx


title: primary mammary tumor, pre-treatment, Patient3

value: mammary tumor

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

tag: unifocal

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Arimidex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient2

tag: tissue

tag: timing biopsies

value: pre-surgery

tag: patient id

value: female

value: TNBC

value: extensive residual disease

value: yes

tag: grade

tag: node invasion

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node


title: hop1-loop2_Spikein_Hop1_ChIP_rep2

value: meiotic nucleus

tag: cell line

tag: timepoint

value: meiosis Hr3

tag: genotype


title: primary mammary tumor, pre-treatment, Patient1

tag: Sex

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

value: moderate residual disease

tag: nac category

tag: nac herceptin_binary

value: Femara


title: ChIPinput_iXist-ChrX-Cast_ES_d6_Rep2

tag: xist (dox)_induction

value: iXist-ChrX-Cast

tag: cell type

value: Mouse embryonic stem cell (mESC)

tag: strain

value: Dom/129S x Cast

tag: chip antibody


title: hop1-loop2rec8_Hop1_ChIP_rep2

description:
ChIP-seq
11689-antiHop1-20220125_20220331-Reps-SK1Yue-PM-PE_B4_W3_MACS2_FE.bedgraph

tag: tissue


title: Pancreas, CIP injected, 30 days, rep1

description:
TMA1_021
QC_BQC_raw_matrixonly.xlsx

value: Pancreas

tag: treatment


title: hop1-loop2rec8_input_rep2


title: Pancreas, CIP injected, 14 days, rep7

description:
TMA2_022
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 14 days, rep6

description:
TMA2_021
QC_BQC_raw_matrixonly.xlsx


title: Z133

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

data_processing:
library strategy: nano-hmC-Seal
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg38  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted for Refseq annotated gene body regions using featureCounts.
Assembly: hg38
Supplementary files format and content: txt file for all sample with raw reads count summarised to Refseq annotated gene bodies.

source_name: Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).

value: Plasma

tag: gender

tag: age

tag: training/validation group in pan-cancer diagnostic model


title: Pancreas, CIP injected, 14 days, rep5

description:
TMA2_020
QC_BQC_raw_matrixonly.xlsx


title: hop1-loop2rec8_Hop1_ChIP_rep1

tag: cell line

tag: timepoint


title: Z131

value: Control


title: Pancreas, CIP injected, 14 days, rep4

description:
TMA1_028
QC_BQC_raw_matrixonly.xlsx


title: wildtype_Hop1_input_SpikeIn_Rep2

description: MidOutput 2x150-300

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: 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)). Rapamycin was added at 0h where indicated.

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 MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
 libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

value: Nucleus

value: Meiosis Hour 3

tag: genotype

value: wild type


title: Z120

value: female


title: Pancreas, CIP injected, 14 days, rep3

description:
TMA1_020
QC_BQC_raw_matrixonly.xlsx


title: Z168

value: male

value: Test


title: hop1-loop2_Spikein_input_rep2

value: meiotic nucleus


title: wildtype_Hop1_input_SpikeIn_Rep1

description: MidOutput 2x150-300


title: Z188


title: Z194


title: wildtype_Hop1_chip_SpikeIn_Rep1

description: MidOutput 2x150-300


title: Pancreas, CIP injected, 14 days, rep1

description:
TMA1_018
QC_BQC_raw_matrixonly.xlsx


title: Primary_tumor_AKP_replicate3 [ATAC_1027_Primary]

city: Cambridge

first: Norihiro

last: Goto

address: 500 Main Street, Building 76

department: Department of Biology

institute: Massachusetts Institute of Technology

description: ngoto_ATACseq_peak_tiled_reads.matrix.gz

data_processing:
Paired-end ATAC-seq reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were merged using Samtools.
Peaks were called on the merged BAM using MACS2.
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: Matrix file of counts for filtered peaks

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated by TrypLE Express for 10 min at 37ºC, passed through a 40 μm filter, and a total of 50,000 cells were centrifuged and washed twice with PBS. Cells are resuspended in 50 μl of buffer with TDE1 enzyme and incubated at 37°C for 30 min with gentle agitation. DNA was isolated using the Qiagen MinElute PCR Purification Kit.
ATAC-seq libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. 2 x 75 paired-end sequencing was performed on an Illumina NextSeq 500.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: pch2_Hop1_input_SpikeIn_Rep2

description:
MidOutput 2x150-300
11758-hop1NH-20220125-20220721-20221004-Reps-SK1Yue-PM-PE_B4_W3_MACS2_FE.bdg.gz


title: Pancreas, CIP injected, 7 days, rep6

description:
TMA2_027
QC_BQC_raw_matrixonly.xlsx


title: Z183


title: pch2_Hop1_chip_SpikeIn_Rep2


title: Z179


title: hop1-loop2rec8_input_rep1

value: meiosis Hr3


title: Primary_tumor_AKP_replicate1 [ATAC_1010_Primary]


title: Z177


title: Pancreas, CIP injected, 7 days, rep5

description:
TMA2_026
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 7 days, rep4

description:
TMA2_019
QC_BQC_raw_matrixonly.xlsx


title: pch2_Hop1_input_SpikeIn_Rep1


title: wildtype_Hop1_chip_SpikeIn_Rep2

description: MidOutput 2x150-300


title: Naïve_AKP_replicate3 [ATAC_Naive_3]


title: pch2_Hop1_chip_SpikeIn_Rep1


title: Z181


title: hop1loop2-pch2_Hop1_input_SpikeIn_Rep2

description:
MidOutput 2x150-300
11757-hop1NH-20220125-20220721-20221004-Reps-SK1Yue-PM-PE_B4_W3_MACS2_FE.bdg.gz

value: hop1-loop2; pch2


title: Pancreas, CIP injected, 7 days, rep2

description:
TMA1_025
QC_BQC_raw_matrixonly.xlsx


title: Naïve_AKP_replicate2 [ATAC_Naive_2]


title: Pancreas, CIP injected, 14 days, rep2

description:
TMA1_019
QC_BQC_raw_matrixonly.xlsx


title: Naïve_AKP_replicate1 [ATAC_Naive_1]


title: Z197


title: Pancreas, CIP injected, 7 days, rep1

description:
TMA1_017
QC_BQC_raw_matrixonly.xlsx


title: Z166


title: hop1loop2-pch2_Hop1_ChIP_SpikeIn_Rep2


title: SOX17KO [scRNA-seq]

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
Supplementary files format and content: components of filtered_feature_bc_matrix

