title: U2OS, siLONP2, biol rep 3

city: Montreal

first: Akihiro

last: Yamashita

address: 3801 University Ave

country: Canada

institute: McGill University

data_processing:
STAR version 2.7.1a
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequence reads were aligned to the reference Chlorocebus sabaeus genome version ChlSab1.1 (gene annotation from Ensembl 104) or Homo sapiens genome version GRCh38 (gene annotation from Gencode version 37) using STAR version 2.7.1a.
Raw gene expression counts were obtained directly from STAR, and normalization and differential expression analysis were performed using DESeq2 version 1.30.1.
For comparison analyses between COS-7 and U2OS, gene identifiers were converted from C. sabaeus to H. sapiens using the R/Bioconductor package biomaRt (version 2.48.3).
Assembly: ChlSab1.1 and GRCh38
Supplementary files format and content: tab-delimited excel file includes normilised read counts for genes and differential expression analysis for each samples

source_name: bone

extract_protocol:
Total RNA was extracted from each cell using RNeasy Plus (QIAGEN) after 168 h siRNA transfection.
RNA libraries for RNA-seq were prepared using KAPA stranded RNA‐seq LibraryPrep Kit following manufacturer's protocols.

value: bone

value: osteosarcoma epithelial cell

value: LONP2 knockdown


title: S1611_synovium_RNA

status: Public on Sep 27 2023

type: SRA

city: Cambridge

first: Anika

last: Gupta

state: Massachusetts

address: 95 Dunster St, 110 Kirkland Mail Center

country: USA

institute: Harvard University

description:
10x Genomics
genesXcells_ALL_raw.h5ad
B_RNA_processed.h5ad
T_RNA_processed.h5ad
myeloid_RNA_processed.h5ad
fibroblast_RNA_processed.h5ad
endothelial_RNA_processed.h5ad

library_source: transcriptomic single cell

data_processing:
Samples were initially processed using 10x Genomics Cell Ranger ARC 2.0.0, which includes barcode processing and read alignment, for both ATAC and RNA information.
Assembly: hg38
Supplementary files format and content: Comma-separated metadata files and h5ad (Hierarchical Data Formats) matrix files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Synovial tissue

extract_protocol:
Synovial tissue samples were collected and cryopreserved, then thawed and disaggregated, and the resulting single-cell suspensions were stained with anti-CD235a antibodies (clone 11E4B-7-6 (KC16), Beckman Coulter) and Fixable Viability Dye (FVD) eFlour 780 (eBioscience/ThermoFisher). Live non-erythrocyte (i.e., FVD- CD235-) cells were collected by fluorescence-activated cell sorting (BD FACSAria Fusion). The sorted live cells were then re-frozen in Cryostor and stored in liquid nitrogen.
Each sample was processed separately in the cell capture step. Nuclei were isolated using an adaptation of the manufacturer’s protocol (10X Genomics). Approximately ten thousand nuclei transposed nuclei were loaded on Chromium Next GEM Chip J followed by GEM generation. 10x Barcoded DNA from the transposed DNA (for ATAC) and 10x Barcoded, full-length cDNA from poly-adenylated mRNA (for Gene Expression) were produced during GEM incubation. The ATAC libraries and Gene Expression libraries were then generated separately. Both library types were sequenced to an average of 30,000 reads per cell on different flow cells with recommended sequencing cycles according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, 10X Genomics) using Illumina Novaseq.

tag: tissue

value: Synovial tissue

tag: disease

value: RA

tag: synovial lymphocytic_inflammation

value: Marked (both perivascular and widespread interstitial aggregates) (3)

tag: synovial lining_hyperplasia

value: 3-4 cells Thick (2)


title: S1281_synovium_ATAC

description:
10x Genomics
peaksXcells_ALL_raw.h5ad
ATAC_ALL_CT_processed.h5ad

library_source: genomic single cell

molecule: genomic DNA

value: OA

value: Mild (OA)


title: AM1

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: total RNA

source_name: biopsy of periapical tissues

extract_protocol:
Tissues were homogenized using pre-chilled Omni Bead Ruptor 24 Cryo Cooling Unit in 2.8mm ceramic tubes and pre-chilled 700 µl QIAzol Lysis reagent. Total RNA was extracted using the Qiagen RNAeasy PLUS Universal Mini Kit per the manufacturer's instructions.
Total RNA samples about 500ng were used for sequencing library preparation according to Illumina TruSeq Stradned mRNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Tissue of 3-8 mm^3 biopsies were collected patients who underwent endodontic microsurgery procedures, and snap-frozen in liquid nitrogen. Samples were then transferred to -80C before RNA extraction.

tag: gender

value: Male

value: periapical tissues

tag: pain status

value: Asymptomatic Apical Periodontitis

tag: age

tag: race/ethnicity

value: Asian


title: S1607_synovium_RNA

value: Band-like (4)

value: 1-3 cells Thick (1)


title: S1609_synovium_RNA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration) (2)


title: CAGE_dhh1D_Replicate_2

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy  file contains two columns providing: systemmatic gene name (ORF) and avg occupancy.

organism: Saccharomyces cerevisiae

source_name: Whole cells

extract_protocol: CAGE libraries were constructed from 5µg of total RNA of each strain using the nAnT-iCAGE protocol (Murata et al. 2014) by K.K. DNAFORM of Japan. Briefly, first strand cDNAs were transcribed to the 5’ end of capped RNAs and attached to CAGE “barcode” tags. Each nAnT-iCAGE library used linkers with specific barcodes and was sequenced using Illumina NextSeq500 (single-end, 75-bp reads).

tag: genotype

tag: cell type

value: yeast cells

tag: fraction

value: capped RNA


title: U2OS, siLONP2, biol rep 2

value: bone

tag: cell line

value: osteosarcoma epithelial cell


title: the plasma of healthy people_rep1

type: RNA

city: Chongqing

first: Ziyue

last: Lin

state: Chongqing

address: Medical College Road

country: China

institute: Chongqing Medical University

description: circRNA expression in human plasma

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).After quantile normalization of the raw data, circRNAs that at least 6 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.Differentially expressed circRNAs with statistical significance were identified through Volcano Plot filtering

source_name: healthy people

label_protocol: Rnase R (Epicentre, Madison, WI) was used to remove linear RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA by using a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: plasma

value: female


title: CAGE_dhh1D_Replicate_1


title: SF2

value: Female

value: Symptomatic Apical Periodontitis

value: White


title: U2OS, siNT, biol rep 3

value: WT


title: SF3

value: Hispanic


title: S1594_synovium_RNA

value: Synovial tissue

value: RA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration)


title: S1592_synovium_RNA

value: Band-like (4)

value: 3-4 cells Thick (2)


title: CAGE_pat1D_Replicate_2


title: U2OS, siNT, biol rep 2


title: U2OS, siNT, biol rep 1


title: AF3

value: periapical tissues

value: Asymptomatic Apical Periodontitis


title: S1590_synovium_RNA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration) (2)

value: > 4 cells Thick (3)


title: SF1


title: AM3

value: Male


title: S1588_synovium_RNA


title: AF2


title: S1586_synovium_RNA

value: 1-3 cells Thick (1)


title: AF1


title: U2OS, siLONP2, biol rep 1

value: bone

value: osteosarcoma epithelial cell

value: LONP2 knockdown


title: PB RNA-seq rep1

city: Taipei

first: Pao-Yang

address: 128 Section 2, Academia Road, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

data_processing:
Clean RNA-seq reads were mapped to the genome using Tophat.
Fragments per kilobase of transcript per million mapped reads (FPKM) was obtained to represent the gene expression level. Count table was generated using Cuffnorm and DEGs were identified using Cuffdiff. Genes with adjusted p-values <=0.05 and 1.5-fold difference in expression were considered differentially expressed.
BS-seq reads were aligned against the rice genome (MSU7) using BS Seeker2
BS Seeker2 post-processes the alignments to remove non-unique and low-quality mappings.
The DNA methylation level was calculated as ((#C)/(#C+#T)), each of which covered at least four reads for an accurate estimation
Assembly: MSU7
Supplementary files format and content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

organism: Oryza sativa

source_name: leaf

growth_protocol: Plants derived derectly from seeds or regenerated from calli were cultivated until the tillering stage in an Academia Sinica greenhouse under natural light.

extract_protocol:
RNA was isolated from leaves of transgenic rice under different treatment groups using RNeasy Plant mini kit (Qiagen) or Trizol for RNA-seq libraries. Genomic DNA was extracted from leaves by using a DNeasy Plant Mini Kit (Qiagen).
RNA-seq libraries were prepared following standard Illumina protocols according to manufacturer’s instructions. The fragmented DNA was then used for library preparation using Illumina's library preparation kits. Premethylated adapter ligated fragments were bisulfite converted using the EZ DNA methylation kit (Zymo Research). The BS-seq libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2500 (Illumina) sequencers.

treatment_protocol: Calli were treated with different combinations of transformation treatments.

tag: ecotype

value: japonica

tag: developmental stage

value: PB


title: AMT+Hb RNA-seq rep2

value: AMTHb


title: H syndrome patient 8

city: Petach Tikva

first: Ruth

last: Shiloh

address: Felsenstein Medical Research Center

country: Israel

institute: Schneider Children's Medical Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software  v3.1.0
Data was analyzed using Seurat v4
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol: 10X library was prepared from 4000–10,000 cells (10X V3 library preparation kit, 10X, USA) and sequenced on NextSeq 500 System (Illumina, USA).

value: blood

value: PBMCs enriched for monocytes

value: SLC29A3 Homozygous c.1279G>A


title: H syndrome patient 1

value: SLC29A3 Homozygous c.1045delC


title: S1389_synovium_RNA

value: Synovial tissue

value: RA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration)


title: H syndrome patient 5


title: H syndrome patient 7


title: CAGE_pat1D_Replicate_1

value: yeast cells

value: capped RNA


title: S1387_synovium_RNA

value: Moderate (>1 perivascular aggregate + focal interstitial infiltration) (2)

value: 3-4 cells Thick (2)


title: 24h_Naive_GEX

city: Oxford

first: Audrey

last: Gerard

address: Roosevelt Dr.

