title: MOC1 cells (passage 10), rep4

city: Ljubljana

first: Maja

last: Cemazar

address: Zaloska 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

description: column MOC1_L in fpkm_sample.txt

data_processing:
quality control: fastp
mapping to reference genome: HISAT2
quantification: featurecounts
differential expression analysis: DESeq2
Assembly: grcm38
Supplementary files format and content: fpkm_sample.xls includes fpkm values for each sample

source_name: cell line

growth_protocol: Cells were cultured in MOC medium, consisting of  of Iscove's Modified Dulbecco's Medium (IMDM)/Ham’s F12 Nutrient Mixture in a ratio of 2:1, supplemented with 5% (v/v) fetal bovine serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 5 µg/mL insulin, 40 ng/mL hydrocortisone and 5 ng/mL epidermal growth factor. Cells were maintained at 37 °C in a 5 % CO2 humidified atmosphere.

extract_protocol:
Cells were trypsinized with 0.25 % trypsin and the RNA was extracted using the peqGOLD Total RNA Kit (VWR, West Chester, PA, USA) following the manufacturer’s instructions. The purity of the isolated RNA was assessed spectrophotometrically using the A260/A280 and A260/A230 ratios. The quality of the RNA was assessed using the RNA Assay for LabChip® GX Touch (PerkinElmer, Waltham, Massachusetts, ZDA) according to the manufacturer’s instructions. Samples with an RNA Quality Score higher than 6.8 were used for transcriptome sequencing
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: cell line

tag: cell line

value: murine oral squamous cell carcinoma

value: WT


title: mRNA_22_T1

status: Public on Jun 14 2023

type: SRA

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

library_source: transcriptomic

data_processing:
Fastqc
Trimming of reads using trimmomatic and fastp
Hisat2 alignment using Ensemble Grch38
Raw Gene ocunt generation using htseq-count program
Assembly: Grch38
Supplementary files format and content: htseq-Count text fiile

molecule: total RNA

organism: Homo sapiens

source_name: Female - NO ICU

extract_protocol:
Total RNA
NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads

tag: disease state

tag: Sex

value: Female

tag: tissue

value: Blood

tag: visit

tag: outcome

value: NO ICU


title: T1245_GS6_4N_M_D3

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)

molecule: genomic DNA

source_name: Single prostate tumor cell

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: cell type

value: Single prostate tumor cell

tag: patient donor/cell_line

tag: genome build

tag: cpg coverage

tag: bisulfite conversion_rate

tag: qc

value: fail


title: CD8+ T cells, FIH_KO_2

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-sequencing: 2x75-nt sequence reads using Illumina NextSeq 550.
Basecalling and demultiplexing was performed using Illumina bcl2fastq.
Reads were aligned to the mm10 reference genome using STAR.
Read summarization to gene counts was performed using featureCounts.
Normalization of raw counts and differential gene expression were performed using DESeq2.
Assembly: mm10.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Mus musculus

source_name: Spleen

growth_protocol: Splenic CD8+ T cells from Hif1an-floxed dLck Cre- or Vhl-floxed dLck Cre- (‘WT’) , Hif1an-floxed dLck Cre+ (‘FIH KO’), Vhl-floxed dLck Cre+ (‘VHL KO’) and Hif1an--floxed/Vhl--floxed dLck Cre+ (‘FIH/VHL KO’) C57BL6/J mice were activated in complete RPMI (Gibco) with anti-CD3/anti-CD28 Dynabeads and 10units/ml recombinant human IL-2 for 3 days.

extract_protocol:
On day 3 CD8+ T cells were washed twice with ice cold PBS (Gibco) and lysed with RLT buffer containing 1% β-mercaptoethanol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD8+ T cells were activated in complete RPMI (Gibco) with anti-CD3/anti-CD28 Dynabeads and 10units/ml recombinant human IL-2 for 3 days.

value: Spleen

value: CD8+ T cells

tag: genotype

value: fih knockout


title: MOC1 cells (passage 10), rep3

description: column MOC1_K in fpkm_sample.txt


title: CD8+ T cells, VHL_KO_3

value: vhl knockout


title: ID8_R_Ola_rep1

city: Denver

first: Lily

last: Nguyen

state: CO

address: 220 Roslyn Street, Apt 706

institute: UNIVERSITY OF COLORADO DENVER

data_processing:
quality assessement using FastQC (v0.11.8) and MultiQC (v1.7)
adapter trimming using BBDuk/BBMap (v38.05)
genome alignment using using hisat2 (v2.1.0)
Assembly: hg38, mm10
Supplementary files format and content: bigwig tracks were generated using the bamCoverage function of deepTools (v3.0.1)

source_name: OC

growth_protocol: Cell Culture- PEO1 (RRID:CVCL_2686), Kuramochi (RRID:CVCL_1345), and OVCA420 (RRID:CVCL_3935) cell lines were provided through the Gynecologic Tumor and Fluid Bank (GTFB). ID8 cell line was kindly gifted from Dr. Iain McNeish lab (Imperial College London). All cells were authenticated via STR at The University of Arizona Arizona Genetics Core (RRID:SCR_012429). All cells undergo monthly mycoplasma testing using Sigma LookOut Mycoplasma Detection kit (Cat. #MP0035) and are only culture up to 20 passages or two months. Cells are cultured in RPMI1640 (Gibco) in 10% FBS (Phoenix Scientific Cat. #PS-100) and Penicillin Streptomycin (Cat. #SV30010) at 37C in 5% CO2. ID8 cells are cultured in DMEM (Gibco, Cat. #11995-065) supplemented with 4% FBS, Penicillin Streptomycin and 1x ITS (Gibco Cat. #41400-045).   Ex vivo Culture - Primary ovarian cancer tumors (Table S1) were collected at The University of Colorado Cancer Center under the Colorado Multiple Institutional Review Board (COMIRB) Gynecologic Tumor and Fluid Bank protocol #07-935. All patients are consented under the GTFB protocol and collected specimens are deidentified. Tumors are collected by the Biorepository Shared Resource and delivered to the lab within one hour of surgical dissection. Tumors are sliced using a Krumdeick Tissue Slicer into 300 micron thick discs and placed in warmed culture media. Tumor sections treated for 72 hours, are either stored at -80C  in RLT plus buffer (Qiagen, Cat. #74136 ) or fixed in 10% buffered formalin. RNA was extracted from tissues stored in the RLT buffer and used for RNA-sequencing. Fixed tissues were embedded in paraffin at the University of Colorado Histopathology Shared Resources.   Cell culture and generation of EHMT1 and 2 overexpression - PEO1 cells were maintained in RPMI+ 10% heat inactivated FBS (Avantor, Cat. #10803-034) + 100 μg/mL Penicilin/Streptomycin (Lonza, Cat. #09-757F). EHMT1 or EHMT2 overexpression cells were obtained by using lentivirus to infect cells with either TRE_EHMT1_hygromycin or TRE_EHMT2_hygromycin. To produce lentivirus, 500,000 Lenti-X 293T cells were seeded on 6-well plate. Twenty-four hours later, the cells were transfected with packaging plasmids (0.5µg pCMV-VSV-G, 1.1µg pD8.9), 0.85µg transfer plasmid, 7.35µg of PEI MAX (Polysciences Inc., Cat. #24765-1) and 10mM HEPES. Media was changed 24 hours later. Supernatant with virus was collected 48 and 72 hours post transfection. The supernatant was filtered using a 0.45µm PES Filter membrane (Whatman Uniflo, Cat. #9914-2504). Cells were then infected using 1mL of supernatant with 5 µg/mL polybrene (EMD Millipore, Cat. #TR-1003-G). Media was changed 24 hours later. 48 hours post transduction, cells were selected using 200μg/ml Hygromycin B (Biosciences, Cat. #31282-04-9). Cells were selected until death of non-transduced cells. Once cells were selected, they were induced for EHMT1 or EHMT2 expression using Doxycycline (1µg/ml, TCI, Cat. #D4116) for four days and collected. Cells were immunoblotted for EHMT1 (Bethyl, Cat. #A301-642A; dilution 1:500), EHMT2 (Cell Signaling, Cat. #3306; RRID:AB_2097647; dilution 1:1000), alpha-tubulin (Cell Signaling Cat. #3873; RRID:AB_1904178; dilution 1:3000), and H3K9me2 (Cell Signaling Cat. #4658; RRID:AB_10544405; diluted 1:1000).

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Sequencing libraries were prepared from RNA harvested from treatment or transfection replicates. Total RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Cat. #D4209). Ribosome depletion and library preparation was performed using the Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581) according to the manufacturer’s protocols. Briefly, 500ng of RNA was used as input, and KAPA BioSystems single-index adapters were added at a final concentration of 1.5mM. Purified, adapter-ligated library was amplified for a total of 11 cycles following the manufacturer’s protocol. The final libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core) as 150 bp paired-end reads.

treatment_protocol: Cells were treated with DMSO, olaparib, UNC0642, or olaparib + UNC0642 for 72 hours

tag: phenotype

tag: treatment

value: olaparib

tag: timepoint


title: T1245_GS6_4N_M_E1

value: pass


title: mRNA_20_T1

source_name: Male - NO ICU

value: Male


title: T1245_GS6_4N_M_D2


title: MOC1 cells (passage 9), rep2

description: column MOC1_J in fpkm_sample.txt


title: CD8+ T cells, FIH_KO_1


title: mRNA_15_T1

source_name: Male - ICU

value: ICU


title: CD8+ T cells, WT_4

value: wild type


title: T1245_GS6_4N_M_D1


title: mRNA_13_T1


title: T1245_GS6_4N_M_C3


title: CD8+ T cells, WT_3


title: MOC1-HPV K3 cells (passage 15), rep4

description: column K3_H in fpkm_sample.txt

value: cell line

value: MOC1-HPV K3

value: colony 3 of murine oral squamous cell carcinoma expressing HPV-16 E6 and E7

value: HPV-16 E6E7 insertion


title: T1245_GS6_4N_M_E2


title: MOC1 cells (passage 8), rep1

description: column MOC1_I in fpkm_sample.txt

value: murine oral squamous cell carcinoma

value: WT


title: CD8+ T cells, WT_2


title: MOC1-HPV K3 cells (passage 15), rep3

description: column K3_G in fpkm_sample.txt


title: T1245_GS6_4N_M_C2

value: Single prostate tumor cell


title: mRNA_7_T1

value: Blood


title: mRNA_12_T1

value: NO ICU


title: T1245_GS6_4N_M_B3

value: fail


title: T1245_GS6_4N_M_B2


title: mRNA_17_T1


title: dipc_Z5_OMP_47

city: New York

first: Elizaveta

last: Bashkirova

state: NY

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

description:
Dip-C
150PE
B6_and_129P2_vs_CAST_merged.snps.chr.txt.gz

data_processing:
The ".con" files contain haplotype reloved long-range contacts. The SNP file used to resolve haplotypes is in the supplementary files. The ".3dg" (3D genome) files contain the x,y,z coordinates of genomic positions at 20kb resolution in the 3D model. The ".cif" files storing structures of the 3D genome at 20kb resolution with OR gene clusters annotated can be viewed with PyMol as described in (https://github.com/tanlongzhi/dip-c).
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN and Dip-C adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler. For Dip-C, the haplotype of aligned contacts was resolved with hickit (followint the Dip-C) pipeline (https://github.com/tanlongzhi/dip-c) and 3D models of nuclei were generated.
Genome_build: mm10

source_name: GFP+ cells from zone5 of the olfactory epithelium

growth_protocol: adult mice > 8 weeks

extract_protocol:
Fixed sorted cells were used for Dip-C as described in Tan et al 2019
Dip-C libraries were prepared as described in  in Tan et al 2019