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: Pancreas, CIP injected, 5 day, rep6

description:
TMA2_018
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2-pch2_Hop1_input_SpikeIn_Rep1


title: Z191


title: Primary_tumor_AKP_replicate2 [ATAC_1026_Primary]


title: Control [scRNA-seq]

description: 10x Genomics


title: Z209


title: Pancreas, CIP injected, 5 day, rep5

description:
TMA2_017
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 7 days, rep3

description:
TMA1_026
QC_BQC_raw_matrixonly.xlsx


title: In_vivo_AKP_SOX17KO3 replicate 3 [In_vivo_AKP_SOX17KO3 RNA-seq]

data_processing:
Paired-end RNA-seq data were mapped to the UCSC mm9 mouse genome build using Bowtie and gene counts were quantified using RSEM.
Assembly: mm9
Supplementary files format and content: ngoto_201102YilA_Ct.txt.gz is a tab delimited text of count data

source_name: In vivo tumor-derived AKP organoid

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

value: In vivo tumor-derived AKP organoid


title: hop1loop2_Hop1_input_SpikeIn_Rep1

description:
MidOutput 2x150-300
11644-NHantiHop1-20220331-20220125-20221004-Reps-SK1Yue-PM-PE_B4_W3_MACS2_FE.bdg.gz


title: Z206


title: In_vivo_AKP_SOX17KO2 replicate 2 [In_vivo_AKP_SOX17KO2 RNA-seq]


title: Pancreas, CIP injected, 5 day, rep3

description:
TMA1_016
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: Z161

value: Plasma


title: Pancreas, CIP injected, 5 day, rep4

description:
TMA2_016
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2_Hop1_ChIP_SpikeIn_Rep1


title: pch2_Hop1_input_Rep3


title: pch2_Hop1_ChIP_Rep3


title: Z158


title: Z155


title: In_vivo_AKP_Control replicate 3 [In_vivo_AKP_Control3 RNA-seq]

value: Control


title: In_vivo_AKP_Control replicate 2 [In_vivo_AKP_Control2 RNA-seq]


title: Z152


title: Pancreas, CIP injected, 72 hours, rep4

description:
TMA2_015
QC_BQC_raw_matrixonly.xlsx


title: pch2_Hop1_input_Rep2

value: Nucleus


title: In_vivo_AKP_Control replicate 1 [In_vivo_AKP_Control1 RNA-seq]


title: pch2_Hop1_ChIP_Rep2

value: Meiosis Hour 3


title: hop1loop2-pch2_Hop1_ChIP_SpikeIn_Rep1


title: pch2_Hop1_input_Rep1


title: Z171


title: Inducible_SOX17OE_AKP [Inducible_SOX17OE RNA-seq]

data_processing:
Paired-end RNA-seq data were mapped to the UCSC mm9 mouse genome build using Bowtie and gene counts were quantified using RSEM.
Assembly: mm9
Supplementary files format and content: ngoto_200615Yil_Ct.txt.gz is a tab delimited text of count data


title: In_vivo_AKP_SOX17KO replicate 1 [In_vivo_AKP_SOX17KO1 RNA-seq]


title: pch2_Hop1_ChIP_Rep1


title: Z145

value: Validation


title: Pancreas, CIP injected, 72 hours, rep1

description:
TMA1_013
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 48 hours, rep5

description:
TMA2_028
QC_BQC_raw_matrixonly.xlsx


title: Constitutive_SOX17OE_AKP [Constitutive_SOX17OE RNA-seq]


title: RAG2KO_Primary_tumor_AKP_replicate3 [1216_RAG2KO_Primary RNA-seq]


title: Pancreas, CIP injected, 5 day, rep2

description:
TMA1_015
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 5 day, rep1

description:
TMA1_014
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 48 hours, rep4

description:
TMA2_012
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2-pch2_Hop1_ChIP_Rep3


title: hop1loop2-pch2_Hop1_input_Rep3


title: Z137


title: Z144

value: female


title: RAG2KO_Primary_tumor_AKP_replicate2 [1204_RAG2KO_Primary RNA-seq]


title: Pancreas, CIP injected, 48 hours, rep3

description:
TMA1_027
QC_BQC_raw_matrixonly.xlsx


title: Z149


title: RAG2KO_Primary_tumor_AKP_replicate1 [1200_RAG2KO_Primary RNA-seq]


title: Pancreas, CIP injected, 72 hours, rep3

description:
TMA2_014
QC_BQC_raw_matrixonly.xlsx


title: Primary_tumor_AKP_replicate3 [1027_Primary RNA-seq]


title: hop1loop2-pch2_Hop1_input_Rep2


title: hop1loop2-pch2_Hop1_ChIP_Rep2


title: Z121


title: Z124

value: Training


title: Primary_tumor_AKP_replicate2 [1026_Primary RNA-seq]


title: Pancreas, CIP injected, 72 hours, rep2

description:
TMA2_013
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 48 hours, rep1

description:
TMA1_012
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2-pch2_Hop1_input_Rep1


title: Healthy_9

city: Athens

first: Tina

last: Bagratuni

address: Lourou 4-2

department: Department of Therapeutics

country: Greece

institute: NKUA

description:
Healthy
ScRNA-seq 10X Genomics v3

data_processing:
Demultiplexing, alignment and gene counts were performed with ‘Cell Ranger’ Single-Cell Software Suite (v4.0, 10X Genomics).
The Cell Ranger output was further processed with ‘Seurat’ (v4.1) in R (v4.0.5) to filter out cell doublets and non-viable cells as well as genes that were consistently not expressed among all cells.
Cells expressing more than 200 and less than 2500 genes with a mitochondrial gene percentage less than 15% were retrieved for further analysis.
The counts matrix was also filtered, removing rows corresponding to genes being expressed in less than 10 cells.
Assembly: GRCh38
Supplementary files format and content: A matrix of UMI counts associated with a feature (row) and a barcode (column), in H5 format, including both the GEX and CMO feature counts.

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
For scRNAseq, sorted CD19+ bone marrow viable cells were loaded in the 10x-Genomics Chromium instrument (10X Genomics, USA).
Single cell RNA sequencing libraries were prepared following 10X-Genomics v3 protocol recommendations (10X Genomics, USA).

value: Bone marrow

value: patient derived CD19+ bone marrow cells

value: CD19+ sorted B cells

value: Healthy donor


title: Primary_tumor_AKP_replicate1 [1010_Primary RNA-seq]

value: Colon cancer organoids

value: AKP


title: Pancreas, CIP injected, 24 hours, rep5

description:
TMA2_009
QC_BQC_raw_matrixonly.xlsx


title: Naïve_AKP_replicate3 [Naive_3 RNA-seq]


title: hop1loop2_Hop1_input_Rep3


title: Pancreas, CIP injected, 24 hours, rep6

description:
TMA2_010
QC_BQC_raw_matrixonly.xlsx


title: Patient_7

description:
MYD88wt
ScRNA-seq 10X Genomics v3

value: MYD88 WT


title: Naïve_AKP_replicate2 [Naive_2 RNA-seq]


title: hop1loop2_Hop1_ChIP_Rep3


title: Pancreas, CIP injected, 24 hours, rep4

description:
TMA2_008
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2-pch2_Hop1_ChIP_Rep1

value: hop1-loop2; pch2


title: Pancreas, CIP injected, 24 hours, rep3

description:
TMA1_010
QC_BQC_raw_matrixonly.xlsx


title: Pancreas, CIP injected, 48 hours, rep2

description:
TMA1_024
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2_Hop1_input_Rep2


title: hop1loop2_Hop1_ChIP_Rep2


title: Pancreas, CIP injected, 24 hours, rep2

description:
TMA1_009
QC_BQC_raw_matrixonly.xlsx


title: Patient_4

description:
MYD88mut
ScRNA-seq 10X Genomics v3

value: MYD88 L265P


title: anaplastic ependymoma (EPN), scRNA-seq

city: Shenzhen

first: Qian

last: Chen

address: 7019 Yitian Road

country: China

institute: Shenzhen Children's Hospital

data_processing:
The official 10× software CellRanger (V6.1.1) was used to filter, align, and map raw library reads for analysis[25]. The reads were aligned to the reference genome (GRCh38-2020-A) using STAR[26] alignment software. After alignment, the expression of each gene in each cell was obtained.
Cells were clustered according to the Seurat v4.0.4[27] Guided Clustering Tutorial.
Assembly: hg18
Supplementary files format and content: matrix files