country: United Kingdom

institute: The Kennedy Institute of Rheumatology

description: 10X Genomics

data_processing:
Sequence reads were mapped using CellRanger multi (version 6.0.0) with the 10x mouse reference transcriptome (version 2020-A).
Paired chain TCR sequences were obtained through targeted amplification of full-length V(D)J segments during library preparation. Sequence assembly and clonotype calling was done through cellranger’s immune profiling pipeline (cellranger multi).
Assembly: mm10
Supplementary files format and content: 24h samples - independent Cellranger output filtered matrices for naïve and listeria-infected samples
Supplementary files format and content: d9 samples - independent Cellranger output filtered matrices for each biological replicate; combined contig output for TCR sequences

organism: Mus musculus

source_name: spleen

extract_protocol:
splenocytes mechanically dissociated and flow sorted for CD8+ T cells binding to the ovalbumin SIINFEKL tetramer
Gene expression, feature barcoding and TCR sequencing libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B). The final libraries were diluted to ~10nM for storage. The 10nM library was denatured and further diluted prior to loading on the NovaSeq6000 sequencing platform (Illumina, v1.5 chemistry, 28bp/98bp paired end for gene expression and feature barcoding, 150bp paired end for TCR libraries).
24h samples are composed of a combined three biological replicates in equal proportion, and sequenced as four technical replicates for naïve and listeria-infected
d9 samples were hashed using BioLegend TotalSeq™-C03 series antibodies, Hashtags 1-4 for each biological replicate

value: spleen

tag: time

value: CD8 T cells

value: WT

tag: treatment

value: naïve


title: H syndrome patient 6


title: S1385_synovium_RNA

value: 1-3 cells Thick (1)


title: S1281_synovium_RNA

value: OA

value: Mild (OA)


title: AMT+Ab RNA-seq rep1

value: japonica

value: AMTAb


title: 24h_Listeria_GEX

description: 10X Genomics

value: Listeria-OVA infected 24 hrs


title: AMT+Ab RNA-seq rep2


title: AgBi RNA-seq rep2

value: AgBi


title: d9_WT_TCR

description: 10X Genomics

data_processing:
Sequence reads were mapped using CellRanger multi (version 6.0.0) with the 10x mouse reference transcriptome (version 2020-A).
Paired chain TCR sequences were obtained through targeted amplification of full-length V(D)J segments during library preparation. Sequence assembly and clonotype calling was done through cellranger’s immune profiling pipeline (cellranger multi).
Assembly: mm10
Supplementary files format and content: 24h samples - independent Cellranger output filtered matrices for naïve and listeria-infected samples
Supplementary files format and content: d9 samples - independent Cellranger output filtered matrices for each biological replicate; combined contig output for TCR sequences
Library strategy: TCR-seq


title: d9_KO_HTO

description:
10X Genomics
d9_KO1_barcodes.tsv.gz
d9_KO1_features.tsv.gz
d9_KO1_matrix.tsv.gz
d9_KO2_barcodes.tsv.gz
d9_KO2_features.tsv.gz
d9_KO2_matrix.tsv.gz
d9_KO3_barcodes.tsv.gz
d9_KO3_features.tsv.gz
d9_KO3_matrix.tsv.gz
d9_KO4_barcodes.tsv.gz
d9_KO4_features.tsv.gz
d9_KO4_matrix.tsv.gz

library_source: other

molecule: protein


title: Healthy donor C8

value: blood

value: PBMCs enriched for monocytes


title: PB RNA-seq rep2

value: PB


title: Healthy donor C7


title: AgBi RNA-seq rep1


title: d9_WT_HTO

description:
10X Genomics
d9_WT1_barcodes.tsv.gz
d9_WT1_features.tsv.gz
d9_WT1_matrix.tsv.gz
d9_WT2_barcodes.tsv.gz
d9_WT2_features.tsv.gz
d9_WT2_matrix.tsv.gz
d9_WT3_barcodes.tsv.gz
d9_WT3_features.tsv.gz
d9_WT3_matrix.tsv.gz
d9_WT4_barcodes.tsv.gz
d9_WT4_features.tsv.gz
d9_WT4_matrix.tsv.gz


title: d9_KO_GEX


title: AMT+Hb RNA-seq rep1

value: AMTHb


title: AgTi RNA-seq rep2

value: AgTi


title: Healthy donor C6


title: kidney, NC, replicate 1, scRNAseq

city: Kunshan

first: Manman

last: Shi

address: South Zuchongzhi Road

institute: Traditional Chinese Medicine Hospital of Kunshan

data_processing:
Raw data from three IMN patients and one normal control from the sequencer was first processed by CellRanger (version 3.0) to get the FASTQ files, which were then aligned to the human genome reference sequence GRCh38. Finally, a collection of files, including barcodes, gene features and gene expression matrix, was obtained through CellRanger.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
For single cell isolation, renal samples were cut into 0.5mm2 pieces and then transferred to a 1.5mL-tube containing 1ml collagenase II and collagenase IV mixtures for digestion, subsequently filtered to remove cell debris and impurities. Next, 1 ml Red Blood Cell Lysis was added and incubated on ice for 2-10 min to lyse remaining red blood cells. After incubation, the cell suspension was centrifuged at 300g for 5 min at room temperature and then resuspended in 100 μl Dead Cell Removal MicroBeads. Subsequently, we removed dead cells using Dead Cell Removal Kit and resuspended cell samples in 1× PBS (0.04% BSA). Finally, cell suspension was centrifuged at 300 g for 3 min at 4 °C and resuspended in 50 μl of 1× PBS (0.04% BSA).
The single-cell transcriptomic amplification and library preparation after single-cell suspension loaded onto the microfluidic chip were performed according to the manufacturer’s instructions for 10×Genomics single-cell 3’ kit (V3). The following mRNA trapping, reverse transcription, cDNA purification and amplification were prepared according to the manufacturer’s protocol. The constructed library was sequenced using a Novaseq 6000 system.

value: kidney

tag: subject status

value: healthy control


title: d9_WT_GEX

tag: tissue

value: spleen

value: CD8 T cells


title: kidney, MN, replicate 1, scRNAseq

value: IMN patient


title: kidney, MN, replicate 2, scRNAseq


title: Ag RNA-seq rep2

value: Ag


title: H syndrome patient 4

value: SLC29A3 Homozygous c.1045delC


title: H syndrome patient 3

value: SLC29A3 Compound heterozygous c.1157G>A/ c.1309G>A


title: Healthy donor C4


title: H syndrome patient 2


title: d9_KO_TCR

description: 10X Genomics


title: Ag RNA-seq rep1

value: japonica


title: Callus+AM RNA-seq rep2

value: CallusAM


title: Ctrl2

city: Hangzhou

first: Fengchao

last: Zhao

address: No.79 Qingchun Road

institute: he First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Samples were sequenced by NovaSeq 6000 (Illumina) after quality inspection, and paired-end reads of 150nt length were obtained.
Sequence reads were trimmed for adaptor seauence/ow-gualty secuence using cutadapt(v2.7).
Trimmed sequence reads were aligned to human genome (ensembl GRCh38) with bwa (v0.7.17).
CIRI (V2.0.6) was applied to identify circRNAs and estimate the junction reads as circRNA counts.
Junction reads counts normalization were performed using DESeq2 .
Assembly: Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include normalization values for each sample

source_name: chondrocytes

extract_protocol:
The circRNA-seq data was generated using a standard RNA extraction protocol. Briefly, total RNA was isolated from the sample using TRIzol (Invitrogen) , according to the manufacturer's instructions. The extracted RNA was treated with DNase to remove any genomic DNA contamination, followed by purification steps to obtain high-quality RNA suitable for downstream applications.The circRNA-seq library was prepared using a modified version of the standard circRNA-seq library construction protocol. The library construction process involved several steps. First, use the kit to deplete rRNA, then deplete linear RNA to enrich circRNA. Then， the circRNA was subjected to a reverse transcription reaction using random primers to convert the RNA into cDNA. The enriched circRNA was fragmented and ligated with adapters. Subsequently, PCR amplification was performed to amplify the library and generate sufficient material for sequencing.The library strategy used for circRNA-seq was strand-specific RNA-seq. This strategy allows the identification and characterization of circular RNAs by preserving the information regarding their originating strands. It provides insights into the differential expression, alternative splicing, and other features of circular RNAs in the sample.
RNA libraries were prepared for sequening using standard Illumina protocols

value: chondrocytes

value: CTRL


title: Ctrl1


title: Ctrl3


title: H syndrome patient 1 during trametinib

value: blood

value: trametinib


title: NCIH460-INPUT

city: Milan

first: Francesco

last: Ferrari

address: Via Adamello 16

country: Italy

institute: IFOM ETS, the AIRC Institute of Molecular Oncology

library_source: genomic

data_processing:
Paired-end raw reads were filtered based on the quality value obtained from FastQC v0.11.9 (-q 10 and -p 30) using the Trim Galore! software v0.6.4_dev. The filtered reads were aligned to the hg19 reference genome using BWA v0.7.17-r1188 to produce the alignment file (BAM). The PCR duplicates were removed from the aligned BAM files using PICARD tools v2.23.1. The BAM files were sorted and indexed for peak calling using SAMtools. The BedGraph files were generated by comparing BAM files of IP and input (IP read coverage/input read coverage) resulting in a ratio for every base across the whole genome using bamCompare from deepTools v3.4.3. To call the peaks MACS2 v2.2.7.1 was used. This framework was implemented using nfcore ChIP-seq v1.2.1.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: bigWig

source_name: Lung

extract_protocol:
phenol/chloroform extraction
The Input and IP samples were ligated with illumina barcodes and amplified using the Kapa library amplification kit, followed by size-selection with AMPure XP Beads. ASPRI cleanup with a 1.5× AMPure XP Bead: DNA ratio was performed and final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 High Output Kit v2.5. For each sample (IP and Input) approximately 90 million paired-end reads were obtained.

treatment_protocol: Immunoprecipitation (IP) was performed with H3K27ac antibody (Catalogue No. AB4729) or control IgG (AB37415).