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 2% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then inactivated with 1% BSA.  Fixed cells were pelleted , washed with cold PBS with 1% BSA, and passed through a 40um filter, before FAC-sorting GFP+ fluorescent cells.

tag: genotype/variation

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)

tag: tissue/cell type

value: mature olfactory sensory neurons (mOSN)


title: dipc_Z5_OMP_46


title: A454

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

data_processing:
Fastq files were uploaded to the DolphinNext platform (34) at the UMass Chan Medical School Bioinformatics Core for mapping and quantification. The reads were subjected to FastQC (v0.11.8) analysis, and the quality of reads was assessed. Nine nt molecular labels were trimmed from both 5’ends of the pair-end reads and quality-filtered with Trimmomatic (0.32). Reads were mapped to the genome assembly GRCh38 (hg38) version 34 using the STAR (v2.5.3a) aligner. Gene and isoform expression levels were quantified by RSEM (1.2.11). Gene Ontology (GO) enrichment analysis was done using the clusterProfiler package (31) for biological processes enriched in the differentially expressed genes.
Differential gene expression analysis: DESeq2 (v3.9) was used to obtain differentially expressed genes from the estimated counts table. After normalization by the median of ratios method, genes with minimal 5 counts average across all samples were kept for the Differential Gene expression analysis. The Padj < 5% was used as a cutoff. The TDF files generated were uploaded on the Integrative Genomics Viewer (2.6.2) for visualization.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Human Leukocytes

extract_protocol:
Eight mL fresh blood were collected from FXS male individuals (N=29) and age-matched typically developing (TD) males (N=13)  in a K2EDTA Tube and the leukocytes collected on a LeukoLOCKTM filter prior to RNA extraction using a LeukoLOCK Fractionation & Stabilization Kit, Ambion #1933 as per the manufacturer’s instructions. Briefly, the blood samples were passed through LeukoLOCKTM filters that were then rinsed with 3 mL phosphate buffered saline (PBS) followed by 3 mL of RNAlater®. The filters were capped and stored in -80 deg C. To extract RNA, the filters were thawed at room temperature for 5 mins and then the remaining few drops of RNAlater were removed. The filter was flushed with 4 ml of TRIzol™ LS Reagent (ThermoFisher Scientific #10296028) and the lysate collected in a 15 ml tube. 800 μl bromo-3-chloro-propane (BCP) (Sigma #B9673) was added to each tube and vortexed vigorously for 30 sec. The tube was then incubated at room temp for 5 min and centrifed for 10 min at 40C at ~2,000 x g;  the aqueous phase containing the RNA was recovered. To recover the long RNA fraction, 0.5 volumes of 100% ethanol were added and mixed well. The RNA was then recovered using an RNA clean and concentrator kit (Zymo Research, #11-325 / R1015), DNase treated with TURBO™ DNAse (Invitrogen # AM2238) and the RNA resuspended in RNAse free water and stored at –80°C.
Three mg of RNA sample was used for directional mRNA library preparation using polyA enrichment (Novogene Co) and the libraries sequenced on the NovaSeq platform to generate paired end, 150bp reads at a sequencing depth of 60 million reads per sample

tag: gender

value: Human Leukocytes

value: TD

value: Isolated from blood using LeukoLOCK filter


title: CD8+ T cells, WT_1

value: Spleen

value: CD8+ T cells


title: MOC1-HPV K1 cells (passage 15), rep3

description: column K1_C in fpkm_sample.txt

value: cell line

tag: cell line

value: MOC1-HPV K1

value: colony 1 of murine oral squamous cell carcinoma expressing HPV-16 E6 and E7


title: dipc_Z5_OMP_48


title: A455

value: Male


title: A422


title: MOC1-HPV K1 cells (passage 15), rep4

description: column K1_D in fpkm_sample.txt

tag: tissue

value: HPV-16 E6E7 insertion


title: MOC1-HPV K3 cells (passage 10), rep1

description: column K3_E in fpkm_sample.txt

value: MOC1-HPV K3

value: colony 3 of murine oral squamous cell carcinoma expressing HPV-16 E6 and E7


title: T1245_GS6_4N_M_A3

value: Single prostate tumor cell

value: pass


title: dipc_Z5_OMP_45


title: MOC1-HPV K1 cells (passage 10), rep2

description: column K1_B in fpkm_sample.txt


title: MOC1-HPV K1 cells (passage 10), rep1

description: column K1_A in fpkm_sample.txt


title: T1245_GS6_4N_M_B1

value: fail


title: A401


title: A400


title: T1245_GS6_4N_M_A2


title: MOC1-HPV K3 cells (passage 10), rep2

description: column K3_F in fpkm_sample.txt


title: dipc_Z5_OMP_44

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)


title: T1245_GS6_4N_M_A1


title: A457

value: FXS


title: dipc_Z5_OMP_43

value: mature olfactory sensory neurons (mOSN)


title: N1484_2N_M_H2

source_name: Single normal prostate cell

value: Single normal prostate cell


title: KO-3 colon, dss-treated, Day5

city: Chuncheon

first: Hyun-Jeong

last: Ko

address: Kangwondaehak-gil 1

department: Department of Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic 0.38
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0, Bowtie2 2.3.4.1
Read count extraction and normalization were performed using StringTie version 2.1.3b
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM/RPKM and TPM values for each Sample

source_name: colon

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: colon

value: ERdj5 Knockout

value: DSS-treated

tag: time

value: Day 5


title: T1245_GS6_4N_M_C1


title: A427

value: Human Leukocytes

value: TD

value: Isolated from blood using LeukoLOCK filter


title: A453

value: Male


title: KO-2 colon, untreated, Day5

value: Control


title: dipc_Z5_OMP_42


title: A435


title: KO-1 colon, dss-treated, Day5


title: KO-2 colon, dss-treated, Day5


title: N1484_2N_M_G2


title: A426


title: KO-1 colon, untreated, Day5


title: N1484_2N_M_F3


title: WT-3 colon, dss-treated, Day5

value: WT


title: dipc_Z5_OMP_40


title: dipc_Z5_OMP_41


title: N1484_2N_M_F1


title: WT-2 colon, dss-treated, Day5


title: A420


title: dipc_Z5_OMP_38


title: N1484_2N_M_G1


title: WT-1 colon, dss-treated, Day5


title: A395


title: N1484_2N_M_E3


title: A394


title: dipc_Z5_OMP_37


title: dipc_Z5_OMP_36


title: A393


title: N1484_2N_M_E2


title: WT-2 colon, untreated, Day5


title: dipc_Z5_OMP_35


title: N1484_2N_M_G3


title: WT-1 colon, untreated, Day5


title: N1484_2N_M_D3


title: N1484_2N_M_E1


title: A388


title: dipc_Z5_OMP_34


title: dipc_Z5_OMP_39


title: A379


title: A387


title: dipc_Z5_OMP_32


title: N2a-2.Nova

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

country: China

institute: Huaqiao University

description: N2a cells, sequenced on Illumina NovaSeq 6000 platform, replica2

data_processing:
Only paired-end raw reads, where read 1 started with 9-11 Gs, read 2 started with 11-13 Ts and each base of each read had Phred quality score >20 were selected.
These reads were then aligned to the chrM of GRCh37/hg19, GRCm38/mm10, and GRCg6a/galGal6 assemblies of human, mouse, and chicken genomes from UCSC Genome Browser (PMID: 12045153) respectively using BWA-MEM (v0.7.12) with default settings.
Only pairs of reads where both reads 1 and 2 uniquely mapped to the genome with appropriate configuration and spacing were kept.
The 5’-end was defined as the first base after 9-11 Gs in read 1.
Read count of each position was obtained and normalized depth was calculated with read count of each position being normalized to total number of aligned reads.
Assembly: GRCh37/hg19, GRCm38/mm10, and GRCg6a/galGal6
Supplementary files format and content: Processed data are in BED files containing coordinates of mitochondrial genome positions with free DNA 5'-end signals. The 4th and 5th columns show the raw and normalized count of each position.

growth_protocol: Human breast cancer cell line BT549, human cervical carcinoma cell line HeLa, human liver cancer cell line HepG2, and human chronic myeloid leukemia cell line K562 were maintained in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco). Mouse neuroblastoma cell line N2a was cultured in MEM/EBSS (HyClone) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Uruguay) and 1% penicillin-streptomycin (Gibco). All cell lines were cultured at 37℃ in 5% CO2. Adult male mice (three-month-old) of C57BL/6J strain were used to extract heart and liver. The tissues were frozen in liquid nitrogen immediately after isolation. Chicken heart and liver samples were bought from the fresh market and frozen in liquid nitrogen within 30 min. The animal tissues were cut into pieces and ground with mortar in liquid nitrogen. The ground tissues were stored at -80 ℃ prior to DNA isolation.