source_name: anaplastic ependymoma

extract_protocol:
Tumor samples were separated into single cell suspensions using a combination of mechanical dissociation and enzymatic degradation of the extracellular matrix. Enzymatic digestion of the samples was performed using a Tumor Dissociation Kit (Miltenyi Biotec, Gladbach, Germany) following the manufacturer's instructions. In short, tissues were minced and mixed with 200 μL enzyme H, 25 μL enzyme A, 100 μL enzyme R, and 4.7 mL Dulbecco’s Modified Essential Medium and loaded into MACS C Tube (130-094-392, Miltenyi Biotec). It was then dissociated three times using mild MACS™ dissociation reagent (130-093-235, Miltenyi Biotec) and the samples were incubated at 37 °C for 30 minutes between each dissociation step. Large particles, erythrocytes, and dead cells were removed using a filter (40 μm), Red Blood Cell Lysis Solution (130-094-183, Miltenyi Biotec), and Dead Cell Removal Kit (Miltenyi Biotec), respectively.
A Chromium Single Cell 3' Reagent kit (10× Genomics, Pleasanton, CA, USA) was used to create scRNA-seq libraries. The suspension of single cells was loaded into the Chromium Single Cell Controller Instrument (10× Genomics) to generate Gel Beads-in-emulsion (GEMs). Then, barcoded full-length cDNA was then used for the reverse transcription reactions, followed by the disruption of emulsions using the recovery agent. DynaBeadsMyone Silane Beads (Thermo Fisher Scientific, Waltham, MA, USA) were used to clean the cDNA. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adapter ligated, and library amplified. Qubit dsDNA HS Assay Kit (Q32854, Agilent, USA) was used for library quantification, and the standard of charge was about 400-500bp for the main peak.

value: anaplastic ependymoma


title: hop1loop2_Hop1_input_Rep1


title: Pancreas, CIP injected, 24 hours, rep1

description:
TMA1_008
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: Patient_5

description:
MYD88mut
ScRNA-seq 10X Genomics v3


title: Patient_3

description:
MYD88mut
ScRNA-seq 10X Genomics v3


title: Species Mixing (RNA-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)

organism:
Homo sapiens
Mus musculus

source_name: OP-9 & HEK

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: OP-9 & HEK


title: Pancreas, CIP injected, 12 hours, rep6

description:
TMA2_007
QC_BQC_raw_matrixonly.xlsx


title: hop1loop2_Hop1_ChIP_Rep1

value: Nucleus


title: Patient_2

description:
MYD88wt
ScRNA-seq 10X Genomics v3


title: Patient_6

description:
MYD88mut
ScRNA-seq 10X Genomics v3


title: Healthy_8

description:
Healthy
ScRNA-seq 10X Genomics v3


title: Species Mixing (ATAC-seq)

description: easySHARE-seq


title: Pancreas, CIP injected, 12 hours, rep5

description:
TMA2_006
QC_BQC_raw_matrixonly.xlsx


title: Naïve_AKP_replicate1 [Naive_1 RNA-seq]


title: Pancreas, CIP injected, 12 hours, rep4

description:
TMA2_005
QC_BQC_raw_matrixonly.xlsx


title: NT control 54h rep 2

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NovaSeq 6000 using v3 chemistry. NovaSeq Software: Control v1.7.0, RTA 3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using Salmon version 1.3.0 with a transcriptome target consisting of human and mouse transcripts. Human transcripts were derived from the hg38 primary assembly and the ensembl version 101 annotation and mouse transcripts were derived from the mm10 primary assembly and the ensembl 101 annotation. Gene level summaries were prepared using tximport version 1.18.0 running under R version 4.0.3.
Assembly: hg38 and mm10 with ensembl version 101 assembly
Supplementary files format and content: 210308Bha_set3_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 210308Bha_set3_l2tpm.txt.gz is a tab delimited text file of log2 tpm data including a +1 offset

source_name: Primary human hepatocytes, mouse embryonic fibroblasts

growth_protocol: Hepatocytes were maintained in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM with L-glutamine, Corning) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences), 7 ng/ml glucagon (Sigma), 40 ng/ml dexamethasone (Sigma), 15 mM HEPES (Gibco), and 1% (v/v) penicillin-streptomycin (Corning). J2-3T3 male murine embryonic fibroblasts  were cultured at <18 passages in fibroblast medium comprising of DMEM with high glucose, 10% (v/v) bovine serum (Thermo Fisher), and 1% (v/v) penicillin-streptomycin (Corning). Primary human hepatocytes were seeded on collagen-coated micropatterned plates as detailed previously (March et al., 2015).

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher) and purified using RNeasy Mini Kit (Qiagen)
RNA integrity was determined using an Agilent Fragment Analyzer and purity and quantity determined using a Thermo Scientific Nanodrop1000 Spectrophotometer. High throughput RNAseq libraries were prepared as previously described (M using 100ng of total RNA input and sequenced on a NovaSeq6000 using 50nt paired-end sequencing

treatment_protocol: siRNA oligonucleotides were added to patterned hepatocytes after washing off the unbound hepatocytes. ON-TARGETplus SMARTpool siRNA oligonucleotides (Dharmacon) were delivered to hepatocytes by using RNAiMAX Transfection Reagent (Thermo Fisher Scientific) per manufacture’s protocols at final concentration 100nM in antibiotic-free DMEM media supplemented with 10% FBS (final volume 100 mL). Duplicate or triplicate wells-containing hepatocytes were exposed to siRNA duplexes overnight for 20-24 hr and subsequently surrounded by 3T3-J2 fibroblasts. To perform circadian synchronization, the cultures were placed in Non-HEPES-buffered CO2 Independent Medium (COI, Thermofisher) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences) and 7 ng/ml glucagon (Sigma). 36, 42, 48 and 54 hour post-synchronization, RNA was extracted.

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: Non-targeting control siRNA

tag: time

value: 54 hours post-synchronization


title: BMAL knock-down 54h rep 2

value: Primary human hepatocytes, mouse embryonic fibroblasts


title: EVT_d3_Input

city: Rensselaer

first: Bum-Kyu

last: Lee

state: New York

address: One Discovery Drive, Cancer Research Center, RM332

institute: University of Albany-SUNY

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to human hg38 genome using Bowtie 2.4.5
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: wiggle file

source_name: Placenta

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in human TSCs. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E7370L ) following by manufacturer’s instructions.

value: Placenta

value: CT27, EVT differentiation for 3 days

value: Extravillous trophoblast

value: none(input)


title: 24hr_rep3

first: Julia

middle: M

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

institute: Harvard Medical School

data_processing:
Reads were first mapped to ERCC spike in sequences using bowtie1.2.2 with the following parameters: -n2 -l 40 -X1000 --best -3. Reads not mapping to the spike in sequences were mapped to hg38 using STAR version 2.7.3a with the following arguments: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outWigType bedGraph --outWigNorm None --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.
Reads per gene in the Gencodev33 gtf file were counted using the featureCounts function of Subread1.6.2
This count matrix was used as input for DESeq2 to identify differentially expressed genes, calculating each time point versus the mock washout condition. As reads mapping to the ERCC spike sequences were not different between conditions, the DESeq2 size factors were used the normalize samples.
Assembly: hg38
Supplementary files format and content: gene_counts.xlsx contains the FeatureCounts output of the number of reads per sample mapping to each gene
Supplementary files format and content: DESeq_output.xlsx contains the log2 Fold Change and Adjusted p value for each gene at 2hrs, 4hrs, and 24hrs compared to the mock washout control.