value: Lung

value: large-cell lung carcinoma

value: Input


title: Ch3

value: 10 ug/ml cholesterol


title: kidney, MN, replicate 3, scRNAseq

value: kidney


title: MIP Mouse SVZ p7

city: Durham

first: Adrian

middle: Aryeh

last: Epstein

state: NC

address: 300 N Duke St

department: Pediatrics

institute: Duke Univeristy School of Medicine

data_processing:
Basecalling and fastq files generated using 10X Cellranger v5.0.1  with default parameters
Alignment, counting and filtering of single cell RNA-Seq samples:- Control and MIP  using 10X Cellranger v5.0.1 with default parameters.
Assembly: mm10-2020-A
Supplementary files format and content: raw read counts in gene-barcode matrix

source_name: subventricular zone

growth_protocol: Standard mouse breeding

extract_protocol: nuclear isolation from tissue

treatment_protocol: SVZ was removed and snap frozen with liquid N2 and stored at -80 until processed

tag: sample type

value: MIP (modeled intestinal perforation)


title: mixed sample of MC38mOVA_Control_DIVA2treated_day20

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Raw fastq-sequencing reads were loaded into BD Rhapsody WTA Analysis Pipeline hosted by SevenBridgesGenomics and analyzed using version 1.9 of the pipeline.
Single cell RNA-seq libraries for Whole Transcriptome Analysis (WTA) and Sample Tags were created, following the BD Rhapsody System mRNA Whole Transcriptome analysis (WTA) and Sample Tag Library Preparation protocol with the BD WTA Amplification Kit (BD Biosciences, Franklin Lakes, USA). Short read sequences were processed using the Seven Bridges analytic workflow. Two to three independent biological replicates of single-cell libraries were sequenced on Illumina sequencer instruments. The dataset was annotated to gene-level information based on  ENSEMBL [v92]. Quality control was performed on each dataset independently to remove poor-quality cells, using the scater package [version 1.24.0]. The proportion of mitochondrial gene content was used as a proxy for damaged cells, using three median absolute deviations as a threshold, following the recommendations of the OSCA resource (https://bioconductor.org/books/release/OSCA/). Normalization of cell-specific biases was performed on the sets of cells passing the quality control filters using the deconvolution method of Lun et al. ran normalization, version 1.24.0]. Counts were divided by size factors to obtain normalized expression values that were log-transformed after adding a pseudocount of one. Integration of different biological samples was performed using the MNN method. Highly variable genes were identified on the pooled set of cells after decomposing the per-gene variability into technical and biological components based on a fitted mean-variance trend. Next, we performed dimension reduction and clustering. Principal Component Analysis (PCA) was performed, and provided as initialization to the t-SNE algorithm/UMAP algorithm to obtain a reduced dimensionality representation of the data. Clustering was performed using the highly variable genes (HVGs), building a shared nearest neighbor graph;  the Walktrap community finding algorithm was applied to determine cluster memberships. Cluster annotations were initially performed with the SingleR package [SingleR, version 1.10.0], using the ImmGen database as a reference. Annotations were also refined manually based on [canonical markers; in conjunction with marker genes identified programmatically with the scran function findMarkers]. Complementary exploration was performed with iSEE, which was adopted to generate most single-cell data visualizations included [iSEE, version 2.8.0]. Differential state analyses, as a combination of differential expression analysis and differential abundance analysis, were conducted in the pseudobulk framework, following the implementation of the muscat package [MUSCAT, version 1.10.0].
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every cell, gene and sample

source_name: MC38mOVA tumors

extract_protocol:
At day 16, respectively day 20, single cell suspensions were prepared from excised whole tumors by tissue digestion using Collagenase 4 (800 U/ml) and DNAse I (1:100) and gentleMACS dissociator (Miltenyi Biotec). CD45+ cells were enriched by murine CD45 (TIL) MicroBeads (Miltenyi Biotec) using MACS technology.
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). For multiplexing samples, tumorinfiltrating CD45+ cells from WT mice were labeled on d16 or d20 by sample tags against CD45 conjugated with unique oligos as indicated in the processed data file section. Sequence of sample tags can be found under BD; Doc ID 210970. Cells were loaded on BD Rhapsody cartridge. Capture of single RNA molecules on barcoded magnetic Oligo-dT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). mRNA and Sample Tag Libraries were prepared following the manual (mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol; 23--21712-00). Upon purifying WTA and Sample tag library, concentration of libraries was assessed by Qubit 2.0 using the DNA high sensitivity kit and average library size was determined on a bioanalyzer 2100 using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling of mRNA and Sample tag library following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on Illumina's NovaSeq 6000 at Novogene (Cambridge, UK). For processing of the sequencing raw data BD Rhapsody WTA analysis pipeline version 1.9 was used. Single-cell RNA-sequencing data were processed with R (further described below) and visualized using the R package iSEE.

treatment_protocol: WT mice were injected s.c. with 5x10^4 MC38mOVA colon adenocarcinoma cells on the right flank. Mice were treated by transcutaneous immunization (TCI) at day 6/7 and 13/14 after inoculation or left untreated. For TCI mice were treated on the ear skin with 25 mg/ear dithranol (300 ng/mg in vaseline) at days 6 and 13 and 50 mg IMI-Sol (5% Imiquimod) at days 7 and 14. 100 µg/ear OVA257-264 + 100 µg/ear OVA323-337 peptides were stirred into cremor basalis and administered after IMI-Sol treatment at days 7 and 14. Tumor growth was measured three times per week using a digital caliper.

value: MC38mOVA tumors

value: tumor-infiltrating CD45+ cells

value: WT

value: untreated and treated

tag: timepoint

tag: group

value: evasion phase - untreated and DIVA2

tag: single cell_capture_device

value: BD Rhapsody


title: mixed sample of MC38mOVA_Control_DIVA2treated_day16

value: control phase - untreated and DIVA2


title: Healthy Mouse SVZ p7

value: Control


title: Ch2

value: chondrocytes


title: Callus RNA-seq rep1

value: japonica

value: Callus


title: NCIH460-ChIP-H3K27ac_rep2

value: Lung

value: ChIP H3K27ac


title: AgTi RNA-seq rep1

value: AgTi


title: Do_2

city: ChunCheon-si

first: Jun Won

last: Park

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Mus musculus  (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2  implementations.
Gene-level and Transcript-level quantification were  calculated as raw read count, FPKM (Fragments Per Kilobase of transcript  per Million mapped reads) and TPM (Transcripts Per Million).
Aligned data (SAM file format) were sorted and  indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include  FPKM, TPM and Read Count values for each Sample

source_name: Gastric cancer

growth_protocol: S1 cells were maintained in RPMI1640 with 10% fetal bovine serum (FBS) and reagent in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using HiYield Total RNA Mini Kit (YRB100, Real Biotech Corporation, Taipei, Taiwan). 0.5 ug of total RNA was used for the construction of sequencing libraries.
A library was independently prepared using 0.5ug of total RNA from each sample using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina; Cat# 20020599).

treatment_protocol: 1×104 cells were seeded as single-cell suspensions in advanced DMEM/F-12 medium (12634010, Gibco), supplemented with 10 mM HEPES (15630-080, Gibco), 1 mM N-Acetylcysteine (A9165-5G, Sigma-Aldrich), 50 ng/ml epidermal growth factor (PMG8043, Gibco), 2mM GlutaMAX (35050061, Gibco), 2% B-27™ Supplement (17504044, Gibco), 1% N-2 Supplement (17502048, Gibco), and 1% penicillin-streptomycin (PS; LS202-02, Welgene) or 3D Tumorsphere Medium XF (C-28070, Promocell, Heidelberg, Germany) on low attachment 24-well plates (SPL3D™ Cell Floater; 39724, SPL).

value: Gastric cancer

value: monolayer cell

value: Rasa1 KO, Nf2 KO


title: Do_3


title: Callus+AM RNA-seq rep1

value: CallusAM


title: Ch1

value: 10 ug/ml cholesterol


title: NCIH460-ChIP-H3K27ac_rep1

value: large-cell lung carcinoma


title: HBEC-Input

value: Lung Epithelium

value: Input


title: Do_1


title: Seedling RNA-seq rep2

value: Seedling


title: Seedling RNA-seq rep1


title: XMOOl WT DAY 21, scRNAseq

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger Single-Cell Software Suite (v 3.1.0) using the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes, features, matrix)

molecule: polyA RNA

source_name: cerebral organoids

extract_protocol:
Nine organoids were collected and placed in a 1.5 ml tube. The samples were washed briefly in PBS, before adding 200 ul of TrypLE Express solution (12604-013 Gibco). The samples were mixed by gentle pipetting and incubated at 37C for 5 minutes. Then, the samples were manually dissociated by further pipetting and incubation for additional 5 minutes. This manual dissociation step was repeated three times. Thereafter, the dissociation reaction was stopped by addition of 800 ul of E8 Stem Flex medium and the cells were counted an automated cell counter (Countess II, Invitrogen) using the viability dye Trypan blue (0.4%, T10282, Invitrogen). To obtain a single cell preparation, the cell suspension was filtered through a 40 um filter (22363547, Thermo fisher). Filtered cells were centrifuged for 2 min at 200g, washed once with 1 ml of PBS containing 0.04% BSA (130-091-376, Miltenyibiotec), and resuspended by gentle pipetting to remove cell clumps. After this final step, cell viability was around 98%. The cells were centrifuged like above, and pellet was resuspended in PBS containing 0.04% BSA. Precisely, 5000 cells were collected at a concentration of 1000 cells/ul in PBS, 0.04% BSA for library preparation and sequencing.
Libraries were generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Dual Index (10X Genomics Inc., USA). Briefly, a droplet emulsion targeting 5,000 cells was generated in a microfluidic Next GEM Chip G, followed by barcoded cDNA generation inside the droplets. Purified and amplified cDNA was then subjected to library preparation and sequenced on a NovaSeq 6000 instrument (Illumina, USA) using a SP100 flow cell kit to a depth of 400M read-pairs per sample. Sequencing was performed as a service at the Department of Molecular Medicine (MOMA) of Aarhus University Hospital, Denmark (https://www.moma.dk/).

value: cerebral organoids

value: iPSC line HMGUi001 (https://www.ebi.ac.uk/biosamples/samples/SAMEA5696688)

value: neuronal progenitors

value: WT

value: Cerebral organoid differentiation


title: Callus RNA-seq rep2

value: japonica

value: Callus


title: PB BS-seq rep2

value: PB


title: NC_rep3

city: Shanghai

first: Zhonghua

last: Tao

address: No. 270, Dong’an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
After evaluation and cleaning, sequencing reads were aligned to hg38 ensemble-94 using bowtie2 V2.3.5.1
Following alignment, macs2 callpeak V2.2.6  was used for peak calling.
In addition,macs2 bdgdiff V2.2.6 was applied to identify significantly different ATAC-seq peaks between samples.
Assembly: hg38
Supplementary files format and content: text files showing enriched peaks for each sample

extract_protocol:
ATAC-seq was performed using the protocol from Corces et al., 2015 with small modifications.  MDA-MB-231 cells were lysed and subjected to tagmentation using Tn5 transposase.
The tagmented DNA fragments were amplified by PCR and purified using MinElute Reaction Cleanup Kit (Qiagen, no. 28206). Library size and quality were checked usingHS DNA Bioanalyzer chip (Agilent, no. 5067-4626).