extract_protocol:
DNA was isolated with TIANamp Genomic DNA Kit (Tiangen)
The biochemistry part of 3’ ends tailing was based on the SSiNGLe-ILM protocol from our previous study (PMID: 31862872). Briefly, 100 ng of the purified DNA was denatured at 95℃ for 5 min in 19 µl volume containing 2 µl of 10x TdT buffer and 2 µl of 2.5 mM CoCl2 followed by rapid snap-cooling on ice. TdT (5 units, NEB) and 2 µl of 10 mM dATP (Takara) were then added to denatured DNA to a total volume of 22 µl and incubated at 37°C for 30 min. To block free 3′-OH ends, samples was mix with 2 µl of 10 mM ddNTP (Roche) and incubated at 37℃ for additional 30 min, followed by enzyme of VAHTS DNA clean beads to a final volumn of 15 μl and mixed with 2 µl of 10x Taq buffer (Tiangen), 1.6 µl of 2.5 mM dNTP mix (Takara), 1 µl of 10 µM of polyT primer (a chimeric DNA-RNA oligo-d(T)50-r(T)3 oligonucleotide) and 1 unit of Taq DNA polymerase (Tiangen). The amplification conditions were as follows: initial denaturation at 94℃ for 3 min, followed by 10 cycles of denaturation at 94 °C for 30 s, annealing at 55℃ for 30 s and extension at 72℃ for 30 s. The PCR products were purified with 2x volumes of VAHTS DNA clean beads and tailed with dCTP (Takara) with the same procedure used for polyA tailing, followed by blocking of 3’-OH ends as described above. The tailing products were purified with 2x volume of VAHTS DNA clean beads and all purified DNA was PCR-amplified with P5_10N10G (CTACACGACGCTCTTCCGATCTAGTTGCGGATGGGGGGGGGGHN) and P7_T12 (GTTCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTVN) primers with the following amplification conditions: initial denaturation at 94℃ for 3 min; 1 cycle of denaturation at 94℃ for 30 s, annealing at 55℃ for 1 min and extension at 72℃ for 1 min; 1 cycle of denaturation at 94℃ for 30 s, annealing at 37℃ for 1 min and slow ramp at 2℃ per minute to 72℃; 30 cycles at 94℃ for 30 s, annealing at 60℃ for 30 s, and extension at 72℃ for 30 s; final extension at 72℃ for 7 min. The amplified DNA was purified with 2x volumes of VAHTS DNA clean beads to a final volumn of 17 μl of water, and 4 µl PCR products were used as the template for the second round of nested PCR with lIlumina_P5 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and primer Illumina_P7 (CAAGCAGAAGACGGCATACGAGATcgtgatGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) as primers under the following conditions.: 94℃ for 3 min; 6 cycles of 94℃ for 30 s, 55℃ for 30 s and 72℃ for 30 s; 72℃ for 7 min. PCR products were purified with 2x volumes of VAHTS DNA Clean Beads.

value: mouse neuroblastoma cell line


title: dipc_Z5_OMP_31


title: N2a-1.Nova

description: N2a cells, sequenced on Illumina NovaSeq 6000 platform, replica1


title: A376


title: N1484_2N_M_C3


title: N1484_2N_M_D1

value: pass


title: Mouse-L-2.Nova

description: Mouse liver, sequenced on Illumina NovaSeq 6000 platform, replica2

source_name: Liver

value: Liver


title: A377


title: dipc_Z5_OMP_29

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)


title: N1484_2N_M_C2

value: fail


title: dipc_Z5_OMP_33

value: mature olfactory sensory neurons (mOSN)


title: A372

value: FXS


title: A373


title: N1484_2N_M_C1

value: Single normal prostate cell


title: Mouse-L-1.Nova

description: Mouse liver, sequenced on Illumina NovaSeq 6000 platform, replica1


title: dipc_Z5_OMP_28


title: dipc_Z5_OMP_30


title: A369


title: N2a-3.Nova

description: N2a cells, sequenced on Illumina NovaSeq 6000 platform, replica3


title: N1484_2N_M_D2


title: N1484_2N_M_B3


title: Mouse-H-3.Nova

description: Mouse heart, sequenced on Illumina NovaSeq 6000 platform, replica3

source_name: Heart

value: Heart


title: Mouse-H-2.Nova

description: Mouse heart, sequenced on Illumina NovaSeq 6000 platform, replica2


title: N1484_2N_M_B2


title: dipc_Z5_OMP_27


title: dipc_Z5_OMP_26


title: A367


title: Mouse-H-1.Nova

description: Mouse heart, sequenced on Illumina NovaSeq 6000 platform, replica1


title: Mouse-L-3.Nova

description: Mouse liver, sequenced on Illumina NovaSeq 6000 platform, replica3


title: Mouse-B-3.Nova

description: Mouse brain, sequenced on Illumina NovaSeq 6000 platform, replica3

source_name: Brain

value: Brain


title: N1484_2N_M_B1


title: A365


title: N1484_2N_M_A3


title: 33-4

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

data_processing:
adapter trimming with Trim Galore
genome alignment with STAR v2.6.1
Raw counts generated with Subread FeatureCounts v1.6.3
Assembly: GRCh38
Supplementary files format and content: mir33.bulk.RNAseq.log2.normalized.tpm.matrix.6.7.21.txt: tab delimited table of log2 transformed transcripts per million mapped reads

source_name: IPF Precision Cut Lung Slice; treated with PNA-33

extract_protocol:
miRNeasy Mini Kit
KAPA Stranded mRNA-Seq Kit

treatment_protocol: Treatment with either PNA-33 or scramble control for 5 days

value: Lung

value: assorted

value: Day 5


title: dipc_Z5_OMP_25


title: N1484_2N_M_A2


title: dipc_Z5_OMP_23


title: dipc_Z5_OMP_22


title: dipc_Z5_OMP_24


title: 33-3


title: N1484_2N_M_A1


title: 33-2


title: Mouse-B-1.Nova

description: Mouse brain, sequenced on Illumina NovaSeq 6000 platform, replica1


title: N1245_2N_M_H3


title: NSC, TFBTBOA, Glut, Rep3

city: Columbus

first: Elizabeth

middle: Diana

last: Kirby

state: OH

address: 1835 Neil Ave, 55 Psycholgy

department: Psychology

institute: The Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Assembly: GRCh38
Supplementary files format and content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

molecule: polyA RNA

source_name: mouse dentate gyrus

growth_protocol: Grown on poly-d-lysine laminin coated plates in neurobasal A media with 1x B27 (without vitamin A), 1 x glutaMAX, 20 ng/ml recombinant epidermal growth factor and 20 ng/ml basic fibroblast grwoth factor.

extract_protocol:
After 48 hours, cells were harvested with Accutase (StemCell technologies) and a subset (approximately 75,000 cells) was pelleted prior to RNA extraction using the NucleoSpin RNA Plus XS kit (Takara) following manufacturer protocol. Assessment of RNA quality with Qubit RNA HS assay kit (Invitrogen) revealed RIN values of at least 8 for all samples.
Libraries were generated with the Clontech SMART/Seq HT kit (Takara).

treatment_protocol: NSCs of passage 4 were plated 75,000 cells per well in a 12 well plate and treated with 1 µM TFB-TBOA or vehicle for 15 minutes prior to the addition of 100 µM glutamate or vehicle (n = 3 wells per treatment).

value: mouse dentate gyrus

value: neural stem cells

tag: strain

value: wild type

value: TFBTBOA-Glut


title: dipc_Z5_OMP_20


title: A366

value: Male

tag: cell type

value: Human Leukocytes

value: Isolated from blood using LeukoLOCK filter


title: 33-1


title: N1245_2N_M_H2

tag: patient donor/cell_line


title: CTR-4

source_name: IPF Precision Cut Lung Slice; treated with scramble

value: scramble


title: NSC, TFBTBOA, Glut, Rep1


title: N1245_2N_M_H1

tag: genome build

value: fail


title: dipc_Z5_OMP_18

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)

value: mature olfactory sensory neurons (mOSN)


title: NSC, TFBTBOA, Glut, Rep2


title: dipc_Z5_OMP_19


title: Mouse-B-2.Nova

description: Mouse brain, sequenced on Illumina NovaSeq 6000 platform, replica2

value: WT


title: CTR-3


title: dipc_Z5_OMP_17


title: NSC, TFBTBOA, Veh, Rep2

value: TFBTBOA-Veh


title: NSC, TFBTBOA, Veh, Rep3


title: N1245_2N_M_G3

value: Single normal prostate cell

tag: cpg coverage

value: pass


title: CTR-1

value: Lung

value: assorted


title: dipc_Z5_OMP_16


title: N1245_2N_M_G2

tag: bisulfite conversion_rate


title: N1245_2N_M_G1

tag: qc


title: NSC, TFBTBOA, Veh, Rep1

value: mouse dentate gyrus

tag: genotype


title: dipc_Z5_OMP_14


title: dipc_Z5_OMP_13


title: N1245_2N_M_F3


title: MDA-MB-436_shMUC1_3

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.9a).
The number of fragments in each known gene from GENCODE (version 33) was quantified using featureCounts.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Assembly: GRCh38.p7
Supplementary files format and content: The first columns represent gene symbol. The other columns are raw counts for all the samples.

source_name: Cell Line

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: Triple-Negative Breast Cancer Cell Line

value: doxycycline


title: N1245_2N_M_F2


title: NSC, Veh, Glut, Rep2

value: neural stem cells

value: wild type

value: Veh-Glut


title: MDA-MB-436_shMUC1_2


title: dipc_Z5_OMP_12


title: N1245_2N_M_F1


title: MDA-MB-436_shMUC1_1


title: NSC, Veh, Glut, Rep1


title: dipc_Z5_OMP_11


title: MDA-MB-436_control_shRNA_3

value: DMSO


title: NSC, Veh, Veh, Rep3

value: Veh-Veh


title: N1245_2N_M_E3


title: N1245_2N_M_E2


title: dipc_Z5_OMP_10


title: MDA-MB-436_control_shRNA_2


title: CTR-2

value: Day 5

value: scramble


title: dipc_Z5_OMP_9

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)

value: mature olfactory sensory neurons (mOSN)


title: NSC, Veh, Veh, Rep2


title: NSC, Veh, Veh, Rep1


title: N1245_2N_M_E1


title: N1245_2N_M_D3

value: fail


title: BT549_shPBRM1_3

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.9a).
The number of fragments in each known gene from GENCODE (version 33) was quantified using featureCounts.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Assembly: GRCh38.p7
Supplementary files format and content: The first column represents gene symbol. The other columns are raw counts for each sample.