source_name: SVG-A

growth_protocol: SVG-A cells were grown in DMEM +10% fetal bovine serum+1% Penicillin/Streptomycin at 37°C with 5%CO2.

extract_protocol:
Samples in Trizol were thawed, and ERCC spike-in RNAs (Thermo Scientific 4456740) were added at 10 L per million cells. RNA was isolated using chloroform following the MaXtract tube protocol (Qiagen 129056). 5 g of RNA was treated with DNaseI (Thermo Scientific 18068015) in the presence of SUPERase-In (Thermo AM2696). RNA quality was evaluated by HS RNA ScreenTape (Agilent 5067-5579) on a TapeStation; all samples had RIN score > 8.
500 ng RNA was used as input for the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina 20020598).

treatment_protocol: Cells were removed from plates using 0.5 mM EDTA for 3min, quenched with media, and counted. 400,000 cells per well were plated in media containing 100 nM Compound E (Millipore Sigma 565790) on non-tissue-culture treated 6-well plates that were prepared overnight with PBS + 0.1 mg/mL Poly-D-lysine (Thermo Scientific A3890401) and 200 g/ml Fc-tagged human JAGGED1 extracellular domain protein. After 18 hr overnight incubation on the JAG1-Fc-coated plates with Compound E, SVG-A cells were washed three times in 4 mL of media, and incubated for 2, 4, or 24 hrs before harvesting by resuspension in 1 mL Trizol (Thermo Scientific 15-596-026). A “0 hr” reference control was collected by performing a mock washout with media containing 100 nM Compound E and immediately harvesting in Trizol.

value: SVG-A

value: 24hr post washout


title: EVT_d3_H3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: Pancreas, CIP injected, 12 hours, rep3

description:
TMA1_007
QC_BQC_raw_matrixonly.xlsx

data_processing:
*library strategy: spatial transcriptomics
FASTQ read data was then processed through the GeoMx NGS Pipeline software to generate digital count conversion files (.dcc files), which were uploaded back to the GeoMx Digital Spatial Profiler instrument for subsequent processing and analysis.
Initial steps of data processing were performed in the GeoMx Digital Spatial Profiler Analysis Suite (v2.3.3.10). Counts were deduplicated based on UMIs and ROIs and filtered for those containing greater than 5% of genes detected (~1000 gene targets). Negative probes were filtered using the Grubbs outlier test to remove outliers, with 119/120 probes passing filter. Gene probes were filtered for those detected 2% above the limit of quantification (LOQ), with LOQ defined as two standard deviations greater than the geometric mean of the negative probes. Upper quartile (Q3) normalization was performed using all targets. Scaling was not performed.
Downstream analysis was performed in python (v3.10) using rpy2 (v3.5.1) to integrate R tools. The batch effect of slide was regressed out using limma’s (v3.56.1) ‘removeBatchEffect’19 and ‘voom’ normalization was performed prior to PCA visualization. Differentially expressed genes (DEGs) were determined using a linear mixed model with slide as a covariable and Benjamini/Hochberg correction for multiple hypothesis testing.
Assembly: mm10
Supplementary files format and content: segmentSummary_readTypes.xlsx: Tab-delimited spreadsheet containing segment information
Supplementary files format and content: TargetProperties_raw.xlsx: Tab-delimited spreadsheet containing target properties information
Supplementary files format and content: BioProbeInformation.xlsx: Tab-delimited spreadsheet containing bioprobe information
Supplementary files format and content: QC_BQC_raw_matrixonly.xlsx: Tab-delimited spreadsheet containing raw gene-counts matrix post filtering
Supplementary files format and content: QC_BQC_Q3Norm_matrixonly.xlsx: Tab-delimited spreadsheet containing Q3 normalized gene-counts matrix


title: EVT_d3_H3K4me3_ChIPseq

description: Chromatin IP against H3K4me3


title: 24hr_rep2


title: NT control 54h rep 1

value: BMAL siRNA


title: H3K27M mutant diffuse midline glioma (BG), scRNA-seq

source_name: diffuse midline glioma

value: diffuse midline glioma


title: Pancreas, CIP injected, 12 hours, rep2

description:
TMA1_006
QC_BQC_raw_matrixonly.xlsx

source_name: Pancreas


title: EVT_Input

value: CT27, EVT differentiation for 8 days


title: 24hr_rep1


title: BMAL knock-down 54h rep 1


title: 4hr_rep3

value: 4hr post washout


title: Pancreas, CIP injected, 12 hours, rep1

description:
TMA1_005
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: NT control 48h rep 2

value: 48 hours post-synchronization


title: EVT_H3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: 4hr_rep2


title: NT control 48h rep 1

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]


title: Pancreas, CIP injected, 3 hours, rep2

description:
TMA2_004
QC_BQC_raw_matrixonly.xlsx


title: 4hr_rep1


title: EVT_H3K9me3_ChIPseq

description: Chromatin IP against H3K9me3


title: Patient_1

description:
MYD88mut
ScRNA-seq 10X Genomics v3

value: Bone marrow

value: patient derived CD19+ bone marrow cells

value: CD19+ sorted B cells

value: MYD88 L265P


title: BMAL knock-down 48h rep 2

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: primary human hepatocyte, mouse embryonic fibroblast


title: Pancreas, CIP injected, 3 hours, rep1

description:
TMA1_004
QC_BQC_raw_matrixonly.xlsx


title: EVT_H3K4me3_ChIPseq

description: Chromatin IP against H3K4me3

value: Placenta

value: Extravillous trophoblast


title: 2hr_rep3

value: SVG-A

value: 2hr post washout


title: ST_d3_Input

value: CT27, ST differentiation for 3 days

value: syncytiotrophoblast

value: none(input)


title: Pancreas, control, rep6

description:
TMA2_002
QC_BQC_raw_matrixonly.xlsx

value: control


title: ST_d1_Input

value: CT27, ST differentiation for 1 day


title: NT control 42h rep 2

value: Non-targeting control siRNA

value: 42 hours post-synchronization


title: 2hr_rep2


title: Pancreas, control, rep7

description:
TMA2_003
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: NT control 42h rep 1

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]


title: Pancreas, control, rep4

description:
TMA1_030
QC_BQC_raw_matrixonly.xlsx


title: 2hr_rep1


title: EVT_H3K27me3_ChIPseq

description: Chromatin IP against H3K27me3

value: CT27, EVT differentiation for 8 days


title: BMAL knock-down 42h rep 2

value: BMAL siRNA


title: mock_washout_rep3

value: mock washout


title: Pancreas, control, rep5

description:
TMA2_001
QC_BQC_raw_matrixonly.xlsx


title: ST_d1_H3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: mock_washout_rep2


title: ST_d3_H3K4me3_ChIPseq

description: Chromatin IP against H3K4me3


title: Pancreas, control, rep3

description:
TMA1_003
QC_BQC_raw_matrixonly.xlsx


title: BMAL knock-down 42h rep 1

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: primary human hepatocyte, mouse embryonic fibroblast


title: ST_Input

value: Placenta

value: CT27, ST differentiation for 6 days


title: Frontal cortex, Sporadic, donor id 277

city: Santa Barbara

first: Kenneth

last: Kosik

state: CA

address: 5165 Biology II

department: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

description:
C277_C01 (Sporadic 8)
10X Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the 10x Genomics CellRanger pipeline (version 3.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Downstream analysis was performed using Seurat 4.0 (https://satijalab.org/seurat/index.html) in RStudio Version 4.1.0. Data was imputed for missing values using single-cell RNA-Seq Gene Expression Recovery package SAVER (v1.1.2).
Assembly: GRch38-3.0.0
Supplementary files format and content: BrainFRONTAL_counts.csv: Comma-separated values file includes processed count matrix for all samples: Samples Control 1-8 (donor ids: 226, 240, 262, 291, 327, 342, 350, 364); Samples E280A 1-8 (donor ids: 114, 135, 140, 142, 361, 363, 379, 377); Samples Sporadic 1-8 (donor ids: 381, 323, 255, 210, 269, 99, 181, 277).
Supplementary files format and content: BrainFRONTAL_metadata.csv: Comma-separated values file includes meta.data information and cell type annotation.