value: triple negative breast cancer cells

value: control


title: NF2_KO_3

value: Gastric cancer

value: monolayer cell

value: Nf2 KO


title: HBEC-ChIP-biol_rep_1

value: Lung

value: ChIP H3K27ac


title: NF2_KO_1


title: PB BS-seq rep1


title: AMT+Hb BS-seq rep2

value: AMTHb


title: H3K27ac NC_IP_2

data_processing:
After evaluation and cleaning, sequencing reads were aligned to hg38 ensemble-94 using bowtie2 V2.3.5.1
Following alignment, macs2 callpeak V2.2.6  was used for peak calling.
In addition,macs2 bdgdiff V2.2.6 was applied to identify significantly different ChIP-seq peaks between samples.
Assembly: hg38
Supplementary files format and content: text files showing enriched peaks for each sample

source_name: triple negative breast cancer

extract_protocol:
ChIP assay was conducted using SimpleChIP Enzymatic Chromatin IP kit (9002S, Cell Signaling Technology) according to the manufacturer’s instruction.
Chromatin was digested with micrococcal nuclease, and nuclear membrane was broken through several pulses. DNA fragment length was checked to be between 150–900 bp. Chromatin was immunoprecipitated by either control IgG or H3K4me3 (ab8895; Abcam; 2 μg) primary antibody and reverse cross-linked. The eluted DNAs were proceeded by QIAseq ultralow input library kit (QIAGEN, 180495) and quantified by qPCR.

value: triple negative breast cancer

tag: antibody

value: immunoprecipitated using anti-H3K27ac antibody (C15210016; Diagenode)


title: NCIH460-ATACseq-biol_rep_3

data_processing:
Paired-end raw reads were filtered based on the quality value obtained from FastQC v0.11.9 (-q 10 and -p 30) using the Trim Galore! software v0.6.4_dev. The filtered reads were aligned to the hg19 reference genome using BWA v0.7.17-r1188 to produce the alignment file (BAM). The PCR duplicates were removed from the aligned BAM files using PICARD tools v2.23.1. The BAM files were sorted and indexed for peak calling using SAMtools. The BedGraph files were generated by comparing BAM files of IP and input (IP read coverage/input read coverage) resulting in a ratio for every base across the whole genome using bamCompare from deepTools v3.4.3. To call the peaks MACS2 v2.2.7.1 was used. This framework was implemented using nfcore ATAC-seq v1.2.1 pipeline .
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

extract_protocol:
Samples were purified using the Qiagen Mini elute PCR Purification kit
Libraries were PCR-amplified using the NEBNext High-Fidelity PCR Master Mix and amplified for 5 cycles using NEBNext 2x MasterMix and custom primers.Libraries were sufficiently amplified individually in addition to 5 cycles of PCR as computed from qPCR fluorescence curves. Libraries were purified using Zymo DNA Clean and Concentrator. The libraries were then size selected withwith a 1.5× AMPure XP Bead: DNA ratio. Final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 mid Output Kit v2.5.

treatment_protocol: as previously described (Corces et al., 2018)

value: large-cell lung carcinoma

value: transposase


title: NCIH460-ATACseq-biol_rep_2


title: HBEC-ChIP-biol_rep_2

value: Lung Epithelium


title: H3K27ac KO_IP_1

value: ARID1A knockout


title: AMT+Hb BS-seq rep1

value: japonica


title: NCIH460-ATACseq-biol_rep_1


title: H3K27ac NC_IP_1


title: Rasal_KO_1

value: Rasa1 KO


title: AMT+Ab BS-seq rep2

value: AMTAb


title: Rasal_KO


title: HBEC-ATACseq-biol_rep_2


title: H3K27ac KO_Input_2

value: triple negative breast cancer cells

value: input


title: NF2_KO_2

value: Gastric cancer


title: Con_2

value: monolayer cell

value: Control


title: HBEC-ATACseq-biol_rep_1

value: Lung


title: Con_1


title: H3K27ac KO_IP_2


title: H3K27ac KO_Input_1


title: AgBi BS-seq rep2

value: AgBi


title: AgBi BS-seq rep1


title: Rasal_KO_2


title: H3K27ac NC_Input_2

value: control


title: HCEC cells, Ct serovar L2-infected, rep3

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Expression_Browser.xlsx
HCEC_L2wt_R3
Re-analysis of GSM5942939

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
An initial ANOVA-like pass of differential expression testing was performed. Genes that did not significantly vary between any treatment were culled from downstream analysis.
Differential expression testing was performed using default paramters to identify genes differentially expressed in either mock-infected (HCEC v HVE) or Ct L2-infected (HCEC v HVE) cells.
Assembly: hg19
Supplementary files format and content: xlsx files containing raw counts, TPM, and FDRP values for every gene and sample.
Supplementary files format and content: xlsx file containing results of differential expression testing.

source_name: primary human cervical epithelial cell

growth_protocol: Primary human vaginal epithelial cells (HVEs, ATCC PCS-480-010, Lot 80924222) were cultured at 37° C with 5% atmospheric CO2 in Vaginal Epithelial Cell Basal Medium (VECBM, ATCC PCS-480-030) supplemented with all contents of a Vaginal Epithelial Cell Growth Kit (ATCC PCS-480-040), per manufacturer’s instructions.

extract_protocol:
HVEs were harvested for total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), per manufacturer's instructions.
Polyadenylated transcript enrichment and cDNA library preparation of intact samples was performed using the NuGEN Universal mRNA-Seq Library Preparation kit, per manufacturer's instructions.

treatment_protocol: HVEs seeded at 5000 cells/cm^2 were cultured to confluence over 6-7 days, then washed with pre-warmed Hanks Buffered Saline Solution prior to inoculation with Chlamydia-containing culture media at a multiplicity of infection (MOI) of 2.

value: primary human cervical epithelial cell

value: WT

tag: infection

value: Chlamydia trachomatis, serovar L2/434/bu-infected

value: 24 hours post-infection


title: HCEC cells, Ct serovar L2-infected, rep2

description:
Expression_Browser.xlsx
HCEC_L2wt_R2
Re-analysis of GSM5942938


title: AgTi BS-seq rep2

value: AgTi


title: Con


title: F08_5

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

institute: University of Leicester

data_processing:
For RNA sequencing, FASTQ files sequencing quality was assessed using FastQC (v0.11.9). Sequencing adapter content was trimmed using FastP (v0.20.0), (Chen, et al., 2018).
The pre-processed reads were then aligned to the mouse GRCm38/mm10 reference genome using Spliced Transcripts Alignment to a Reference (STAR) (v2.7.3a), (Dobin et al., 2013).
Gene mapping and quantification was performed using TEtranscripts (v2.1.4), (Jin et al., 2015), and DE analysis using DESeq2 (v1.34.0), (Love eta l., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text containing normalized read count

source_name: Intestinal tissue

extract_protocol:
RNA was extracted on a Promega Maxwell 16 using the Maxwell 16 LEV simplyRNA Cells Kit (Reference AS1270)
Indexed RNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB ref # E6420S) according to manufacturer’s standard protocol

treatment_protocol: four VillinCreER/0/BrafV600E-LSL/+ 8-12-week old mice were induced with tamoxifen and four were treated with vehicle to be left uninduced and used as controls to identify differentially expressed (DE) genes. Each experimental group contained two male and two female animals. Mice received intraperitoneal injections of 2 mg tamoxifen on two consecutive days. Intestinal tissue was harvested 6 months post-induction

value: Intestinal tissue

value: Mutant


title: H3K4me1 KO_IP_2

value: triple negative breast cancer

value: ARID1A knockout

value: immunoprecipitated using anti-H3K4me1 antibody (ab8895; Abcam)


title: AgTi BS-seq rep1

value: japonica


title: F011_5


title: HCEC cells, mock-infected, rep3

description:
Expression_Browser.xlsx
HCEC_Mock_R3
Re-analysis of GSM5942936

value: mock-infected


title: HCEC cells, Ct serovar L2-infected, rep1

description:
Expression_Browser.xlsx
HCEC_L2wt_R1
Re-analysis of GSM5942937


title: H3K4me1 KO_IP_1

value: triple negative breast cancer cells


title: Ag BS-seq rep2

value: Ag


title: F014_5

value: Control


title: H3K4me1 NC_IP_2


title: Ag BS-seq rep1


title: AMT+Ab BS-seq rep1

value: AMTAb


title: F019_5


title: H3K4me1 NC_IP_1

value: control


title: HCEC cells, mock-infected, rep1

description:
Expression_Browser.xlsx
HCEC_Mock_R1
Re-analysis of GSM5942934

value: primary human cervical epithelial cell


title: Callus+AM BS-seq rep2

value: CallusAM


title: HVE cells, Ct serovar L2-infected, rep3

description:
Expression_Browser.xlsx
HVE_L2wt_R3

source_name: primary human vaginal epithelial cell

value: primary human vaginal epithelial cell

value: WT

value: Chlamydia trachomatis, serovar L2/434/bu-infected


title: Callus+AM BS-seq rep1


title: H3K4me1 KO_Input_2

value: input


title: F017_5

value: Intestinal tissue


title: H3K4me1 KO_Input_1

value: triple negative breast cancer


title: HCEC cells, mock-infected, rep2

description:
Expression_Browser.xlsx
HCEC_Mock_R2
Re-analysis of GSM5942935

value: 24 hours post-infection


title: HVE cells, Ct serovar L2-infected, rep2

description:
Expression_Browser.xlsx
HVE_L2wt_R2


title: H3K27ac NC_Input_1


title: HVE cells, Ct serovar L2-infected, rep1

description:
Expression_Browser.xlsx
HVE_L2wt_R1


title: F023_5

value: Mutant


title: H3K4me1 NC_Input_2


title: F013_5


title: Callus BS-seq rep1

value: japonica

value: Callus


title: H3K4me1 NC_Input_1

value: triple negative breast cancer cells


title: HVE cells, mock-infected, rep3

description:
Expression_Browser.xlsx
HVE_Mock_R3

value: mock-infected


title: HVE cells, mock-infected, rep2

description:
Expression_Browser.xlsx
HVE_Mock_R2


title: Seedling BS-seq rep2

value: Seedling


title: F018_5

value: Control


title: d10_3 IND

city: Helsinki

first: Juha

middle: Samuli

last: Tapanainen

state: Uusimaa

address: Haartmaninkatu 8

department: Obstetrics and Gynaecology

country: Finland

institute: University of Helsinki

data_processing:
Library quality checks were performed using LabChip GX Touch HT High Sensitivity assays (PerkinElmer, USA).
The libraries were quantified for sequencing using KAPA Library Quantification Kits (KAPA Biosystems, Wilmington, MA, USA).
Sequencing was performed by using Illumina equipment (NovaSeq system using an S1 flow cell with lane divider, Illumina, San Diego, CA, USA). Read length for the paired-end run was 2 × 151 bp.
Quality control of raw sequence data was performed with FastQC v0.11.9.
Trim-Galore v0.6.5 was used for adapter trimming and quality filtering.
RNA-seq reads were then aligned against the human reference genome (GRCh38 release 82) using STAR-2.7.6a.
The quality of RNA-Seq quality matrices was inspected with RNA-SeQC v2.4.2 and the quality of RNA-Seq data was assessed with RSeQC v4.0.0.
FeatureCounts software was then used to summarise the read distribution over several genomic features.
Assembly: GRCh38 release 82
Supplementary files format and content: tab-delimited text file containing the expression count matrix

source_name: H9-DDdCas9VP192-NR5A1 clone 10

growth_protocol: Gonadal-like cells were derived by differentiating 2.24 x 10^5 iPSCs on 0.5 µg/cm2 human placental-derived type I collagen in DMEM/F12 + 2% B27 supplemented with 100 ng/ml Activin A + 5 µM CHIR-99021 + 2 µM dorsomorphin + 10 µM Y-27632 for 24 h, in 3 µM CHIR-99021 + 10 ng/ml BMP7 for 24 h, in 3 µM CHIR-99021 + 2 µM dorsomorphin for 48 h and finally in plain DMEM/F12 + 2% B27 for 6 days.