title: dipc_Z5_OMP_7


title: WGBS_E8.5 Whole Embryo_Zmym2KO_M_sample8

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

data_processing:
Reads were trimmed using Trim Galore! (v0.6.6) software (parameters: -q 20, --clip_r1 10 --clip_r2 15 --three_prime_clip_r1 15 --three_prime_clip_r2 10).
Trimmed reads were then aligned to the mm10 genome or lambda genome (for assessing conversion efficiency) using Bismark (v0.22.3) using default parameters.
Aligned reads (BAMs) were then deduplicated (using the deduplicate_bismark function)  and were subsequently  filtered for incomplete bisulfite conversion (using filter_non_conversion functions) in Bismark(v0.22.3). Replicate samples were merged using Samtools(v1.12).
Methylation calls were made using the bismark_methylation_extractor function in Bismark(v0.22.3)
Methylation calling over cytosines was then done using Bismark and overall DNA methylation was then calculated as a mean of all cytosine bases in CpG context
Assembly: GRCm38/mm10
Supplementary files format and content: Coverage file (tab-delimited text file) containing base-resolution (columns 1-3) % CpG methylation (column 4) and overall coverage (columns 5+6)

source_name: Whole Embryo

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA mini kit (Qiagen, 51304) or AllPrep DNA/RNA Micro Kit (Qiagen, 82084). 500 ng of genomic DNA and 1.25ng of Lambda spike-in DNA was sheared using the M220 ultrasound sonicator (Covaris) to an average genomic size of 350 bp. 200 ng of sheared DNA was bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zmyo Research, D5005) using manufacturer’s instructions.
Up to 100 ng of genomic DNA was then used to generate WGBS libraries with the Accel-NGS Methyl-Seq DNA Library prep kit (Swift Biosciences, 30024) according with manufacturer’s instructions and 13 cycles of PCR for final library amplification.

tag: developmental stage

value: Whole Embryo

tag: Sex

value: Male

value: Zmym2 Knockout


title: dipc_Z5_OMP_8


title: NSC, Veh, Glut, Rep3

tag: treatment


title: WGBS_E8.5 Whole Embryo_Zmym2KO_M_sample7


title: N1245_2N_M_D2

value: Single normal prostate cell


title: WGBS_E8.5 Whole Embryo_Zmym2KO_M_sample6


title: BT549_shPBRM1_1


title: dipc_Z5_OMP_6

tag: genotype/variation


title: N1245_2N_M_D1

value: pass


title: dipc_Z5_OMP_5

tag: tissue/cell type


title: BT549_control_shRNA_3

value: Triple-Negative Breast Cancer Cell Line


title: N1245_2N_M_C3


title: WGBS_E8.5 Whole Embryo_Zmym2KO_M_sample5_rep2


title: BT549_control_shRNA_2


title: WGBS_E8.5 Whole Embryo_Zmym2KO_M_sample5_rep1


title: MDA-MB-436_control_shRNA_1


title: dipc_Z5_OMP_4


title: BT549_control_shRNA_1


title: dipc_Z5_OMP_3


title: dipc_Z5_OMP_2


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample4

value: Female


title: BT549_shPBRM1_2

value: doxycycline


title: BT549_shIRF1_2


title: dipc_Z5_OMP_1


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample3


title: BT549_shIRF1_3


title: N1245_2N_M_B3


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample2_rep2


title: BT549_shIRF1_1


title: N1245_2N_M_B1


title: N1245_2N_M_B2


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample2_rep1


title: BT549_control_shRNA_3


title: dipc_Z1_OMP_46

source_name: GFP+ cells from zone1 of the olfactory epithelium


title: dipc_Z1_OMP_48


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample1_rep2


title: BT549_control_shRNA_2


title: WGBS_E8.5 Whole Embryo_Zmym2KO_F_sample1_rep1


title: N1245_2N_M_A2


title: dipc_Z1_OMP_45


title: BT549_control_shRNA_1


title: WGBS_E8.5 Whole Embryo_WT_M_sample8

value: Wild-Type


title: N1245_2N_M_C1


title: dipc_Z1_OMP_44


title: N1245_2N_M_A1


title: Human hepatocytes, replicate 2, snRNAseq

city: Westmead

first: Suzanne

last: Scott

state: NSW

address: 214 Hawkesbury Rd

country: Australia

institute: Children's Medical Research Institute

description:
ROD_C3
hep2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Combined GRCh38, mm10, AAV reference
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
To identify and characterize cell states associated with AAV transduction in human heptocytes, we employed a droplet-based (10x chromium) single nucleus transcriptomics approach. Hepatic nuclei were isolated and profiled from (a) human hepatocytes before engraftment, (b) liver samples from FRG mice engrafted with human hepatocytes, and (c) liver samples from FRG mice engrafted with human hepatocytes, treated with two AAV vectors (LLK03, REDH).
Libraries were prepared from single nucei.  Breifly, nuclei were isoalted from flash-frozen chunks of tissue, which were homogenized using a Kimble Dounce tissue grinder, followed by straining with a 40 μm cell strainers, two rounds of centrifugation at 500g.  Nuclei were stained with DAPI and proridium iodide, followed by FACS sorting to isolate PI-positive nuclei. Libraries were then prepared using a 10x Genomics Chromium Single Cell 3’v3 Reagent Kits were used according to manufacturer’s instructions.
snRNA-seq

value: Liver

value: Hepatocytes

value: Unengrafted


title: dipc_Z1_OMP_43


title: HPrEC_M_H3

source_name: ATCC cell line cells

value: ATCC cell line cells

value: HPrEC


title: WGBS_E8.5 Whole Embryo_WT_M_sample7_rep2


title: HPrEC_M_H2


title: dipc_Z1_OMP_42

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)


title: dipc_Z1_OMP_41

value: mature olfactory sensory neurons (mOSN)


title: Villous tissue 3, RPL, replicate 1, scRNAseq

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced reads were initially processed by the CellRanger pipeline which includes FASTQ creation, read alignment, gene counting, and cell calling. The Cell Ranger GRCh38(v2020-A) genome was used as the reference for alignment.
Assembly: Cell Ranger GRCh38(v2020-A) genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Villous tissue of fetal placenta

extract_protocol:
Product of conception (POC) including placental and decidual tissue were collected from 3 patients (Supplementary Table 17) suffering from idiopathic (unexplained) recurrent pregnancy loss defined as 2 or more failed pregnancies where common risk factors were excluded (i.e. obesity, use of alcohol/tobacco/drugs, Mullerian anomaly (septum), balanced translocation, uncontrolled diabetes, uncontrolled hypothyroidism, anti-phospholipid antibody syndrome (or other coagulopathy). All samples had normal karyotype based on clinical cytogenetics testing including chromosomal analysis (GTG banded chromosomes analyzed at the 450-550 band levels) and array comparative genomic hybridization performed in accordance with current International Standing Committee on Human Cytogenetic Nomenclature (ISCN 2009). Prior to single-cell capture, samples were thawed in 10ml of Thawing Medium consisting of DMEM/F-12 (Thermo Fisher Cat No. 11320033) supplemented with 10% FBS and 100 units/mL of penicillin and 100 µg/mL of streptomycin (Thermo Fisher Cat No. 15140122) that was prewarmed in a 37°C bead bath and centrifuged at 300 x g for 8 min. The supernatant was carefully removed without disturbing the cell pellets. The cell pellets were each resuspended in 0.5 mL of Thawing Medium, and the cell suspensions were placed on ice and passed through a prewetted 40-µm nylon mesh cell strainer. Cell suspensions were centrifuged at 300 x g for 8 min at 4°C, and the supernatant was carefully aspirated without disturbing the cell pellets.Each sample was rinsed in PBS before the addition of 5ml of digestion media (MEM/F12 +10% FBS +P/S with 2.0mg/mL collagenase type 1A) and incubated for 50min at 37⁰C. The sample was strained through a pre-wetted 100um filter in a 50ml conical tube and rinsed twice with 5 mL of DMEM/F12 +10% FBS +P/S and centrifuged at 300g for 8 min. The cell pellets were resuspended in 1 mL of cold Recovery Cell Culture Freezing Medium (Thermo Fisher Cat No. 12648010) , and the cell suspension was transferred to a cryogenic storage vial. The cryogenic storage vial was placed in a Corning CoolCell FTS30, which was then placed in a -80°C freezer overnight. Samples were stored at -80°C before being thawed and processed for single-cell RNA-Seq.
The cell pellets were resuspended in 100 µL of cold Thawing Medium, and cell count and viability were assessed using 0.4% Trypan Blue and a Countess II automated cell counter. For each sample, Chromium Chip B (10x Genomics Cat No. 1000153) were loaded (Supplementary Table 17). Following cell loading, cDNA and library preparation was performed identically for all samples using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics Cat No. 1000075) according to the manufacturer’s protocol. Libraries were sequenced using an Illumina NovaSeq 6000 using 2x94 cycle paired-end.

value: Villous tissue of fetal placenta

value: male

tag: disease state

value: Idiopathic recurrent pregnancy loss


title: WGBS_E8.5 Whole Embryo_WT_M_sample7_rep1

value: Whole Embryo

value: Male


title: WGBS_E8.5 Whole Embryo_WT_M_sample6_rep2


title: N1245_2N_M_A3

value: Single normal prostate cell

value: fail


title: dipc_Z1_OMP_40


title: WGBS_E8.5 Whole Embryo_WT_M_sample6_rep1


title: HPrEC_M_G2

value: pass


title: Villous tissue 2, RPL, replicate 2, scRNAseq

description: 10x Genomics


title: Villous tissue 2, RPL, replicate 1, scRNAseq

description: 10x Genomics


title: WGBS_E8.5 Whole Embryo_WT_M_sample5_rep2


title: HPrEC_M_F2


title: Villous tissue 1, RPL, replicate 1, scRNAseq

description: 10x Genomics


title: dipc_Z1_OMP_39


title: dipc_Z1_OMP_38


title: WGBS_E8.5 Whole Embryo_WT_M_sample5_rep1


title: dipc_Z1_OMP_37


title: WGBS_E8.5 Whole Embryo_WT_F_sample4

value: Female


title: HPrEC_M_E2


title: dipc_Z1_OMP_36


title: CT27_EVT_rep3

data_processing:
Raw FASTQ files were trimmed using default parameters (-r 0.1 -d 0.03) in Skewer (Version 0.2.2), and reads shorter than 18 bp were discarded.
Transcripts were quantified using Kallisto (Version 0.46.2).
Differentially expressed genes at FDR of 0.05 were discovered using the Bioconductor package DESeq2 in R (Version 1.32.0)

growth_protocol: Human TS cells (Okae et al. 2018) were cultured in 100 mm tissue culture dishes coated with 5 μg/mL collagen IV (CB40233, Thermo-Fisher, Waltham, MA). Human TS cells were maintained in Complete human TS cell medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) fetal bovine serum (FBS), 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 1.5 μg/mL L-ascorbic acid (A8960, Sigma-Aldrich, St. Louis, MO), 50 ng/mL epidermal growth factor (EGF, E9644, Sigma-Aldrich), 2 μM CHIR99021 (04-0004, Reprocell, Beltsville, MD), 0.5 μM A83-01 (04-0014, Reprocell), 1 μM SB431542 (04-0010, Reprocell), 0.8 mM valproic acid (P4543, Sigma-Aldrich), and 5 μM Y27632 (04-0012-02, Reprocell). EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) FBS, 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 100 ng/mL of neuregulin 1 (NRG1, 5218SC, Cell Signaling, Danvers, MA), 7.5 μM A83-01 (04-0014, Reprocell, Beltsville, MD), 2.5 μM Y27632 (04-0012, Reprocell), 4% KnockOut Serum Replacement (KSR, 10828028, Thermo-Fisher), and 2% Matrigel® (CB-40234, Thermo-Fisher). On day 3 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and with a reduced Matrigel® concentration of 0.5%. On culture day 6 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and KSR, and with a Matrigel concentration of 0.5%. Cells were analyzed on day 8 of EVT cell differentiation.