source_name: Brain (frontal cortex)

extract_protocol:
Frontal cortex (FC) from E280A-PSEN1 mutant, Sporadic Alzheimer's disease or non-diseased controls were dissociated, and nuclei isolation was performed separately for each of these samples using the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, #NUC101) as described in (https://doi.org/10.1038/nmeth.4407).  Briefly, tissue samples were dounce homogenized in 2 ml of ice-cold EZ PREP and incubated on ice for 5 min. Following initial dounce homogenization, an additional 2ml of EZ PREP was added and the samples were incubated for 5 min. Nuclei suspension was centrifuged (500 × g, 5 min and 4°C) washed 1X in ice-cold EZ PREP buffer, and 1X in Nuclei Suspension Buffer (NSB; consisting of 1× PBS, 1% (w/v) BSA and 0.2 U/μl RNase inhibitor (Clontech, #2313A)), resuspended in 1 ml of NSB and filtered through a 40 μm cell strainer. Nuclei were stained with SYTOX green (1:1000) and counted twice. A final concentration of 1000 nuclei per µl was used for loading onto the 10X Chromium (10X Genomics).
Library construction was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10X Genomics) using manufacturer instructions.

value: Brain (frontal cortex)

value: diverse brain cell types

tag: disease

value: Sporadic Alzheimer's Disease

value: no treatment

tag: Sex

value: Female

tag: donor


title: Pancreas, control, rep2

description:
TMA1_002
QC_BQC_raw_matrixonly.xlsx

extract_protocol:
For GeoMx WTA profiling, we generated two 12-core tissue blocks containing each time point. Formalin-fixed paraffin-embedded tissue sections (5 μm) were processed according to the Nanostring Manual Slide Preparation guide (MAN-10150-01). A total of 57 regions of interest (ROIs, 650 μm x 650 μm) were profiled, with 2-4 ROIs selected from each tissue sample.
The GeoMX Digital Spatial Profiler instrument selectively illuminated each ROI with UV light, permitting the photocleavage of a 66 bp-long DNA barcode from each oligonucleotide probe that was hybridized to an mRNA target within the ROI. The DNA barcodes from each ROI were deposited in a collection plate, and PCR was used to uniquely index each ROI’s barcodes with specific Illumina i5/i7 dual indexing primers. Amplified, indexed libraries were then pooled, purified with SPRI beads (Beckman Coulter) and the library quality assessed by capillary electrophoresis using a Fragment Analyzer (Agilent). Paired-end sequencing was performed on a NovaSeq6000 (Illumina), targeting the Nanostring recommended read depth of 2.5 billion read-pairs (calculated using the sum of each ROI’s area).

value: control


title: NT control 36h rep 2

value: Non-targeting control siRNA

value: 36 hour post-synchronization


title: NT control 36h rep 1


title: ST_H3K27me3_ChIPseq

description: Chromatin IP against H3K27me3

value: syncytiotrophoblast


title: BMAL knock-down 48h rep 1

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: 48 hours post-synchronization


title: Pancreas, control, rep1

description:
TMA1_001
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: ST_H3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: Frontal cortex, Sporadic, donor id 99

description:
C99_C01 (Sporadic 6)
10X Genomics


title: BMAL knock-down 36h rep 2

value: BMAL siRNA


title: BMAL knock-down 36h rep 1

value: Primary human hepatocytes, mouse embryonic fibroblasts


title: ST_H3K9me3_ChIPseq

description: Chromatin IP against H3K9me3


title: ST_H3K4me3_ChIPseq

description: Chromatin IP against H3K4me3


title: CRIF1 KO Treg TCR stim (rep4), ATAC-seq

city: Seoul

first: Sangsin

address: Daehakro

country: South Korea

institute: Seoul National University

description: CRIF1 KO Regulatory T cells (1 day TCR stimulated)

data_processing:
Read alignment to the mm10 mouse genome was conducted by using Bowtie2 software with the “-X 2000” option, which resulted in a Binary Alignment Map (BAM) file.
The BAM file was converted to the Browser Extensible Data (BED) format by using the “bamToBed” function in BEDtools software.
The alignment positions of the fragments were corrected by shifting +4 bp for the positive strands and -5 bp for the negative strands to compensate for 9 bp
this was conducted with the “makeTagDirectory” function in the Homer-Suite, which created an intermediate folder.
Genome browser tracks were generated for each sample by using the "MakeUCSCfile" function in the Homer Suite with the “--bigwig” option.
Assembly: mm10
Supplementary files format and content: A BED file includes the ATAC-peak coordinates in BED format (chromosome, start, end positons)

source_name: Spleen and Lymph node

extract_protocol:
DNA was extracted by lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin)
ATAC-seq libraries were prepared by using the indexing primers fromINextera XT DNA Library Preparation Kit (Illumina)

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells

value: CRIF1 KO

value: 1 day TCR stimulated


title: CRIF1 KO Treg TCR stim (rep3), ATAC-seq


title: Frontal cortex, Sporadic, donor id 210

description:
C210_C01 (Sporadic 4)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Sporadic Alzheimer's Disease

value: Male


title: CRIF1 KO Treg TCR stim (rep2), ATAC-seq


title: TSC_Input

value: Placenta

value: Human trophoblast stem cells

value: none(input)


title: CRIF1 KO Treg TCR stim (rep1), ATAC-seq


title: UBV PHH at 72hr rep2

data_processing:
Illumina NovaSeq 6000 using v3 chemistry. NovaSeq Software: Control v1.6.0, RTA 3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.1 and STAR version 2.7.1a alignment to a transcriptome derived from the human hg38 primary assembly and ensembl version 98 annotation.
Assembly: hg38 with the ensembl 98 annotation
Supplementary files format and content: 190712Bha_set1_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 190712Bha_set1_l2tpm.txt.gz is a tab delimited text file of log2 tpm data including a +1 offset

treatment_protocol: To perform circadian synchronization, the cultures were placed in Non-HEPES-buffered CO2 Independent Medium (COI, Thermofisher) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences) and 7 ng/ml glucagon (Sigma)