extract_protocol:
Cells were disrupted directly on culture wells with QlAzol Lysis Reagent (Qiagen, MD, USA). Total RNA was extracted and purified with miRNeasy Mini Kit (Qiagen, Hilden, Germany) including an additional On-Column DNase Digestion with the RNase-Free DNase Set.
Library preparation from 800 ng of total RNA was performed according to Illumina methodology (stranded total RNA prep with Ribo-Zero Plus Reference Guide, Illumina, San Diego, CA, USA).

treatment_protocol: Cells in IND condition were treated with 1 µg/ml doxycycline and 1 µM trimethoprim at days 4 to 10 of differentiation (for 6 days in total). Cells in CTRL condition were not treated with doxycycline and trimethoprim.

value: H9-DDdCas9VP192-NR5A1 clone 10

value: Embryonic stem cell-derived gonadal-like cells

value: 1 µg/ml doxycycline and 1 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: Seedling BS-seq rep1

data_processing:
Clean RNA-seq reads were mapped to the genome using Tophat.
Fragments per kilobase of transcript per million mapped reads (FPKM) was obtained to represent the gene expression level. Count table was generated using Cuffnorm and DEGs were identified using Cuffdiff. Genes with adjusted p-values <=0.05 and 1.5-fold difference in expression were considered differentially expressed.
BS-seq reads were aligned against the rice genome (MSU7) using BS Seeker2
BS Seeker2 post-processes the alignments to remove non-unique and low-quality mappings.
The DNA methylation level was calculated as ((#C)/(#C+#T)), each of which covered at least four reads for an accurate estimation
Assembly: MSU7
Supplementary files format and content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.


title: HVE cells, mock-infected, rep1

description:
Expression_Browser.xlsx
HVE_Mock_R1

value: primary human vaginal epithelial cell


title: NL6

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

institute: University of Liverpool

data_processing:
The raw Fastq files are trimmed using Cutadapt version 1.2.1
The reads are further trimmed using Sickle version 1.200 with a minimum window quality score of 20. Reads shorter than 15 bp after trimming were removed.
The processed reads were then pseudo-aligned to the Ensemble release mus musculus transcriptomes v96 with Kallisto quant version 0.46.1
Read count extraction and normalization were performed using DESe2.
Assembly: mus musculus transcriptomes v96
Supplementary files format and content: tab-delimited tsv files contain abundance, count and length values for each sample

source_name: gastrocnemius muscle

extract_protocol:
RNA was harvested usingTRizol reagent and Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. Samples treated with Dnase to avoid genomic DNA contamination.
Preparation of dual-indexed, strand-specific RNASeq library from submitted total RNA was performed using the NEBNext polyA selection and Ultra II Directional RNA library preparation kits (New England Biolabs, UK).

value: gastrocnemius muscle

value: lactational protein restriction


title: p974s865-ctrl

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

data_processing:
STAR v.2.4 alignment to genome
featurCounts v.1.5.1 for gene loci counting
DESeq2 for differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw gene counts of every sample

growth_protocol: BMDCs were cultures for 6 days before stimulation.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using poly A enrichment with Illumina TruSeq sample prep Kit / Illumina TruSeq SR Cluster Kit v3 HiSeq4000 according to manufacturers protocol.

treatment_protocol: BMDCs were stimulated with 500 µM ATP for 30 min and either harvested directly or after 24h.

value: BMDC


title: NL4


title: NL5


title: d10_3 CTRL

value: No treatment


title: p974s865-24h


title: KCO2s only, TGFβ1-treated, rep2

data_processing:
Sequencing data was demultiplexed and aligned to the hg38 reference genome via CellRanger (10X Genomics, version 6.0.1), using an expected cell count of 1000.
After aggregating the mock- and Ct L2-infected alignment results for each replicate (n = 2), initial cell type determination was performed in Loupe Cell Browser (10X Genomics, version 3.1.1). Epithelial cell (End1) and fibroblast (KCO2) populations were identified on the basis of keratin 19 and vimentin expression, respectively.
Subclustering analysis of the epithelial/fibroblast populations was performed in the Seurat R package. After associating per-cell expression data with their respective treatment (mock- or Ct¬ L2-infected) and cell type (epithelial cell or fibroblast) metadata, per-cell expression data were separated into separate End1/KCO2 Seurat objects.
Subsequent quality control and dimensionality reduction was performed analogously to the Seurat guided vignette on single-cell expression analysis. After trimming cells with extreme unique feature counts (200 < n < 8000), outlier features were identified using the vst method (local polynomial regression of log-transformed mean/variance, selecting top 2000 features). The dimensionality of each data set was determined via the Seurat JackStraw method; for both the End1 and KCO2 cell populations, the top 15 principal components encompassed the majority of variance in the data.
Dimensionality reduction via uniform manifold approximation and projection (UMAP) was then performed on each data set, using their respective top 15 principal components, followed by cluster identification via Seurat’s shared nearest neighbor algorithm (using a clustering resolution of 0.5).
Assembly: GRCh38
Supplementary files format and content: Loupe Cell Browser output files (.cloupe)
Supplementary files format and content: Raw unfiltered matrix files (.h5)

growth_protocol: Human endocervical epithelial HPV-16 E6/E7-immortalized End1s (End1 E6/E7, ATCC CRL-2615) were cultured at 37° C with 5% atmospheric CO2 in Keratinocyte Serum-Free Medium (KSFM, Thermo Fisher Scientific) supplemented with human recombinant epidermal growth factor, bovine pituitary extract, 5 micrograms/mL gentamicin, and 0.4 mM CaCl2 (unless otherwise indicated). Human endometrial hTERT-immortalized fibroblasts (KCO2-44D hTERT, ATCC SC-6000) were cultured in Dulbecco’s modification of Eagle’s medium (DMEM, Thermo Fisher Scientific 11960069) supplemented with 10% Fetal Bovine Serum (FBS, Fisher Scientific NC0327704), 2 mM L-Glutamine (Thermo Fisher Scientific 25030081), and 5 ug/mL gentamicin.

extract_protocol:
Cocultures were harvested as single-cell suspensions via the 10X Genomics Sample Preparation Demonstrated Protocol (Revision B).
Approx. 1000-cell libraries of each sample were prepared according to the 10X single-cell protocol (10X Genomics, Chromium Single Cell 3’ v2 Chemistry).

treatment_protocol: End1s were seeded at 35% of confluence on 6-well tissue culture plates, incubated for 16 hours, then infected at an MOI of 5. Infected End1 cultures were returned to a tissue culture incubator until 1 hpi, at which time cultures were washed three times with pre-warmed HBSS containing 100 ug/mL heparin to remove any transiently adhered chlamydial organisms. After aspiration of the final wash, KCO2s in complete DMEM were seeded in each well, at 75% of confluence. Tissue culture plates were subsequently incubated until 24 hpi.

value: fibroblasts

value: WT

value: TGFβ1-treated (20 ng/mL)

value: 24 hours post-treatment


title: KCO2s only, TGFβ1-treated, rep1


title: d10_2 CTRL


title: End1/KCO2 coculture, Ct serovar L2-infected, rep2

source_name: End1/E6E7, KCO2

value: End1/E6E7, KCO2

value: epithelial cells, fibroblasts

value: Chlamydia trachomatis, serovar L2/434/bu-infected

value: 24 hours post-infection


title: NL2


title: Callus BS-seq rep2

last: Chen

source_name: leaf

extract_protocol:
RNA was isolated from leaves of transgenic rice under different treatment groups using RNeasy Plant mini kit (Qiagen) or Trizol for RNA-seq libraries. Genomic DNA was extracted from leaves by using a DNeasy Plant Mini Kit (Qiagen).
RNA-seq libraries were prepared following standard Illumina protocols according to manufacturer’s instructions. The fragmented DNA was then used for library preparation using Illumina's library preparation kits. Premethylated adapter ligated fragments were bisulfite converted using the EZ DNA methylation kit (Zymo Research). The BS-seq libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2500 (Illumina) sequencers.

value: japonica

value: Callus


title: NL1


title: p974s864-ctrl


title: p974s865-0p5h

value: vehicle


title: p974s864-24h


title: End1/KCO2 coculture, Ct serovar L2-infected, rep1


title: d10_1 CTRL

value: H9-DDdCas9VP192-NR5A1 clone 10

value: Embryonic stem cell-derived gonadal-like cells


title: NN6

value: gastrocnemius muscle

value: control


title: d8_3 IND

value: 1 µg/ml doxycycline and 1 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: End1/KCO2 coculture, mock-infected, rep2

value: Mock-infected


title: d10_2 IND


title: NN4


title: p974s864-0p5h

value: BMDC


title: p974s856-24h

value: WT


title: p974s856-ctrl


title: NN5


title: NN3


title: End1/KCO2 coculture, mock-infected, rep1


title: d8_3 CTRL

value: No treatment


title: d8_2 IND


title: p974s856-0p5h


title: d10_1 IND


title: Child3_Day7

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

country: Australia

institute: QIMR Berghofer

description: 10x Genomics

data_processing:
Single cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger software v6.0.1  (10x Genomics) against the human reference genome, with default parameters. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control of the data, normalization, integration, clustering and sub-clustering was done using Seurat version 4.0.2.
Gene set enrichment analysis software was used to identify significantly enriched gene ontology terms
the HOMER v4.9 package was used to identify significantly overrepresented upstream regulators
Assembly: GRCh38 v 2.7.1a
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
PBMCs were isolated from whole blood via density centrifugation with Ficoll-Paque prior to cryopreservation. PBMC samples were thawed in RPMI 1640 (Gibco) containing 10% FCS and 0.02% Benzonase. 1E6 PBMCs were stained for viability with Propidium iodide (PI) and live cells were sorted on BD FACSAria™ III Cell Sorter into 2% FBS/PBS and counted on hemocytometer
Up to 10 000 cells were loaded into each lane of Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Gel Bead-in-Emulsion (GEMs) generated in Chromium Controller. 3’ Gene Expression Libraries were then generated according to manufacturer’s instructions. Generated libraries were sequenced in a NextSeq 550 System using High Output Kit (150 Cycles) with the following parameters read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles, read 2: 98 cycles

value: blood

value: PBMCs

tag: strain

tag: age


title: Child2_Day7

description: 10x Genomics

tag: cell type


title: NL3

tag: genotype

value: lactational protein restriction


title: d8_1 IND

tag: cell line


title: p974s855-ctrl


title: d8_1 CTRL


title: NN1


title: Child3_Day28

description: 10x Genomics


title: d6_3 IND


title: d8_2 CTRL


title: Prime_Boost2, replicate 2, scRNAseq

first: Feifei

last: Xiong

address: 350 Anshun Rd，Shanghai

institute: Shanghai Institute of Biological Products

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CeleScope version 1.6.1.
Correcting the deviation between samples using Harmony (https://portals.broadinstitute.org/harmony/).
Use Seurat to filter data, normalize and standardize data, perform PCA, etc.
Assembly: mm9
Supplementary files format and content: *tar: Tar archives include cell barcode file (barcodes.tsv), Feature file (genes.tsv), and Matrix file (matrix.mtx) for each sample.