extract_protocol:
RNA was isolated with a TRIzol/chloroform precipitation followed by a cleanup with a RNeasy Mini Kit (74104, Qiagen, Germantown, MD). Frozen cell isolates in TRIzol were thawed on ice prior to starting the isolation. Once thawed, the samples were placed at room temperature for 5 min to promote dissociation of nucleoprotein complexes. Next, 200 μL of chloroform was added to each sample with vigorous shaking for 15 sec. Samples were placed at room temperature for 3 min before centrifugation at 12,000 g for 15 min at 4°C. After centrifugation, the upper, colorless, aqueous phase was removed and transferred to a new 1.5 mL tube and 1.5 volumes of 100% ethanol added. Isolates containing ethanol were mixed thoroughly by pipetting and 650 μl transferred to a RNeasy spin column. The protocol for the RNeasy Mini Kit was then followed to clean the sample post-TRIzol/chloroform extraction. RNA was then quantified using a Qubit RNA BR Assay Kit and RNA integrity assessed using RNA ScreenTape (5067-5577 and 5067-5576, Agilent) on the Agilent TapeStation platform (Agilent) prior to library preparation
RNA libraries were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (RS-122-2303, Illuminaon a Caliper Sciclone G3 platform (PerkinElmer, Waltham, MA) . Manual bead cleanup was performed using AMPure XP Beads (A63881, Beckman Coulter, Brea, CA) after llibrary preparation to remove primer-dimers. 1.0x volume of beads was added to the entire library volume. Samples were mixed by pipetting and incubated at room temperature for 5 min before being placed on a magnetic stand until the supernatant cleared. Once clear, the supernatant was removed and discarded, and the beads were washed twice with 80% ethanol while still on the magnet. Any residual ethanol was removed, and the beads were air-dried on the magnet for 5 min at room temperature. Once dry, 30 μL of Resuspension Buffer was added to each sample, the beads were resuspended by pipetting, and the solution incubated for 2 min at room temperature. Samples were then placed on a magnet until the supernatant was clear. The supernatant was then transferred to a new plate. A Qubit dsDNA BR Assay kit was used to determine the concentration of the library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit (DNF-473-10000, Agilent) was used to detect the size of the library and to verify removal of excess primer-dimers. Standard Illumina Free-Adapter Blocking was performed on the libraries.
Cleaned, adapter-blocked libraries were loaded on a NovaSeq6000 (Illumina, San Diego, CA) with a run configuration of 151x8x8x151 and an average depth of 70M PE reads per library.

tag: source

value: human trophoblast stem cells

tag: cell line

value: extravillous trophoblast cell


title: WGBS_E8.5 Whole Embryo_WT_F_sample3

tag: tissue

value: Wild-Type


title: HPrEC_M_G3


title: CT27_EVT_rep2


title: Human hepatocytes, replicate 1, snRNAseq

description:
ROD_C2
hep1

value: Liver

value: Hepatocytes

value: Unengrafted

tag: time


title: HPrEC_M_D3

tag: cell type

value: ATCC cell line cells

value: HPrEC


title: N1245_2N_M_C2

tag: patient donor/cell_line


title: CT27_Stem_rep3

value: stem state trophoblast cell


title: HPrEC_M_D2

tag: genome build


title: dipc_Z1_OMP_34

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)

value: mature olfactory sensory neurons (mOSN)


title: HPrEC_M_F3

tag: cpg coverage


title: dipc_Z1_OMP_33


title: CT27_Stem_rep2


title: CT29_Stem_rep3


title: WGBS_E8.5 Whole Embryo_WT_F_sample1_rep1

value: Whole Embryo

tag: strain


title: dipc_Z1_OMP_32


title: HPrEC_M_C3

tag: bisulfite conversion_rate

tag: qc


title: HPrEC_M_E3


title: HPrEC_M_C2


title: dipc_Z1_OMP_31


title: HPrEC_M_B3


title: L3MBTL2_CUTRUN_mESC_Zmym2KO_IgG_rep2

data_processing:
Reads were trimmed using Trimmomatic (v0.6.6) using default parameters and then aligned to the mm10 genome using BWA(v0.7.17).
Removal of PCR duplicates was then done using Picard (v2.0.1). MACS2 was then used for peak identification using default parameters and inputs as controls.
Aligned BAM files were used to generate the bigwigs using DeepTools/Homer. The resulting bigwigs were used for metaplot and heatmaps using the computeMatrix and plotHeatmap functions in DeepTools.
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig

source_name: CCE

growth_protocol: Cells were cultured on 0.1% gelatin (EmbryoMax, ES-006-B) coated plates and media was refreshed every day. Cells were passaged every 2 days using 0.05% Trypsin-EDTA (Gibco, 25300062). These cells were cultured in Knockout™ D-MEM (Gibco, 10829018) media supplemented with 1000U/mL ESGRO Recombinant Mouse LIF (Millipore Sigma, ESG1107), 2 mM GlutaMAX (Gibco, 35050061), 100 μg/mL Primocin (InvivoGen, ant-pm-2), 0.1 mM 2-mercaptoethanol and 15% ES-qualified fetal bovine serum (Gibco, 10439024). All mESCs were mycoplasma-free. For embryoid body culture, mESCs were added to 30 ul hanging drops in embryoid body culture media (mESC media mentioned above but without Lif and a final 20% FBS concentration)

extract_protocol:
Trypsinized mESCs were fixed and crosslinked using 1% paraformaldehyde (diluted in PBS) for 10 minutes. The crosslinking was then quenched using 1 mM of Glycine for 10 minutes. The mESCs were then lysed and sonicated using the M220 ultrasonicator (Covaris) in 1 ML tubes with an AFA Fiber and the following conditions ( cycles/burst = 200, Duty Factor = 20%, Peak Intensity Power = 75, time = 10 minutes and temperature = 7 degrees celcius). The sheared DNA was then pre-cleared using magnetic beads for 1 hour. Antibodies were then added to the DNA and incubated overnight at 4 degrees. Magnetic beads were added to each samples. The DNA samples were then eluted and de-crosslinked overnight at 62 degrees. Residual RNA and protein was then removed using RNAseA and proteinaseK and DNA was isolated using the Qiagen PCR purification Kit using manufacturer's instructions. For ChIP samples that used CUT&RUN (L3MBTL2) was used using manufacturer’s instructions (EpiCypher CUTANA ChIC/CUT&RUN Kit, 14-1048)
The eluted DNA from the CUT&RUN or ChIP was used to construct multiplex libraries with the NEBNext Ultra II DNA library Kit using manufacturer’s instructions.

value: CCE

value: embryonic stem cell

tag: genotype

value: Zmym2 Knockout

tag: chip antibody

value: IgG


title: CT29_Stem_rep2


title: dipc_Z1_OMP_35


title: CT29_Stem_rep1


title: HPrEC_M_A3

value: pass


title: dipc_Z1_OMP_28


title: HPrEC_M_B2


title: L3MBTL2_CUTRUN_mESC_Zmym2KO_IgG_rep1


title: CT29_EVT_rep3

value: human trophoblast stem cells


title: CT29_EVT_rep2

value: extravillous trophoblast cell


title: L3MBTL2_CUTRUN_mESC_WT_IgG_rep2

value: Wild-Type


title: dipc_Z1_OMP_30


title: WGBS_E8.5 Whole Embryo_WT_F_sample2

tag: developmental stage

tag: Sex

value: Female


title: WGBS_E8.5 Whole Embryo_WT_F_sample1_rep2


title: HPrEC_M_A2


title: L3MBTL2_CUTRUN_mESC_WT_IgG_rep1


title: dipc_Z1_OMP_27

tag: genotype/variation

tag: tissue/cell type


title: CT29_EVT_rep1

tag: source


title: L3MBTL2_CUTRUN_mESC_Zmym2KO_rep2

tag: cell line

value: L3MBTL2 (Active Motif, 39570)


title: T1255_GS6_4N_M_C6

source_name: Single prostate tumor cell

value: Single prostate tumor cell

value: fail


title: dipc_Z1_OMP_26


title: CT27_Stem_rep1


title: L3MBTL2_CUTRUN_mESC_Zmym2KO_rep1


title: CT27_EVT_rep1


title: L3MBTL2_CUTRUN_mESC_WT_rep2


title: dipc_Z1_OMP_24


title: T1255_GS6_4N_M_C5


title: CT27, EVT, p20, rep5

data_processing:
PhiX  reads were removed using HTStream's (Version 1.3.2) hts_SeqScreener with default parameters.
Duplicates were removed using HTStream's (Version 1.3.2) hts_SuperDeduper (-e 250000).
Adapter sequences were trimmer using HTStream's (Version 1.3.2) hts_AdapterTrimmer (-p 4).
N's were removed using HTStream's (Version 1.3.2) hts_Ntrimmer.
Base quality trimming was performed using HTStream's (Version 1.3.2) hts_QWindowTrim (-w10 -q 20).
Reads shorted than 50bp were remvoed using HTStream's (Version 1.3.2) hts_LengthFilter (-n -m 50).
Reads were aligned to the human genome (GRCh38) using BWA mem (0.7.17-r1188).
The alignments were shifted using alignmentSieve (Version 3.5.1) using the --ATACshift option.
Alignments in the ENCODE blacklisted regions were removed using Bedtools (Version 2.30.0).
Peaks were called using MACS3 callpeak (Version 3.0.0a6) with the following parameters: -B -q 0.01.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
The Omni-ATAC library preparation was performed on freshly isolated cells according to the established protocol (Corces et al. 2017) until the post-transposition cleanup step. After the cleanup of the transposed DNA was complete, samples were stored at -20°C until library amplification.
The samples underwent 5 cycles of PCR before an aliquot was used in a quantitative PCR (qPCR) reaction to determine whether additional amplification was required. An Applied Biosciences Viia7 Real-Time PCR System (Applied Biosciences, Beverly Hills, CA) was used for qPCR and the number of additional PCR cycles needed was determined from the multicomponent plot, which plots fluorescence versus the number of PCR cycles. The maximum fluorescence for each sample was found from the plot, ¼ of the maximum fluorescence value was calculated, and the number of additional PCR cycles needed was determined by determining the cycle number that reached ¼ maximum fluorescence on the graph. In cases where the ¼ maximum fluorescence value was halfway between two cycle numbers, the lower number of cycles was selected since slight under-amplification was more favorable than overamplification. The original samples were then PCR amplified with their determined number of additional cycles. Cleanup of the samples was performed after PCR amplification according to the published protocol (Corces et al. 2017). Libraries were quantified using a Qubit dsDNA BR Assay Kit (Q32853, Thermo-Fisher) and the size was determined with a High Sensitivity DNA Bioanalyzer Kit (5067-4626, Agilent, Santa Clara, CA).