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction

value: 72 hours post-synchronization


title: Frontal cortex, Sporadic, donor id 269

description:
C269_C01 (Sporadic 5)
10X Genomics

value: no treatment


title: UBV PHH at 72hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts


title: TSC_H3K27me3_ChIPseq

description: Chromatin IP against H3K27me3


title: Frontal cortex, Sporadic, donor id 255

description:
C255_C01 (Sporadic 3)
10X Genomics

value: Female


title: mock_washout_rep1

value: SVG-A

value: mock washout


title: TSC_H3K27ac_ChIPseq

description: Chromatin IP against H3K27ac


title: Frontal cortex, Sporadic, donor id 323

description:
C323_C01 (Sporadic 2)
10X Genomics

value: Brain (frontal cortex)


title: Frontal cortex, Sporadic, donor id 381

description:
C381_C01 (Sporadic 1)
10X Genomics

value: diverse brain cell types


title: TSC_H3K9me3_ChIPseq

description: Chromatin IP against H3K9me3


title: UBV PHH at 69hr rep3

value: 69 hours post-synchronization


title: UBV PHH at 72hr rep1


title: Pancreas, CIP injected, 3 hours, rep3

description:
TMA2_029
QC_BQC_raw_matrixonly.xlsx

value: Pancreas


title: UBV PHH at 69hr rep2


title: Frontal cortex, Sporadic, donor id 181

description:
C181_C01 (Sporadic 7)
10X Genomics

value: Sporadic Alzheimer's Disease


title: TSC_H3K4me3_ChIPseq

description: Chromatin IP against H3K4me3

value: Placenta

value: Human trophoblast stem cells


title: Control Treg TCR stim (rep2), ATAC-seq

description: Control Regulatory T cells (1 day TCR stimulated)

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells

value: Control

value: 1 day TCR stimulated


title: Frontal cortex, Control, donor id 364

description:
C364_C01 (Control 8)
10X Genomics

value: Non-diseased Control

value: no treatment

value: Male


title: Frontal cortex, Control, donor id 350

description:
C350_C01 (Control 7)
10X Genomics


title: UBV PHH at 69hr rep1

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction


title: Control Treg TCR stim (rep1), ATAC-seq


title: UBV PHH at 66hr rep3

value: 66 hours post-synchronization


title: CRIF1 KO Treg unstim (rep4), ATAC-seq

description: CRIF1 KO Regulatory T cells (Unstimulated)

value: CRIF1 KO

value: Unstimulated


title: Frontal cortex, Control, donor id 342

description:
C342_C01 (Control 6)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Female


title: Frontal cortex, Control, donor id 327

description:
C327_C01 (Control 5)
10X Genomics


title: 25486, LUSC, sRNA

city: Zagreb

first: Maja

last: Šutić

address: Bijenicka street 54

department: Division of Molecular Medicine

country: Croatia

institute: Ruder Boskovic Institute

data_processing:
Quality of sequenced reads was checked with FASTQC application on BaseSpace Sequence Hub cloud (Illumina).
Reads were aligned to reference genome (GRCh38_p10) with sRNAbench webtool in batch mode. Alignment set up was: removal of Illumina TruSeq adapters; minimum mean quality Phred Score Treshold of 20; minimal read length of 15nt, and allowed number of mismatches in seed region of one nt.
Assembly: Reference genome- GRCh38_p10, miRNA annotations- miRBase v22
Supplementary files format and content: mature_sense_minExpr1_RCadj_deseq2_RLEnormTable.csv contains DESeq2 normalized miRNA counts

source_name: FFPE tissue

extract_protocol:
Total RNA was isolated from 14 SQC and 4 healthy FFPE tissue samples with miRNeasy FFPE kit (Qiagen), according to manufacturer’s instructions. RNA integrity and quality were assessed using RNA Nano 6000 BioAnalyzer chips (Agilent) and percentage of miRNA fraction was assessed with small RNA BioAnalyzer chips (Agilent).
For library preparation with TruSeq Small RNA Library kit, one µg of total RNA was used, according to manufacturer’s protocol.

value: FFPE tissue

value: male

tag: disease state

value: LUSC


title: 25609, LUSC, sRNA


title: UBV PHH at 66hr rep1

tag: cell type


title: CRIF1 KO Treg unstim (rep2), ATAC-seq

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells


title: Control Treg TCR stim (rep4), ATAC-seq

value: Control

value: 1 day TCR stimulated


title: Frontal cortex, Control, donor id 291

description:
C291_C01 (Control 4)
10X Genomics

value: Non-diseased Control

value: no treatment

value: Male


title: UBV PHH at 63hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction

value: 63 hours post-synchronization


title: Control Treg TCR stim (rep3), ATAC-seq


title: CRIF1 KO Treg unstim (rep1), ATAC-seq

value: CRIF1 KO

value: Unstimulated


title: Frontal cortex, Control, donor id 262

description:
C262_C01 (Control 3)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types


title: 20432, LUSC, sRNA

value: FFPE tissue

value: male

value: LUSC


title: UBV PHH at 63hr rep2


title: Frontal cortex, Control, donor id 240

description:
C240_C01 (Control 2)
10X Genomics

value: Female


title: UBV PHH at 63hr rep1


title: 19694, LUSC, sRNA


title: Control Treg unstim (rep4), ATAC-seq

description: Control Regulatory T cells (Unstimulated)

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells

value: Control


title: Control Treg unstim (rep3), ATAC-seq


title: 25850, LUSC, sRNA


title: Frontal cortex, Control, donor id 226

description:
C226_C01 (Control 1)
10X Genomics

value: Non-diseased Control

value: no treatment


title: 17664, LUSC, sRNA


title: Frontal cortex, PSEN1-E280A, donor id 377

description:
C377_C01 (E280A 8)
10X Genomics

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: Male


title: 16734, LUSC, sRNA

value: female


title: UBV PHH at 60hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction

value: 60 hours post-synchronization


title: UBV PHH at 66hr rep2

value: 66 hours post-synchronization


title: CRIF1 KO Treg unstim (rep3), ATAC-seq

value: Spleen and Lymph node

value: CRIF1 KO

value: Unstimulated


title: Control Treg unstim (rep2), ATAC-seq

value: Primary mouse cells

value: Regulatory T cells

value: Control


title: UBV PHH at 60hr rep2


title: 12545, LUSC, sRNA

value: FFPE tissue

value: LUSC


title: CRIF1 KO Treg TCR stim (rep2), RNA-seq

data_processing:
FASTQ files were trimmed to remove low-quality reads using TrimOmatic software
To align the sequence reads to the mm10 mouse genome, the HISAT2 software was used with default settings.
The 'featureCount' function from the Rsubread R-package was then employed to quantify fragment overlap with exons.
The General Transfer Format (GTF) file from GENCODE vM25 was used for the mouse genome.
To identify expressed genes, we excluded those with a Count Per Million (CPM) value less than 1 in at least one replicate by using the edgeR R-package.
Assembly: mm10
Supplementary files format and content: A text file includes the aligned read count per transcript for each sample

extract_protocol:
RNA was harvested using Trizol (Qiagen). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared by using the Illumina Truseq Stranded Total RNA Sample prep kit with Ribo-zero Human/mouse/rat according to the manufacturer’s protocol (Illumina)

value: 1 day TCR stimulated


title: UBV PHH at 60hr rep1


title: Control Treg unstim (rep1), ATAC-seq


title: 21671, LUSC, sRNA

value: male


title: 8323, LUSC, sRNA


title: Frontal cortex, PSEN1-E280A, donor id 379, repeat

description:
C379_C01_Repeat (E280A 7)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: no treatment