source_name: spleen

extract_protocol:
In each microwell, a magnetic bead was paired with a cell. Each magnetic bead had a unique cell label and multiple molecular labels (unique molecular identifier or UMI) for capturing RNA. When the RNA is released from the captured cells, it can hybridize to the magnetic beads.
The magnetic beads were then collected into a 1.5-ml Eppendorf tube for reverse transcription using GEXSCOPER Single-Cell RNA Library Kit to perform cDNA synthesis on single cells. After cDNA synthesis and PCR amplification, Qubit (Thermo, Waltham, MA, USA) was used for cDNA quantification and Fragment Analyzer was used to determine the cDNA fragment size. Following several steps including fragmentation, adapter ligation, purification, PCR amplification, size selection and QC analysis; libraries were constructed before being sequenced with 150 bp paired end reads on Illumina HiSeq X platform.

value: spleen

value: CD3 T

value: Enhance immunity


title: Child3_Day0

description: 10x Genomics


title: NN2


title: d6_3 CTRL


title: p974s853-ctrl


title: Child2_Day28

description: 10x Genomics


title: p974s853-24h


title: d6_2 CTRL


title: Prime2, replicate 2, scRNAseq

value: primary immunity


title: Child2_Day0

description: 10x Genomics


title: p974s853-0p5h

value: vehicle


title: Prime3, replicate 3, scRNAseq


title: Adult3_Day28

description: 10x Genomics


title: Prime1, replicate 1, scRNAseq


title: p974s852-ctrl


title: Adult3_Day0

description: 10x Genomics


title: d6_1 IND

value: H9-DDdCas9VP192-NR5A1 clone 10


title: d6_1 CTRL

value: Embryonic stem cell-derived gonadal-like cells


title: Adult2_Day7

description: 10x Genomics


title: Prime_Boost3, replicate 3, scRNAseq


title: p974s855-0p5h


title: p974s852-24h


title: p974s855-24h


title: p974s852-0p5h


title: Contrl3, replicate 2, scRNAseq

value: Control


title: Adult2_Day28

description: 10x Genomics


title: Prime_Boost1, replicate 1, scRNAseq


title: d4_2


title: d4_1


title: Adult2_Day0

description: 10x Genomics


title: Cerebellum, WNV, 10 dpi, m8

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

data_processing:
Average base quality was determined by Fastqc
Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model.  After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: processed_data_cerebellum.xlsx represents counts, FPKMs, TPMs for all samples

source_name: Cerebellum

growth_protocol:
Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC)
Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 3, 7 and 10 days post-infection.

extract_protocol:
Total brain RNA was extracted from tissue samples using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol:
Mice were infected intraperitoneally (i.p.) with 10e4 plaque forming units (PFU) of WNV in 200 µL of Minimum Essential Medium Eagle (Corning) mock-infected animals were also inoculated i.p. with 200 µL of culture media
Mock-infected animals were also inoculated i.p. with 200 µL of culture media

value: Cerebellum

value: WNV

value: Day 10


title: p974s851-ctrl

value: BMDC


title: p974s851-24h


title: MPAL Patient 7, Diagnosis

city: Atlanta

first: Hope

last: Mumme

address: 1760 Haygood Dr NE

institute: Emory University

description: 10X Genomics

data_processing:
Raw scRNA-seq data was demultiplexed, aligned to human reference genome, and processed for single cell gene counting using the Cell Ranger Software from 10x Genomics (v7.0.0).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: bone marrow

extract_protocol:
Frozen bone marrow samples were obtained from Aflac Cancer and Blood disorder center from Children’s Healthcare of Atlanta Pediatric Biorepository.The frozen BM were thawed viably using standardized protocol. Briefly the cells were thawed quickly (37C for ~2 minutes till a small ice crystal remains), and warm complete medium (RPMI1640, 5% heat inactivated FBS, 1x Penicillin. Streptomycin) was added gradually. The cells were pelleted (380g, RT, 5min), and washed one more time with complete medium, which was followed by one more wash with PBS containing BSA (0.04 to 1.0%). For cell multiplexing, cells were labelled with specific anti-human TotalSeq-B Hashtag antibodies (Biolegend) according to manufacturer’s protocol. The cells were resuspended in cell staining buffer (Biolegend) or PBS with1% BSA to get an optimal cell concentration of 700-1200 cells/µl. The single cell suspensions were then proceeded using 10x Genomics single cell assay protocols.
The single cell RNA-seq libraries were prepared using the Chromium single cell 3’v3 and 3’ v3.1 reagent kits (10x Genomics). The libraries were quantified using Qubit (Thermo Fisher Scientific) and quality was checked using Bioanalyzer HS DNA chips (Agilent). Sequencing was performed using the massively parallel sequencing NextSeq 500 and Novaseq S4 platforms (Illumina).

tag: individual

value: patient 7

value: bone marrow

value: diagnosis

value: Bone marrow blast and immune cells

tag: disease state

value: MPAL

tag: diagnosis subtype

value: B/My MPAL


title: Cerebellum, WNV, 10 dpi, m5

value: WT

tag: time


title: Cerebellum, WNV, 10 dpi, m4


title: Control2

description: 10x Genomics

value: blood

value: PBMCs


title: Child1_Day28

description: 10x Genomics


title: Child1_Day7

description: 10x Genomics


title: p974s851-0p5h

tag: treatment

value: vehicle


title: Adult3_Day7

description: 10x Genomics

tag: tissue


title: KO_rep5

data_processing:
After evaluation and cleaning, sequencing reads were aligned to hg38 ensemble-94 using bowtie2 V2.3.5.1.
Following alignment, macs2 callpeak V2.2.6  was used for peak calling.
In addition, macs2 bdgdiff V2.2.6 was applied to identify significantly different ATAC-seq peaks between samples.
Assembly: hg38
Supplementary files format and content: *.rpkm.bw: bigWig files showing enriched peaks for each sample.

extract_protocol:
ATAC-seq was performed using the protocol from Corces et al., 2015 with small modifications. MDA-MB-231 cells were lysed and subjected to tagmentation using Tn5 transposase.
The tagmented DNA fragments were amplified by PCR and purified using MinElute Reaction Cleanup Kit (Qiagen, no. 28206). Library size and quality were checked using HS DNA Bioanalyzer chip (Agilent, no. 5067-4626).

value: triple negative breast cancer cells

value: ARID1A knockout


title: Child1_Day0

description: 10x Genomics


title: p974s850-24h


title: d4_3

value: H9-DDdCas9VP192-NR5A1 clone 10

value: Embryonic stem cell-derived gonadal-like cells

value: No treatment


title: Cerebellum, WNV, 10 dpi, m3

value: Cerebellum

value: WNV

value: Day 10


title: Cerebellum, WNV, 10 dpi, m2


title: Control1

description: 10x Genomics


title: KO_rep4


title: p974s850-0p5h

value: BMDC


title: Cerebellum, WNV, 10 dpi, m1


title: Contrl2, replicate 1, scRNAseq

value: spleen

value: CD3 T

value: Control


title: Adult1_Day28

description: 10x Genomics


title: KO_rep3


title: Cerebellum, Mock, 10 dpi, m7

value: Mock


title: Adult1_Day7

description: 10x Genomics


title: d6_2 IND

value: 1 µg/ml doxycycline and 1 µM trimethoprim at days 4-10 of differentiation (total 6 days)


title: MPAL Patient 2, Diagnosis

description: 10X Genomics

value: patient 2

value: bone marrow

tag: sample type

value: diagnosis

value: Bone marrow blast and immune cells

value: MPAL

value: T/My MPAL


title: Cerebellum, Mock, 10 dpi, m6

value: WT


title: p974s846-ctrl


title: KO_rep1

value: triple negative breast cancer cells

value: ARID1A knockout


title: p974s850-ctrl


title: Cerebellum, Mock, 10 dpi, m5

value: Cerebellum


title: Adult1_Day0

description: 10x Genomics

value: blood

value: PBMCs


title: p974s843-ctrl

value: BMDC


title: p974s846-24h


title: Patient BE 26-5

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

data_processing:
Basecall data produced by the NextSeq 550 is automatically uploaded to BaseSpace, a cloud- based data management and analysis service provided by Illumina. Here it is converted into FASTQ files in order to allow analysis using a number of apps accessible directly through BaseSpace, or to download so that alternative analysis pipelines can be used.
Data was processed using the pipeline nf-core/rnaseq v3.0 (b892cc54e3b768dca93d19da30a907a) using Nextflow (20.12.0-edge)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene-level length corrected values for each Sample. Salmon (1.4.0) and bioconductor-tximeta (1.8.0)

source_name: nasal epithelia

growth_protocol: Primary human nasal epithelial cells were expanded at 37 °C in media selective for basal cells or specialized media until 80% confluency. Basal cells were then dissociated and seeded into transwell inserts until confluent.

extract_protocol:
Cells were stored in RNALater until used. Total RNAas purified with miRNA Easy (Qiagen #74004)
Libraries were made with NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #E7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the providers protocol.

treatment_protocol: Apical fluid was then removed and cells were maintained in this air liquid interface (ALI) for at least 3 weeks until fully differentiated into multiciliated ciliated epithelium.