title: T1255_GS6_4N_M_C3

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19 (human); mm9 (mouse)
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)


title: CT27, EVT, p20, rep4


title: dipc_Z1_OMP_23


title: dipc_Z1_OMP_22


title: T1255_GS6_4N_M_B7


title: CT27, EVT, p20, rep3


title: K4me3_input_EmbryoidBody_Zmym2KO_rep2

value: embryoid body

value: input


title: CT27, EVT, p20, rep1


title: dipc_Z1_OMP_21

value: OMPgfp*/+ (F1 cross between OMPgfp (129/Bl6) and CAST/EiJ)


title: T1255_GS6_4N_M_B5


title: dipc_Z1_OMP_20

value: mature olfactory sensory neurons (mOSN)


title: dipc_Z1_OMP_19


title: dipc_Z1_OMP_25


title: CT27, EVT, p19, rep4


title: CT27, EVT, p19, rep5


title: CT27, EVT, p19, rep1


title: K4me3_input_EmbryoidBody_WT_rep2


title: K4me3_input_EmbryoidBody_WT_rep1


title: K4me3_input_mESC_Zmym2KO_rep2


title: dipc_Z1_OMP_18


title: T1255_GS6_4N_M_B3


title: dipc_Z1_OMP_17


title: L3MBTL2_CUTRUN_mESC_WT_rep1


title: T1255_GS6_4N_M_B2


title: K4me3_input_mESC_Zmym2KO_rep1


title: T1255_GS6_4N_M_C2


title: T1255_GS6_4N_M_B1


title: dipc_Z1_OMP_16


title: CT27, Stem, p21, rep3

value: stem state trophoblast cell


title: K4me3_input_mESC_WT_rep2


title: K4me3_input_EmbryoidBody_Zmym2KO_rep1


title: T1255_GS6_4N_M_B6


title: T1255_GS6_4N_M_A8


title: dipc_Z1_OMP_15


title: K4me3_input_mESC_WT_rep1


title: T1255_GS6_4N_M_A7


title: H3K4me3_EmbryoidBody_Zmym2KO_rep2

value: H3K4me3 (Cell Signaling, C42D8)


title: T1255_GS6_4N_M_A5


title: H3K4me3_EmbryoidBody_Zmym2KO_rep1


title: dipc_Z1_OMP_13


title: H3K4me3_EmbryoidBody_WT_rep2


title: CT27, Stem, p21, rep2


title: dipc_Z1_OMP_12


title: CT27, Stem, p21, rep1


title: CT27, Stem, p16, rep4


title: CT27, Stem, p16, rep5


title: CT27, Stem, p21, rep5


title: H3K4me3_EmbryoidBody_WT_rep1


title: CT27, Stem, p16, rep1


title: H3K4me3_mESC_Zmym2KO_rep2

value: embryonic stem cell


title: T1255_GS6_4N_M_A2


title: dipc_Z1_OMP_11


title: dipc_Z1_OMP_10


title: N1255_2N_M_H2

value: Single normal prostate cell


title: dipc_Z1_OMP_9


title: R15

extract_protocol:
Eight mL fresh blood were collected from FXS male individuals (N=10) and age-matched typically developing (TD) males (N=7)  in a K2EDTA Tube and the leukocytes collected on a LeukoLOCKTM filter prior to RNA extraction using a LeukoLOCK Fractionation & Stabilization Kit, Ambion #1933 as per the manufacturer’s instructions. Briefly, the blood samples were passed through LeukoLOCKTM filters that were then rinsed with 3 mL phosphate buffered saline (PBS) followed by 3 mL of RNAlater®. The filters were capped and stored in -80 deg C. To extract RNA, the filters were thawed at room temperature for 5 mins and then the remaining few drops of RNAlater were removed. The filter was flushed with 4 ml of TRIzol™ LS Reagent (ThermoFisher Scientific #10296028) and the lysate collected in a 15 ml tube. 800 μl bromo-3-chloro-propane (BCP) (Sigma #B9673) was added to each tube and vortexed vigorously for 30 sec. The tube was then incubated at room temp for 5 min and centrifed for 10 min at 40C at ~2,000 x g;  the aqueous phase containing the RNA was recovered. To recover the long RNA fraction, 0.5 volumes of 100% ethanol were added and mixed well. The RNA was then recovered using an RNA clean and concentrator kit (Zymo Research, #11-325 / R1015), DNase treated with TURBO™ DNAse (Invitrogen # AM2238) and the RNA resuspended in RNAse free water and stored at –80°C.
Three mg of RNA sample was used for directional mRNA library preparation using polyA enrichment (Novogene Co) and the libraries sequenced on the NovaSeq platform to generate paired end, 150bp reads at a sequencing depth of 60 million reads per sample

tag: gender

value: Male

value: Human Leukocytes

value: FXS


title: H3K4me3_mESC_WT_rep2


title: R14


title: H3K4me3_mESC_Zmym2KO_rep1

value: Zmym2 Knockout


title: R13


title: N1255_2N_M_H3

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.


title: dipc_Z1_OMP_8


title: dipc_Z1_OMP_14


title: N1255_2N_M_G3


title: H3K4me3_mESC_WT_rep1

value: Wild-Type


title: N1255_2N_M_G2


title: dipc_Z1_OMP_7


title: dipc_Z1_OMP_6


title: R12


title: T1255_GS6_4N_M_A3

value: pass


title: K4me2_input_EmbryoidBody_Zmym2KO_rep2


title: T1255_GS6_4N_M_A4


title: R11


title: N1255_2N_M_F3


title: K4me2_input_EmbryoidBody_Zmym2KO_rep1


title: dipc_Z1_OMP_5


title: K4me2_input_EmbryoidBody_WT_rep2


title: R07


title: R09


title: dipc_Z1_OMP_4


title: N1255_2N_M_E3


title: N1255_2N_M_E1


title: K4me2_input_EmbryoidBody_WT_rep1


title: N1255_2N_M_D1


title: dipc_Z1_OMP_3


title: K4me2_input_mESC_Zmym2KO_rep2


title: dipc_Z1_OMP_2


title: R03

value: TD


title: N1255_2N_M_C2


title: N1255_2N_M_B3


title: K4me2_input_mESC_Zmym2KO_rep1


title: dipc_Z1_OMP_1


title: R02


title: HiC_Z1_iOSN_r2

data_processing:
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: cooler format

source_name: TdTomato - GFP +(bright) cells from zone 1 of the olfactory epithelium

growth_protocol: Newborn mice (P2-P4) were injected  IP with tamoxifen. 48 hours later mice were sacrificed and cells were collected

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2030
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2030

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone 1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 1% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted , washed once with PBS + 2% FBS, and then resuspended in sort media.  Cells were passed through a 40um filter, then tdTomato- GFP+(bright)  cells were isolated with FAC-sorting

value: immature olfactory sensory neurons (iOSN)


title: K4me2_input_mESC_WT_rep2


title: N1255_2N_M_B2

value: fail


title: A294

source_name: Human Leukocytes


title: H3K4me2_EmbryoidBody_Zmym2KO_rep2

value: embryoid body

value: H3K4me2 (Cell Signaling, C64G9)


title: K4me2_input_mESC_WT_rep1

value: input


title: N1255_2N_M_B1

source_name: Single normal prostate cell


title: HiC_Z1_iOSN_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2029
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2029


title: HiC_Z5_iOSN_r2

source_name: TdTomato - GFP +(bright) cells from zones 4/5 of the olfactory epithelium

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2028
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2028

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zones4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 1% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted , washed once with PBS + 2% FBS, and then resuspended in sort media.  Cells were passed through a 40um filter, then tdTomato- GFP+(bright) cells were isolated with FAC-sorting


title: N1255_2N_M_A3


title: A293


title: A307


title: HiC_wt_zone5_r2

source_name: TdTomato +/dim cells from zones 4/5 of the olfactory epithelium

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 40 days.