value: Female


title: Frontal cortex, PSEN1-E280A, donor id 379

description:
C379_C01 (E280A 7)
10X Genomics


title: UBV PHH at 57hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction

value: 57 hours post-synchronization


title: CRIF1 KO Treg TCR stim (rep1), RNA-seq

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells

value: CRIF1 KO


title: 7202, LUSC, sRNA

value: FFPE tissue

value: male

value: LUSC


title: UBV PHH at 57hr rep2


title: Control Treg TCR stim (rep2), RNA-seq

value: Control

value: 1 day TCR stimulated


title: 4737, LUSC, sRNA


title: Frontal cortex, PSEN1-E280A, donor id 363

description:
C363_C01 (E280A 6)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: no treatment


title: Frontal cortex, PSEN1-E280A, donor id 361

description:
C361_C01 (E280A 5)
10X Genomics

value: Male


title: Frontal cortex, PSEN1-E280A, donor id 142

description:
C142_C01 (E280A 4)
10X Genomics


title: Control Treg TCR stim (rep1), RNA-seq


title: 4613, LUSC, sRNA


title: UBV PHH at 54hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction

value: 54 hours post-synchronization


title: 3260, LUSC, sRNA

value: FFPE tissue


title: CRIF1 KO Treg unstim(rep2), RNA-seq

value: Spleen and Lymph node

value: Primary mouse cells

value: Regulatory T cells

value: CRIF1 KO

value: Unstimulated


title: CRIF1 KO Treg unstim (rep1), RNA-seq


title: UBV PHH at 57hr rep1

value: 57 hours post-synchronization


title: 55, healthy control, sRNA

value: male

value: healthy control


title: Frontal cortex, PSEN1-E280A, donor id 135, repeat

description:
C135_C01_Repeat (E280A 2)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: no treatment


title: UBV PHH at 54hr rep2

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT


title: Control Treg unstim (rep2), RNA-seq

value: Spleen and Lymph node

value: Control


title: UBV PHH at 54hr rep1

value: circadian synchronization and RNA extraction

value: 54 hours post-synchronization


title: 44, healthy control, sRNA

value: FFPE tissue


title: Frontal cortex, PSEN1-E280A, donor id 135

description:
C135_C01 (E280A 2)
10X Genomics

value: Male


title: UBV PHH at 51hr rep3

value: 51 hours post-synchronization


title: 28, healthy control, sRNA

value: male

value: healthy control


title: Control Treg unstim (rep1), RNA-seq

value: Primary mouse cells

value: Regulatory T cells

value: Unstimulated


title: Frontal cortex, PSEN1-E280A, donor id 114, repeat

description:
C114_C01_Repeat (E280A 1)
10X Genomics

value: Brain (frontal cortex)

value: diverse brain cell types

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: no treatment


title: Frontal cortex, PSEN1-E280A, donor id 114

description:
C114_C01 (E280A 1)
10X Genomics


title: L1072F/L1072F ES ChIP-seq replicate 3

city: Fukuoka

first: Taichi

last: Shiraishi

address: 1-1-3 Maidashi Higashiku Fukuoka

department: Medical institute of bioregulation

country: Japan

institute: Kyushu university

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.2.0.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 v2.4.5
PCR duprication was removed with Picard and bigwig files were generated with bamCoverage (deeptools v3.5.1)
S3norm was used for data normalization and peakcall was conducted using MACS2 bdgpeakcall with parameters -c 4 -l 400.
Assembly: mm10
Supplementary files format and content: BigWig files for Genome Browser

source_name: Embryonic stem cell

growth_protocol: ES cells were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in ES culture medium with 15% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
ES cells were fixed with 1% formalin and digested with sonication and Micrococcal Nuclease (TaKaRa, 2910A) and lysate were isolated using CHD8-antibody.
ChIP-seq libraries were prepared for sequencing with the use of ThruPLEX® DNA-Seq Kit (TaKaRa, R400675).


title: 2, healthy control, sRNA


title: UBV PHH at 51hr rep2

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT


title: UBV PHH at 51hr rep1

value: circadian synchronization and RNA extraction


title: UBV PHH at 48hr rep3

value: 48 hours post-synchronization


title: L1072F/L1072F ES ChIP-seq replicate 2


title: C364, frontal pole, NovaSeq

description:
C364_c1
10X Genomics
Visium Spatial Gene Expression

data_processing:
The Space Ranger pipeline (v1.3.1) for processing of Visium Spatial Gene Expression (GEX) data with brightfield images to align reads and generate Feature Barcode (FB) matrices was used (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger).
Downstream analysis was performed using Seurat 4.1.1 (https://satijalab.org/seurat/index.html).
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: filtered feature barcoded matrix is a spaceranger output .h5 file with counts for every spot.
Supplementary files format and content: tissue low resolution image is a spaceranger output .png file for projecting gene expression values onto
Supplementary files format and content: metadata .csv file includes all demographic and tissue spot information; C140, C363 and C364 are donor ids.

extract_protocol:
Hippocampal and frontal cortical samples were cryosectioned at -20°C. The 10 μm sections were placed on a Visium Tissue Optimization Slide (10x Genomics, #3000394) and Visium Spatial Gene Expression Slide (10x Genomics, #2000233). By following the Visium Spatial Tissue Optimization User Guide (10x Genomics, #CG000238 Rev E), the optimal permeabilization time was determined to be twelve minutes. The gene expression slides underwent methanol fixation, Hematoxylin & Eosin (H&E) staining, and brightfield imaging using a 10x objective on a Nikon Eclipse Ti2-E (10x Genomics, #CG000160 Rev C).
Immediately after imaging, the tissues were permeabilized and the remaining steps for library construction were completed according to the user guide (10x Genomics, #CG000239 Rev F).

value: Healthy Control


title: CRG47_3

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: RNA-seq pair end (PE)

data_processing:
RNA-seq analysis.  (https://docs.google.com/document/d/1yRZevDdjxkEmda9WF5-qoaRjIROZmicndPl3xetFftY/edit?usp=sharing)
RNA-seq analysis. Differential expression (www.dropbox.com/s/026pc48kfuqr88g/RNA_analysis_deseq.2.R?dl=0)
Assembly: hg38

extract_protocol:
RNA was isolated from cells with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer. RNA was subject to Bioanalyzer (for Quality Control [QC]). Libraries were prepared using 1 µg of RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pair-ended (PE) 100-base-long reads.
To detect expression of AE and tRNAs, the RNA-seq library preparation was carried out as above, but without the poly-T purification step. Libraries were prepared using 1 µg of RNA and the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat from Illumina. Libraries were sequenced using Illumina HI-seq-2500 to obtain PE reads 150-base-long reads.
chipseq Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen).