value: nasal epithelia

value: Primary cultures

value: TUBB4B p.P259L

value: Air Liquid Interface


title: Patient BE 26-6


title: Cerebellum, Mock, 10 dpi, m4

value: Mock

value: Day 10


title: NC_rep4

value: control


title: p974s843-24h


title: NC_rep5


title: NC_rep2


title: p974s843-0p5h

value: vehicle


title: Patient BE 26-3


title: Patient BE 26-4


title: Cerebellum, WNV, 7 dpi, m9

value: WNV

value: Day 07


title: Cerebellum, Mock, 10 dpi, m1

value: WT


title: Cerebellum, Mock, 10 dpi, m2


title: Patient BE 26-2


title: EOD rep5

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

description: A whole day fasting for every-other-day regime

data_processing:
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files containing FPKM values and Readcount values for all samples.

source_name: Heart

extract_protocol:
Whole hearts were removed and flash frozen on dry ice before RNA extraction. Frozen tissues were used for total RNA extraction using commercial RNA extraction kit from Bio Basic (EZ-10 DNAaway RNA miniprep kit).
RNA libraries were prepared for sequencing using standard Illumina protocols by NOVOGENE.

value: Heart

value: 9 months


title: KO_IP

description: Immunoprecipitated using anti-H3K4me3 antibody (9751; Cell Signaling Technology).

data_processing:
Samples were sequenced by NovaSeq 6000 (Illumina) after quality inspection, and paired-end reads of 150nt length were obtained.
After evaluation and cleaning, sequencing reads were aligned to human genome (UCSC hg19) with bowtie2 (v2.2.4).
In addition, MACS (v1.4.3) was used for peak calling and diffReps was applied to find significantly different H3K4me3 distribution.
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files showing enriched peaks for each sample (except for input sample).

extract_protocol:
ChIP assay was conducted using SimpleChIP Enzymatic Chromatin IP kit (9002S, Cell Signaling Technology) according to the manufacturer’s instruction.
Chromatin was digested with micrococcal nuclease, and nuclear membrane was broken through several pulses. DNA fragment length was checked to be between 150–900 bp. Chromatin was immunoprecipitated by either control IgG or H3K4me3 (9751; Cell Signaling Technology; 1:50) primary antibody and reverse cross-linked. The eluted DNAs were proceeded by QIAseq ultralow input library kit (QIAGEN, 180495) and quantified by qPCR.

value: triple negative breast cancer cells

value: ARID1A knockout

tag: chip antibody

value: anti-H3K4me3 antibody


title: Cerebellum, WNV, 7 dpi, m8

value: Cerebellum


title: EOD rep4


title: KO_Input

description: Input

value: IgG


title: Cerebellum, WNV, 7 dpi, m6


title: EOD rep3


title: Patient BE 26-1

value: nasal epithelia

value: Primary cultures


title: p974s846-0p5h

value: BMDC


title: Patient Tubb4b W123-2

value: TUBB4B p. P358S

value: Air Liquid Interface


title: KO_rep2


title: EOD rep2


title: Cerebellum, WNV, 7 dpi, m5


title: NC_IP

value: control


title: Patient Tubb4b W123-1


title: EOD rep1


title: Cerebellum, WNV, 7 dpi, m4


title: NC_Input

description: Input


title: NC_rep1


title: XMOOl WT DAY 100, scRNAseq

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger Single-Cell Software Suite (v 3.1.0) using the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes, features, matrix)

extract_protocol:
Five to six 100 day old organoids were collected and placed in a 35 mm plate. To remove dead cells from the organoid core, organoids were cut in half using a syringe needle and washed with PBS. Subsequently, PBS was removed and 200 ul of TrypLE Express solution (12604-013 Gibco) was added. Next, the organoids were cut into smaller fragments using two needles attached to 1 ml syringes. Fragments were collected in a 1.5 ml reaction tube and subjected to gentle pipetting followed by intermittent resting at 37C for 5 minutes. Single cells present in the supernatant after 5 min were collected into a new reaction tube and placed into the incubator. Tissue fragments remaining in the tube were treated with 100 ul of Triple Express and dispersed into small pieces using consecutive pipetting with 1 ml and 200 µl pipette tips. After additional five minutes, the single cells in the supernatant were again collected and added to the tube containing the single-cell suspension. This procedure was repeated 3 time for a total of 15 min. Any remaining tissue fragments were discarded. Triple Express dissociation was stopped by adding an equal volume of E8 Stem Flex medium, resulting in a total volume of 1 ml. Cells viability was assessed using cell viability dye Trypan blue (0.4%, T10282, Invitrogen) and cells were counted using an automated cell counter (Countess II, Invitrogen). Thereafter, the single-cell suspension was filtered through a 40 um filter (22363547, Thermo fisher) placed on top of a 50 ml tube. Filtered cells were collected and cell viability determined as above. Typically, cell viability at this step was around 50%-60%. To increase the precent of live cells in the single-cell suspension, the cells were centrifuged for 2 min at 200g and placed on ice. The cell pellet was washed in 1 ml of PBS with 0.04% BSA (130-091-376, Miltenyibiotec), pipetted gently to remove any cell clumps, and counted again. This washing step was repeated two more times, resulting in a cell viability of approximately 80%. Finally, 5000 cells were collected at a concentration of 1000 cells/ul in PBS, 0.04% BSA for library preparation and sequencing.
Libraries were generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Dual Index (10X Genomics Inc., USA). Briefly, a droplet emulsion targeting 5,000 cells was generated in a microfluidic Next GEM Chip G, followed by barcoded cDNA generation inside the droplets. Purified and amplified cDNA was then subjected to library preparation and sequenced on a NovaSeq 6000 instrument (Illumina, USA) using a SP100 flow cell kit to a depth of 400M read-pairs per sample. Sequencing was performed as a service at the Department of Molecular Medicine (MOMA) of Aarhus University Hospital, Denmark (https://www.moma.dk/).

value: cerebral organoids

value: iPSC line HMGUi001 (https://www.ebi.ac.uk/biosamples/samples/SAMEA5696688)

value: mainly neurons

value: Cerebral organoid differentiation, day 100


title: Control  BE 20- 2

value: TUBB4B WT


title: Control BE 20- 1


title: Cerebellum, WNV, 7 dpi, m2

value: WT

value: WNV

value: Day 07


title: IF16 rep5

description: Daily intermittent fasting for 16 hours

value: Heart

value: 9 months


title: Cerebellum, Mock, 7 dpi, m10

value: Cerebellum

value: Mock


title: IF16 rep3

description: Daily intermittent fasting for 16 hours


title: Cerebellum, Mock, 7 dpi, m9


title: IF16 rep4

description: Daily intermittent fasting for 16 hours


title: Control W123-2

value: nasal epithelia

value: Primary cultures


title: Control W123-1


title: T11, Rel, sc-RNA seq

first: Swati

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

data_processing:
Demultiplexed, aligned to the reference human genome (GRCh38) and processed for single cell gene counting using the Cell Ranger Software (v3.1.0, v4.0.0) from 10X Genomics Inc.
Assembly: hg38
Supplementary files format and content: mtx

source_name: Bone Marrow

extract_protocol:
BM single cells were captured together with uniquely barcoded primer beads in droplets in the Chromium Controller (10x Genomics, 110211).
The scRNA-Seq libraries were prepared using the 10X genomics Chromium single cell 3’V3 and 5’V1 reagent kits (10x Genomics, 1000075 and 1000006) and sequencing was performed using massively parallel sequencing on the Novaseq S4 platform producing >20,000 reads per cell.

value: Bone Marrow

tag: time point

value: diagnosis (Dx)


title: T10, EOI, sc-RNA seq

value: after therapy (EOI) and 1 at relapse


title: IF16 rep2

description: Daily intermittent fasting for 16 hours


title: Cerebellum, Mock, 7 dpi, m6


title: T9, EOI, sc-RNA seq


title: T9, Dx, sc-RNA seq


title: PAO1_pit2_I_3

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

description: total RNA with depletion of rRNA

data_processing:
cDNA reads quality and trimming
The quality of the cDNA reads was analyzed using FastQC (0.11.8) (Andrews, 2010). Adapters and poor quality sequences were trimmed using Trimmomatic (v0.39) (Bolger et al., 2014).
Allignment
BWA-MEM aligner (v0.7.17) was used to map the read pairs to the reference genome of PAO1 (NC_002516.2), which was manually altered to carry the pit2 genomic insert in its Tn7 site.
Normalization
The resulting fragment counts were normalized by gene length and the total number of mapped non-rRNA fragments per sample to yield fragments per kilobase of transcript per million mapped fragments (FPKM) values
statistics
Principal Component Analysis (PCA) was conducted with the prcomp package in R to evaluate sample clustering. Finally, gene expression analysis was performed using the DESeq2 Bioconductor package in R (v1.30.0)
Assembly: PAO1 (NC_002516.2)
Supplementary files format and content: FeatureCounts results containing raw gene feature counts and counts normalized by fragments per kilobase per million mapped non-rRNA fragments

organism: Pseudomonas aeruginosa

growth_protocol: LB overnight cultures of PAO1::empty and PAO1::pit2 in CAA + 150 µM FeCl3 were diluted a 100-fold in 50 mL CAA medium to an OD600nm of 2

extract_protocol:
At OD (600 nm) = 2, 2 mL cells was harvested, 20 % ice cold stop mix solution (95 % v/v ethanol, 5 % v/v phenol, saturated pH 4.5) was added and the mixture was immediately snap-frozen in liquid nitrogen. Next, samples were thawed on ice and their pellets were collected (20 min, 4 °C, 4500 g) for resuspension in 300 µL of a 0.5 mg/mL lysozyme solution in Tris-EDTA buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). Subsequently, samples were treated via the hot phenol method, followed by ethanol precipitation to extract the RNA. Next, the samples were treated with DNase I and the RNA was further purified using ethanol purification.
RNA samples were converted into cDNA using the Illumina Stranded Total RNA Prep Ligation Ribo Zero Plus kit. The Bioanalyzer and the DNA high sensitivity kit (Aligent) were used to verify rRNA depletion and evaluate the average fragment length, aiming for fragments around 500 bp.
All samples (n = 3 per condition) were pooled together in equimolar amounts to obtain a 25 µL sample of 4 nM and the cDNA samples were paired-end sequenced via Illumina next-generation sequencing (Novaseq 6000)