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2026
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2026

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zone4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 1% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted , washed once with PBS + 2% FBS, and then resuspended in sort media.  Cells were passed through a 40um filter, then tomato+(dim) cells were isolated with FAC-sorting

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl

value: tdTomato +(dim) cells from the olfactory epithelium


title: R05


title: A292


title: N1255_2N_M_A2


title: H3K4me2_EmbryoidBody_WT_rep2


title: H3K4me2_EmbryoidBody_Zmym2KO_rep1


title: R04


title: H3K4me2_EmbryoidBody_WT_rep1


title: A285_


title: HiC_wt_zone5_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2025
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2025


title: HiC_NfiABXko_K5CreER_r2

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2024
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2024


title: N1255_2N_M_C1


title: H3K4me2_mESC_Zmym2KO_rep2


title: A284


title: N1255_2N_M_A1


title: H3K4me2_mESC_Zmym2KO_rep1


title: N1255_2N_M_C3


title: H3K4me2_mESC_WT_rep2


title: Disease.DMP1_Yes.Inorganic. Rep 2

city: Chicago

last: Guirado

state: IL

address: 801 S. Paulina St. Room 421

department: Oral Biology

institute: University of Illinois Chicago

description:
GEO071619_016
GEO071619_016

data_processing:
NovaSeq 6000 instrument was used with SP flow cell (2x50 reads), 380+ M reads per lane, approx. 23 M clusters/sample.
Raw sequencing reads were aligned to the human reference genome (HG38) using the STAR aligner and ENSEMBL gene and transcript annotations.
Gene expression levels were quantified using FeatureCounts as raw read counts and as normalized reads-per-million. Normalized expression (in counts per million) accounts for differences in sequencing depth across libraries, allowing expression levels to be directly compared between samples.
Quality control was performed to confirm the depth and quality of the raw sequencing data and the absence of sequencing artifacts and to confirm that the number of reads aligning to the reference genome mapping to coding sequences was sufficient for expression estimates.
Assembly: HG38
Supplementary files format and content: tab-delimited text files include CPM (counts per million) values for each Sample

source_name: dental pulp stem cells

growth_protocol: Cells were maintained in standard growth conditions [Dulbecco’s Modified Eagle Medium 1g/L D-Glucose (DMEM; Invitrogen, Grand island, NY, United States)] supplemented with 10% fetal bovine serum (FBS; Invitrogen), 1% antibiotic-antimycotic 100× (Gibco/Invitrogen, Cat. 15240062), at 37◦ C, 5% CO2.

extract_protocol:
A hybrid Trizol/RNeasy protocol was followed for the isolation of total RNA. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Universal Plus mRNA-seq chemistry by NuGEN.

treatment_protocol: Control and XLH dental pulp cells were transduced with lentivirus containing full-length human DMP1 cDNA Cells were differentiated for eight hours under conditions containing one of two phosphate sources: β- glycerophosphate (10mM, "organic" phosphate source) or sodium phosphate buffer (10mM, pH7.2, "inorganic" phosphate source), plus ascorbic acid(100 μg/ml) and dexamethasone(10nM).

value: dental pulp stem cells

value: XLH

tag: dmp1 gene

value: Yes

tag: phosphate source

value: Sodium Phosphate


title: HiC_Z5_mOSN_r2

source_name: GFP+ cells from zones 4/5 of the olfactory epithelium

growth_protocol: Used adult >8 weeks mice

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2022
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2022

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most ventral segments (zone4/5) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 1% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted , washed once with PBS + 2% FBS, and then resuspended in sort media.  Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN)


title: HiC_Z5_iOSN_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2027
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2027


title: N1255_2N_M_D2

tag: cell type

value: Single normal prostate cell

tag: patient donor/cell_line


title: HiC_Z5_mOSN_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2021
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2021


title: Disease.DMP1_Yes.Inorganic. Rep 1

description:
GEO071619_015
GEO071619_015


title: H2AK119Ub_K9me3_input_EmbryoidBody_Zmym2KO_rep2

value: Zmym2 Knockout


title: H3K4me2_mESC_WT_rep1

value: embryonic stem cell

value: Wild-Type


title: N1255_2N_M_D3

tag: genome build

tag: cpg coverage

value: pass


title: Disease.DMP1_Yes.Organic. Rep 1

description:
GEO071619_013
GEO071619_013

value: Beta-glycerophosphate


title: HiC_Z1_mOSN_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2019
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2019

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The most dorsal segment (zone1) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), then fixed in PBS + 1% methanol-free formaldehyde (Pierce) for 10 minutes at room temperature, and then quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted , washed once with PBS + 2% FBS, and then resuspended in sort media.  Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting


title: Disease.DMP1_Yes.Organic. Rep 2

description:
GEO071619_014
GEO071619_014


title: H2AK119Ub_K9me3_input_EmbryoidBody_Zmym2KO_rep1

tag: strain


title: N1255_2N_M_F2

tag: bisulfite conversion_rate

tag: qc


title: Disease.DMP1_No.Inorganic. Rep 2

description:
GEO071619_012
GEO071619_012

tag: genotype

value: No


title: N1255_2N_M_E2


title: N1255_2N_M_F1


title: CutRun.NfiWT_NFIA_r1

data_processing:
Library strategy: Cut&RUN
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: TdTomato +/dim cells from the olfactory epithelium

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 10 days.

extract_protocol:
Approximatelu 100,000 to 250,000 cells were used for CUT&RUN: bound to activated Concanavalin A beads, and incubated with Nfia antibody (Active Motif 39397) antibody overnight at 4°C , then Protein A-MNase for 1 hour at 4°C.  . MNase cleavage was carried out at 0°C for 5 minutes.
CUT&RUN libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tdTomato+ (dim) cells were isolated with FAC-sorting

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: H2AK119Ub_K9me3_input_EmbryoidBody_WT_rep2

value: embryoid body

tag: chip antibody


title: Disease.DMP1_No.Inorganic. Rep 1

description:
GEO071619_011
GEO071619_011


title: N1255_2N_M_G1


title: CutRun.NfiKO_NFIA_r1


title: Disease.DMP1_No.Organic. Rep 2

description:
GEO071619_010
GEO071619_010


title: H2AK119Ub_K9me3_input_EmbryoidBody_WT_rep1

value: input


title: N1255_2N_M_H1

value: fail


title: HiC_NfiABXko_K5CreER_r1

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2023
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2023

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl

value: tdTomato +(dim) cells from the olfactory epithelium


title: H2AK119Ub_K9me3_input_mESC_Zmym2KO_rep2

extract_protocol:
Trypsinized mESCs were fixed and crosslinked using 1% paraformaldehyde (diluted in PBS) for 10 minutes. The crosslinking was then quenched using 1 mM of Glycine for 10 minutes. The mESCs were then lysed and sonicated using the M220 ultrasonicator (Covaris) in 1 ML tubes with an AFA Fiber and the following conditions ( cycles/burst = 200, Duty Factor = 20%, Peak Intensity Power = 75, time = 10 minutes and temperature = 7 degrees celcius). The sheared DNA was then pre-cleared using magnetic beads for 1 hour. Antibodies were then added to the DNA and incubated overnight at 4 degrees. Magnetic beads were added to each samples. The DNA samples were then eluted and de-crosslinked overnight at 62 degrees. Residual RNA and protein was then removed using RNAseA and proteinaseK and DNA was isolated using the Qiagen PCR purification Kit using manufacturer's instructions. For ChIP samples that used CUT&RUN (L3MBTL2) was used using manufacturer’s instructions (EpiCypher CUTANA ChIC/CUT&RUN Kit, 14-1048)
The eluted DNA from the CUT&RUN or ChIP was used to construct multiplex libraries with the NEBNext Ultra II DNA library Kit using manufacturer’s instructions.


title: CUT&RUN_Ngn1GFPbright_NFIA_r1

source_name: GFP+ cells from the olfactory epithelium

growth_protocol: Used postnatal mice at ~P6

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ (bright) cells were isolated with FAC-sorting

value: immature olfactory sensory neurons (iOSN)


title: H2AK119Ub_K9me3_input_mESC_Zmym2KO_rep1


title: HiC_Z1_mOSN_r2

extract_protocol:
Fixed sorted cells were used for Hi-C as described in Monahan and Horta et al 2020
On bead library preparation fof Hi-C experiments was carried out with NuGEN Ovation V2 DNA-Seq Library Preparation Kit, as described in Monahan and Horta 2020


title: Disease.DMP1_No.Organic. Rep 1

description:
GEO071619_009
GEO071619_009

value: dental pulp stem cells

value: XLH


title: CUT&RUN_Ngn1GFPbright_anti-rabbit_r1

extract_protocol:
Approximatelu 100,000 to 250,000 cells were used for CUT&RUN: bound to activated Concanavalin A beads, and incubated with rabbit-anti-goat antibody (abcam ab97096) overnight at 4°C , then Protein A-MNase for 1 hour at 4°C.  . MNase cleavage was carried out at 0°C for 5 minutes.
CUT&RUN libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)


title: Control.DMP1_Yes.Inorganic. Rep 2

description:
GEO071619_008
GEO071619_008

value: Control

value: Yes

value: Sodium Phosphate


title: T1255_GS6_4N_M_A6

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

value: Single prostate tumor cell


title: H2AK119Ub_K9me3_input_mESC_WT_rep2

value: embryonic stem cell

value: Wild-Type


title: Control.DMP1_Yes.Inorganic. Rep 1

description:
GEO071619_007
GEO071619_007


title: H2AK119Ub_K9me3_input_mESC_WT_rep1


title: nchip_MOE_H3K9me3_r1

data_processing:
For RNA-seq, native ChIP-seq, omni ATAC-seq and CUT&RUN adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). The RNAseq libraries that were sequenced 75PE were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20, single cell RNA-seq were aligned with the Drop-seq pipeline (http://mccarrolllab.org/dropseq/). Native ChIP-seq, omni-ATAC-seq, and CUT&RUN  reads were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000).  HiC data was aligned with the distiller pipeline (https://github.com/mirnylab/distiller-nf). Dip-c data was aligned according to the Dip-C pipeline (https://github.com/tanlongzhi/dip-c).
Filtering:  We filtered out unmapped reads and reads with a mapping quality below q30 with Samtools for RNA-seq, native ChIP-seq, omni-ATAC-seq, Cut&RUN and HiC and below q255 for single cell RNA-seq
For RNA-seq, native ChiP-seq, omni-ATAC-seq and Cut&RUN  BigWig files were generated using HOMER. For single cell RNA-seq digital expression matrices (DGE) were generated with drop-seq. For HiC ".cool" contact matixes were generated with cooler.
genome build: mm10
processed data files format and content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: Cells from the olfactory epithelium

extract_protocol:
Nuclei were extracted with dounce homogenization, then digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K9me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation and the olfactory epithelium was dissected.

value: WT

value: olfactory epithelium cells


title: T1255_GS6_4N_M_C4

value: pass


title: T1255_GS6_4N_M_A1


title: nchip_MOE_H3K79me3_r2

extract_protocol:
Nuclei were extracted with dounce homogenization, then digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)


title: nchip_Z5_wt_K5CreER_H3K9me3_r2

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K9me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Zone 4 and 5  (the most ventral segments) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ tdTomato +(dim) cells were isolated with FAC-sorting.