tag: chip-antibody

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h, followed by re-addition of 10% charcoal-treated (CT) FBS after the indicated time

tag: antibiotics

value: with antibiotics (100 u/ml penicillin, 100 ug/ml streptomycin)

tag: replicate


title: L1072F/L1072F ES ChIP-seq replicate 1


title: CRG47_2

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

tag: treatment


title: C363, frontal pole, NovaSeq

description:
C363_c1
10X Genomics
Visium Spatial Gene Expression

tag: tissue

value: female


title: UBV PHH at 48hr rep2


title: Frontal cortex, PSEN1-E280A, donor id 140

description:
C140_C01 (E280A 3)
10X Genomics

value: Female


title: R910Q/R910Q ES ChIP-seq replicate 3


title: C364, hippocampus, NovaSeq

description:
C364_c12
10X Genomics
Visium Spatial Gene Expression

source_name: Brain (hippocampus)

value: Brain (hippocampus)

value: male


title: CRG47_1

description: RNA-seq pair end (PE)


title: UBV PHH at 48hr rep1


title: Pgr_3

description: RNA-seq pair end (PE)

value: progesterone


title: R910Q/R910Q ES ChIP-seq replicate 2


title: C363, hippocampus, NovaSeq

description:
C363_c12
10X Genomics
Visium Spatial Gene Expression

value: diverse brain cell types

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A


title: UBV PHH at 45hr rep3

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: 45 hours post-synchronization


title: R910Q/R910Q ES ChIP-seq replicate 1


title: Pgr_2

description: RNA-seq pair end (PE)


title: UBV PHH at 45hr rep2

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT

value: circadian synchronization and RNA extraction


title: L834P/L834P ES ChIP-seq replicate 3


title: L834P/L834P ES ChIP-seq replicate 2


title: Pgr_1

description: RNA-seq pair end (PE)


title: UBV PHH at 45hr rep1


title: Late_5

city: Charleston

first: Christina

last: Voelkel-Johnson

state: SC

address: 173 Ashley Ave, MSC 250504 room 201

institute: Medical University of South Carolina

data_processing:
base calling: CASAVA software
alignment: STAR software
quantification: HTSeq
differential analysis on readcounts: DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with readcounts for every gene and every sample provided as a tab delimited text file

source_name: prostate cancer cell line PPC1

growth_protocol: 7 X 10^5 cells plated in 100 mm plate on day 1 in RPMI 1640  growth media.

extract_protocol:
Qiagen RNAEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate cancer cell line PPC1

value: mitotic population post PGCC

value: 8 Gy radiation + 20 days


title: Late_6


title: L834P/L834P ES ChIP-seq replicate 1


title: UBV PHH at 42hr rep3

value: 42 hours post-synchronization


title: EtOH_3

description: RNA-seq pair end (PE)

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

value: with antibiotics (100 u/ml penicillin, 100 ug/ml streptomycin)

value: ethanol


title: Late_4


title: UBV PHH at 42hr rep2


title: WT ES ChIP-seq replicate 3


title: EtOH_2

description: RNA-seq pair end (PE)


title: UBV PHH at 42hr rep1


title: Late_3


title: EtOH_1

description: RNA-seq pair end (PE)


title: WT ES ChIP-seq replicate 2


title: nsyb-4

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: UT

institute: University of Utah

description: flies_vs_neurons_annotated_differential.csv

data_processing:
Fastq files were quality-checked with FastQC v0.11.9
Adapter sequences were trimmed with CutAdapt v3.4
Reads were aligned to the dm6.26 genome assembly using Bowtie2 v2.4.2
Aligned reads were sorted with samtools v1.12 and deduplicated with the markDuplicates function in Picard v2.23.
Differential chromatin accessibility was performed using DiffBind v2.10.0 and DESeq2 v1.32.0
Peaks were annotated using ChIPseekR v1.30.3
Coverage files were generated using Deeptools v3.3.2
Assembly: dm6.26
Supplementary files format and content: Differential chromatin accessibility and peak annotation in .tsv files

organism: Drosophila melanogaster

source_name: Neurons from heads

extract_protocol:
Nuclei were isolated as described in Merrill CB,Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. (2022)  Optimized assay for transposon-accessible chromatin by sequencing (ATAC-seq) preparation from adult Drosophila melanogaster neurons. Scientific Reports 12: 6043.
ATAC-seq libraries were constructed by incubating isolated nuclei with Illumina Tn5 enzyme for 23 min at 37 °C. Tagged DNA was purified using a Qiagen MinElute PCR purification kit. Purified fragments were amplified by PCR using Illumina index primers. Amplified libraries were purified and size-selected using AMPure XP beads.

value: Neurons from heads


title: WT ES ChIP-seq replicate 1


title: Late_2


title: C140, hippocampus, NovaSeq

description:
C140_c12
10X Genomics
Visium Spatial Gene Expression

value: Brain (hippocampus)

value: diverse brain cell types

value: no treatment

value: female


title: Late_1


title: UBV PHH at 39hr rep2

value: Primary human hepatocytes, mouse embryonic fibroblasts

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

value: 39 hours post-synchronization


title: nsyb-3


title: UBV PHH at 39hr rep3

value: primary human hepatocyte, mouse embryonic fibroblast

value: WT


title: L0172F/L1072F ES ChIP-seq input


title: UBV PHH at 39hr rep1

value: circadian synchronization and RNA extraction


title: nsyb-1


title: nsyb-2


title: ErD_5

value: prostate cancer cell line PPC1

value: early progeny of PGCC

value: 8 Gy radiation + 8 days


title: UBV PHH at 36hr rep3

value: 36 hours post-synchronization


title: ErD_4


title: L834P/L834P ES ChIP-seq input


title: elav-4


title: UBV PHH at 36hr rep2


title: elav-3


title: WT ES ChIP-seq input


title: UBV PHH at 36hr rep1


title: ErD_2


title: UBV PHH at 33hr rep2

value: 33 hours post-synchronization


title: R1242Q/+ NPC-2 RNA-seq replicate 2

source_name: Neural progenitor cell

growth_protocol: ES cells were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in ES culture medium with 15% fetal bovine serum (Life Technologies) and antibiotics. ES cell–derived neural progenitor cells were generated by re-plating d 8 and d 14 neural differentiation cultures on low attachment dish in Neural differential medium.

extract_protocol:
ES and Neural progenitor cells were lysed with ISOGEN (Nippon gene, 311-02501). RNA were purified with the use of  PureLink RNA Mini Kit (Invitrogen). NEBNext Library Quant Kit for Illumina (NEB, E7630L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Day14 NPC


title: elav-1

value: Neurons from heads


title: elav-2


title: R1242Q/+ NPC-2 RNA-seq replicate 1


title: ErD_6


title: Gi_6

value: radiation induced PGCC

value: 8 Gy radiation + 2 days


title: UBV PHH at 30hr rep3

value: 30 hours post-synchronization


title: L1072F/+ NPC-2 RNA-seq replicate 3


title: R910Q/R910Q ES ChIP-seq input


title: tub-3

source_name: Whole fly

value: Whole fly


title: tub-4


title: Gi_5


title: ErD_1


title: L1072F/+ NPC-2 RNA-seq replicate 2


title: tub-2


title: UBV PHH at 33hr rep1

value: Primary human hepatocytes, mouse embryonic fibroblasts


title: ErD_3


title: UBV PHH at 30hr rep1

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]


title: L1072F/+ NPC-2 RNA-seq replicate 1


title: tub-1


title: R1242Q/+ NPC-2 RNA-seq replicate 3


title: Gi_4


title: UBV PHH at 27hr rep2

value: 27 hours post-synchronization


title: Gi_3


title: Gi_2


title: R910Q/+ NPC-2 RNA-seq replicate 3


title: UBV PHH at 27hr rep1

value: primary human hepatocyte, mouse embryonic fibroblast


title: R910Q/+ NPC-2 RNA-seq replicate 2


title: actin-4


title: UBV PHH at 24hr rep3

value: WT

value: 24 hours post-synchronization


title: actin-3


title: actin-2


title: UBV PHH at 30hr rep2

value: circadian synchronization and RNA extraction


title: R910Q/+ NPC-2 RNA-seq replicate 1