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: Control.DMP1_Yes.Organic. Rep 1

description:
GEO071619_005
GEO071619_005

value: Beta-glycerophosphate


title: H3K9me3_EmbryoidBody_Zmym2KO_rep2

value: embryoid body

value: Zmym2 Knockout

value: H3K9me3 (Cell Signaling, C42D8)


title: Control.DMP1_Yes.Organic. Rep 2

description:
GEO071619_006
GEO071619_006


title: H3K9me3_EmbryoidBody_Zmym2KO_rep1


title: T1255_GS6_4N_M_B4


title: nchip_Z5_wt_K5CreER_H3K79me3_r2

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

value: tdTomato +(dim) cells from the olfactory epithelium


title: H3K9me3_EmbryoidBody_WT_rep2


title: Control.DMP1_No.Inorganic. Rep 2

description:
GEO071619_004
GEO071619_004

value: dental pulp stem cells

value: No


title: Control.DMP1_No.Inorganic. Rep 1

description:
GEO071619_003
GEO071619_003

value: Control


title: nchip_Z5_NfiABXko_K5CreER_H3K9me3_r2

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: T1255_GS6_4N_M_B8


title: H3K9me3_EmbryoidBody_WT_rep1


title: T1255_GS6_4N_M_C7


title: nchip_Z5_NfiABXko_K5CreER_H3K79me3_r2


title: Control.DMP1_No.Organic. Rep 2

description:
GEO071619_002
GEO071619_002


title: nchip_Z5_wt_K5CreER_H3K9me3_r1


title: H3K9me3_mESC_Zmym2KO_rep2


title: M_WBC9_HD4_180126

source_name: Single WBCs

value: Single WBCs


title: Control.DMP1_No.Organic. Rep 1

description:
GEO071619_001
GEO071619_001


title: M-WBC6_donor1


title: nchip_Z5_wt_K5CreER_H3K79me3_r1


title: nchip_Z5_NfiABXko_K5CreER_H3K9me3_r1


title: H3K9me3_mESC_WT_rep2


title: M_WBC5_HD4_180126


title: H3K9me3_mESC_Zmym2KO_rep1


title: nchip_Z5_OMPgfp_H3K9me3_r2

source_name: GFP+ cells from zone5 the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Zone 4 and 5  (the most ventral segments) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting

value: mature olfactory sensory neurons (mOSN)


title: T1255_GS6_4N_M_C1

value: Single prostate tumor cell


title: H3K9me3_mESC_WT_rep1

value: embryonic stem cell

value: Wild-Type


title: HE_5

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

data_processing:
Bcl files were processed in Space Ranger v.1.2.0 (10X Genomics) and demultiplexed using "spaceranger mkfastq". The resulting fastq files were mapped to the human genome build GRCh38.p13 and annotated using the GENCODE gene annotation release 32 with "spaceranger count" to produce feature-barcode count matrices. Fiducial alignment and tissue assignment was done manually by providing a json file generated in Loupe Browser (10X Genomics) to the "spaceranger count" command.
Genome_build: hg38 (GRCh38.p13)
annotation: GENCODE release 32
Supplementary_files_format_and_content: Tar archive containing an hdf5 file (filtered_feature_bc_matrix.h5), as well as two tsv files (barcodes.tsv.gz and features.tsv.gz) and a mtx file (matrix.mtx.gz). Furthermore, a spatial directory is included which contains two jpg files (aligned_fiducials.jpg and detected_tissue_image.jpg), two png files (tissue_hires_image.png and tissue_lowres_image.png), a json file (scalefactors_json.json), and a csv file (tissue_positions_list.csv). All processed data files are filtered, i.e. containing only spot barcodes. Processed data for sample AD_4_NL is missing due to bad library quality.

source_name: Skin

extract_protocol:
Human skin biopsy samples were snap-frozen in liquid nitrogen-cooled isopentane and placed in a –80 °C freezer for long-term storage. To prepare tissues for cryosectioning, fresh-frozen tissue samples were embedded in ice-cold optimal cutting temperature (OCT) compound (Tissue-Tek, Sakura Finetek, USA) and frozen on powdered dry ice. After solidification, the OCT embedded tissue block was used immediately for cryosectioning. Block was equilibrated in a cryostat for 30 min with a cryostat chamber temperature adjusted to –20 °C and specimen stage temperature set to –15 °C. Embedded tissues were cryosectioned at 12 μm thickness and transferred onto a Visium optimization slide or a gene expression slide (10X Genomics, USA). Slides were kept in chilled slide mailers on dry ice and transferred to the –80 °C freezer.
Visium Spatial Gene Expression Slide with cryosectioned tissue sections were dried for 1 min at 37 °C, fixed in chilled 100% methanol for 20 min and stained with hematoxylin and eosin for 7 min and 1 min, respectively. Brightfield images for the spatial gene expression slides were captured using an Axio Z1 slide scanner (Zeiss, Germany). Gene expression samples were prepared by permeabilization of tissues for 18 minutes, as optimally determined using the Tissue Optimization Kit. Gene expression libraries were constructed according to the Visium Spatial Gene Expression Reagent Kits User Guide (Rev D, 10X Genomics).

tag: individual

tag: disease state

value: Healthy

tag: tissue

value: Skin


title: HE_4


title: HE_6


title: nchip_Z5_NfiABXko_K5CreER_H3K79me3_r1

tag: genotype/variation

tag: tissue/cell type


title: HE_3


title: M-WBC4_donor1

value: pass


title: H2AK119Ub_EmbryoidBody_Zmym2KO_rep1

tag: cell line

value: H2AK119Ub (Cell Signaling, D27C4)


title: nchip_Z2_OMPgfp_H3K9me3_r2

source_name: GFP+ cells from zone2 the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Zone 2 and 3  (the central segments) of the olfactory epithelium were dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting


title: HE_2


title: H2AK119Ub_EmbryoidBody_Zmym2KO_rep2

value: embryoid body


title: M_WBC2_HD6_180202


title: nchip_Z1_OMPgfp_H3K9me3_r2

source_name: GFP+ cells from zone1 the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. Zone 1  (the most dorsal segment) of the olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+ cells were isolated with FAC-sorting


title: H2AK119Ub_EmbryoidBody_WT_rep2


title: H2AK119Ub_EmbryoidBody_WT_rep1


title: nchip_Z5_OMPgfp_H3K9me3_r1


title: M_WBC1_HD5_180129


title: H2AK119Ub_mESC_Zmym2KO_rep2

value: Zmym2 Knockout


title: M_WBC4_HD4_180126


title: nchip_Z5_OMPgfp_H3K79me3_r2


title: M_WBC20_HD6_180202


title: AD_7_NL

source_name: Atopic dermatitis non-lesional skin

value: Atopic dermatitis

value: Atopic dermatitis non-lesional skin


title: H2AK119Ub_mESC_Zmym2KO_rep1


title: AD_6_NL


title: M-WBC1_donor1

value: fail


title: M_WBC3_HD6_180202


title: H2AK119Ub_mESC_WT_rep2


title: M_WBC16_HD4_180126


title: nchip_Z2_OMPgfp_H3K9me3_r1


title: AD_5_NL


title: nchip_Z2_OMPgfp_H3K79me3_r2


title: AD_4_NL

description: Because of low quality, it was not used in further analysis.  No processed data.


title: M_WBC15_HD4_180126


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_F_Sample 6

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7444_9_KO

data_processing:
Reads were trimmed using Trimmomatic (v0.34)
Trimmed reads wre then mapped to the GRCm38/mm10 genome using STAR (v2.7.8a) using default parameters
Picard (v2.9.0) was used to sort, mark and remove duplicates.
Raw and normalized counts were quanitified using HTSeq-counts and the StringTie suite(v1.3.5)
Differential expression analysis was then measured using DESeq2 and EdgeR
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimted text file showing raw and normalized read counts
Supplementary files format and content: tab-delimted text file showing RPKM of samples

source_name: Whole Embryo

extract_protocol:
Total RNA was isolated using a Rneasy Micro Kit (Qiagen, 74084) or AllPrep DNA/RNA Micro Kit (Qiagen, 82084)
Sequencing libraries were prepared by the Genome Quebec Innovation Center using the NEB mRNA stranded library preperation kit

tag: developmental stage

value: Whole Embryo

tag: Sex

value: Female


title: AD_3_NL


title: M_WBC14_HD4_180126

tag: cell type


title: nchip_Z1_OMPgfp_H3K79me3_r2


title: nchip_Z1_OMPgfp_H3K9me3_r1


title: H2AK119Ub_mESC_WT_rep1


title: AD_2_NL


title: HE_1


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_F_Sample 5

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2408_1


title: nchip_Z5_OMPgfp_H3K79me3_r1


title: M-vCAP-3

source_name: ATCC cell line cells

value: ATCC cell line cells

tag: patient donor/cell_line

value: vCAP


title: AD_1_NL


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_F_Sample 4

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2121_4


title: nchip_Z2_OMPgfp_H3K79me3_r1

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation  with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

value: mature olfactory sensory neurons (mOSN)


title: AD_7_LS

source_name: Atopic dermatitis lesional skin

value: Atopic dermatitis lesional skin


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_M_Sample 3

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7484_10_KO

value: Male


title: M-vCAP-2

tag: genome build


title: AD_6_LS


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_M_Sample 2

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7484_4_KO


title: M-vCAP-1

tag: cpg coverage


title: nchip_Z1_OMPgfp_H3K79me3_r1


title: RNASeq_E8.5 Whole Embryo_Zmym2KO_M_Sample 1

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7484_3_KO

tag: strain


title: M-PC3-4

tag: bisulfite conversion_rate


title: RNASeq_E8.5 Whole Embryo_WT_F_Sample 6

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
J_7623_1_WT

value: Wild-Type


title: nchip_Ngn1GFPdim_H3K9me3_r2

source_name: TdTomato - GFP +(dim) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(dim) tdTomato - cells were isolated with FAC-sorting


title: M_WBC13_HD4_180126

value: Single WBCs

tag: qc


title: AD_5_LS


title: AD_4_LS


title: RNASeq_E8.5 Whole Embryo_WT_F_Sample 4

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2121_2

tag: genotype


title: AD_2_LS


title: M-PC3-1


title: RNASeq_E8.5 Whole Embryo_WT_F_Sample 5

description:
Zmym2_normalized_and_raw_counts.txt
Zmym2_RNAseq_matrixRPKM.txt
H2163_1


title: nchip_Ngn1GFPbright_H3K79me3_r2

source_name: TdTomato - GFP +(bright) cells from the olfactory epithelium

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with  500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP+(bright) tdTomato- cells were isolated with FAC-sorting

value: immature olfactory sensory neurons (iOSN)