treatment_protocol: Induced conditions: CAA was supplemented with 1 mM IPTG

value: single genomic integration of pit2 via pUC18mini-Tn7-lac-GW

value: 1 mM IPTG


title: IF16 rep1

description: Daily intermittent fasting for 16 hours


title: T10, Dx, sc-RNA seq


title: PAO1_pit2_I_2

description: total RNA with depletion of rRNA


title: T8, EOI, sc-RNA seq


title: IF12 rep5

description: Daily intermittent fasting for 12 hours


title: Cerebellum, Mock, 7 dpi, m3


title: Cerebellum, Mock, 7 dpi, m5


title: T8, Dx, sc-RNA seq


title: IF12 rep3

description: Daily intermittent fasting for 12 hours


title: PAO1_empty_I_2

description: total RNA with depletion of rRNA

value: single genomic integration of an empty pUC18mini-Tn7-lac-GW

value: 0 mM IPTG


title: PAO1_pit2_I_1

description: total RNA with depletion of rRNA


title: IF12 rep4

description: Daily intermittent fasting for 12 hours


title: IF12 rep2

description: Daily intermittent fasting for 12 hours


title: T7, EOI, sc-RNA seq


title: PAO1_empty_I_3

description: total RNA with depletion of rRNA


title: Cerebellum, WNV, 3 dpi, m9

value: Day 03


title: T7, Dx, sc-RNA seq


title: Cerebellum, WNV, 3 dpi, m6

value: WT


title: Cerebellum, WNV, 3 dpi, m8

value: WNV


title: PAO1_empty_I_1

description: total RNA with depletion of rRNA


title: IF12 rep1

description: Daily intermittent fasting for 12 hours


title: Cerebellum, Mock, 7 dpi, m8

value: Day 07


title: PAO1_pit2_NI_3

description: total RNA with depletion of rRNA


title: AL rep5

description: Ad libitum feeding control

value: Heart


title: T6, EOI, sc-RNA seq


title: T6, Dx, sc-RNA seq


title: PAO1_pit2_NI_2

description: total RNA with depletion of rRNA


title: T5, Dx, sc-RNA seq


title: PAO1_pit2_NI_1

description: total RNA with depletion of rRNA


title: Cerebellum, WNV, 3 dpi, m2


title: AL rep3

description: Ad libitum feeding control

value: 9 months


title: Cerebellum, WNV, 3 dpi, m1

value: Cerebellum


title: PAO1_empty_NI_3

description: total RNA with depletion of rRNA


title: AL rep2

description: Ad libitum feeding control


title: T4, Dx, sc-RNA seq


title: T3, Dx, sc-RNA seq


title: AL rep1

description: Ad libitum feeding control


title: Cerebellum, Mock, 3 dpi, m9

value: Mock


title: PAO1_empty_NI_2

description: total RNA with depletion of rRNA


title: T2, Dx, sc-RNA seq


title: PAO1_empty_NI_1

description: total RNA with depletion of rRNA


title: Mate-Pair_ETP5uM2h-Recovery36h_Replicate2

city: Cambridge

first: Vishnu

last: Dileep

state: MA

address: 43 Vassar St

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

data_processing:
FASTQ files were trimmed to remove Illumina adaptors and paired-end reads were mapped separately using Bowtie2.
Mapped sam files were converted to bam files using samtools view
Bam files were sorted and PCR duplicates were removed using samtools rmdup
Bam files were converted to bed files using bedtools bamtobed
BED files from corresponding paired reads were merged based on FASTQ ID to create the matepair.txt files for each sample
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with mapped location of paired-reads

source_name: Primary culture

extract_protocol:
Mate-Pair library preparation was performed using the Nextera® Mate Pair Library Preparation (FC-132-1001). Briefly, formaldehyde-fixed FANS sorted nuclei were reverse crosslinked and genomic DNA was purified. Genomic DNA was tagmented to a size range of 1-5kb using mate pair transposome containing biotinylated adaptors followed by strand displacement to repair single-stranded gaps. Tagmented genomic DNA was circularized and then fragmented using sonication. The junctions were purified using streptavidin beads.
Sequencing libraries were prepared using TruSeq DNA LT Sample Prep (15027084) provided with the mate pair kit or NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) and NEBNext Multiplex Oligos for Illumina (E6440S).
Illumina libraries were sequenced in 75bp or 40bp paired-end mode using Nextseq500

value: Primary culture

value: Neuron

value: Etoposide


title: T1, Dx, sc-RNA seq

value: Bone Marrow

value: diagnosis (Dx)


title: Cerebellum, Mock, 3 dpi, m7


title: Cerebellum, Mock, 3 dpi, m6


title: Mate-Pair_ETP5uM2h-Recovery36h_Replicate1


title: Cerebellum, Mock, 3 dpi, m3


title: Cerebellum, WNV, 3 dpi, m4


title: CNHCM7V2

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

data_processing:
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using featureCounts from the SubRead package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: iPSC-derived nerons

growth_protocol: Induced pluripotent stem cells (iPSCs) were generated from four subjects (two males and two females). Specifically, we performed iPSC reprogramming using peripheral blood mononuclear cells (PBMCs) and the CytoTune™-iPS 2.0 Sendai Reprogramming Kit (A16517, Thermo Fisher, USA) as described previously. All iPS cell lines showed normal karyotypes, and they all expressed pluripotency markers. Cell lines were regularly characterized and verified to be free from mycoplasma. We then generated iPSC-derived forebrain neurons as reported previously. Briefly, iPS cells were cultured on Matrigel with mTeSR1 Plus media (STEMCELL technology, MA, USA). We suspended 3-D iPSC aggregates in embryoid body (EB) medium, consisting of FGF-2-free iPS cell medium supplemented with 2 μM dorsomorphin (STEMCELL technology, MA, USA) and 2 μM A-83 (STEMCELL technology, MA, USA), in non-treated polystyrene plates for 6 days. EB Medium was renewed every day. After 6 days, we replaced EB medium by neural induction medium (NPC medium) consisting of DMEM/F12, 1x N2 supplement, 1x NEAA, 2 ug ml−1 heparin (Tocris Bioscience) and 2 μM cyclopamine (Tocris Bioscience). The floating EBs were then transferred to Matrigel-coated plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with NPC medium change every other day. On day 22, we transferred the rosettes to low attachment plates in NPC medium containing 1x B27 (Thermo fisher). On day 24, neural progenitor spheres were dissociated and placed onto Matrigel-coated plates in neuron culture medium, consisting of Neurobasal medium supplemented with 1x glutamax, 1x B27, 0.2 mM L-Ascorbic Acid, and 0.5 mM cAMP (Sigma-Aldrich, St Louis, MO), 10 ng ml−1 BDNF and 10 ng ml−1 GDNF. Medium was replaced every three days during continuous culture

extract_protocol:
Total RNA was extracted using Trizol and the RNeasy mini kit (Qiagen, Valencia, CA, USA). The RNA integrity numbers (RIN) were above 9.5 for RNA samples.
RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads

treatment_protocol: The naïve form of FGF21 (100 ng/mL, PeproTech, cat: 100-42) at physiologically relevant concentration was used to perform the proposed experiments. Additionally, the concentrations of the naïve form of FGF21 (Peprotech, cat#100-42) [17; 18] and PF-05231023 (MedChemExpress, cat: HY-113697)  were selected to fall within the range of blood concentrations for this drug observed during preclinical and clinical studies.

value: iPSC-derived nerons

value: vehicle

value: 7 days treatment with drug renew daily


title: AL rep4

description: Ad libitum feeding control


title: Cerebellum, Mock, 3 dpi, m1


title: Mate-Pair_ETP5uM12h-Recovery36h_Replicate2


title: Mate-Pair_ETP5uM12h-Recovery36h_Replicate1


title: CNHCM7L2


title: Brain, WNV, 10 dpi, m8

data_processing:
Average base quality was determined by Fastqc
Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model.  After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: processed_data_brain.xlsx represents counts, FPKMs, TPMs for all samples

source_name: Brain

value: Brain

value: Day 10


title: Mate-Pair_DMSO_Replicate2

value: DMSO


title: CNHCM7L1


title: CNHCM7F2


title: Mate-Pair_DMSO_Replicate1


title: Brain, WNV, 10 dpi, m5

value: WT

value: WNV


title: Brain, WNV, 10 dpi, m4


title: CNHCM7F1


title: Cerebellum, Mock, 3 dpi, m8

value: Day 03


title: Brain, WNV, 10 dpi, m3


title: Mate-Pair_CKp25-Con

source_name: Forebrain

value: Forebrain

value: 2 weeks induction (removal of doxycycline from diet)


title: Brain, WNV, 10 dpi, m2


title: CNHCM3V2


title: CNHCM3V1


title: Brain, WNV, 10 dpi, m1


title: CNHCM3L2


title: Mate-Pair_CKp25-allGH2AX+ve


title: Brain, Mock, 10 dpi, m7

value: Mock


title: Brain, Mock, 10 dpi, m6


title: CNHCM7V1


title: CNHCM3F2


title: CNHCM3F1


title: Brain, Mock, 10 dpi, m5


title: Hi-C_TauWT_11months

data_processing:
Hi-C experiments were analyzed using Homer and Juicer pipeline
For HOMER pipeline, Reads were trimmed for GATC sites and mapped using bowtie2. Mapped reads were analyzed using the makTagDirectory command in the Homer pipeline. Processed files (.hic) were created using the tagDir2hicFile.pl script in Homer.
In addition to homer pipeline, Juicer pipeline was used to create hic files for combined CK-p25 samples Con, Step 1, and Step 2 as described in Rao et al.,2014. In Brief, paired-end read pairs were aligned separately to the mouse genome (mm10) using BWA. Next, duplicates/invalid pairs were removed. Interaction matrices were generated at resolutions of 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb.
Assembly: mm10
Supplementary files format and content: Processed Hi-C data in an indexed binary format (.hic) that can be accessed using the Juicebox tool (https://aidenlab.org/juicebox/)

extract_protocol:
In situ Hi-C was performed as previously described in Rao et al., 2014. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. P301S Tau mice and primary neuronal culture Hi-C were performed using FANS isolated nuclei with the Dovetail Hi-C kit (SKU: 21004) Illumina libraries were sequenced in 38 bp paired-end mode.
Library construction was performed using the custom protocol as described in Rao et al, 2014 or using the library preparation module in the Dovetail Hi-C kit (SKU: 21004)
Illumina libraries were sequenced in 38 bp paired-end mode

value: Tau P301S


title: Brain, Mock, 10 dpi, m4


title: Hi-C_TauWT_3months

value: Neuron


title: Brain, Mock, 10 dpi, m2


title: Hi-C_TauP301S_11months


title: Hi-C_TauP301S_3months


title: Mate-Pair_CKp25-Step2


title: CN1043L2


title: Hi-C_ETP_1uM48h_Replicate1

value: Primary culture

value: Etoposide


title: Mate-Pair_CKp25-NueN+veGH2AX-ve


title: CNHCM3L1


title: Mate-Pair_CKp25-Step1


title: CN1043V1


title: Hi-C_ETP_1uM48h_Replicate2


title: CN1043F1


title: Brain, WNV, 7 dpi, m9

value: Day 07


title: CN1043L1

value: iPSC-derived nerons


title: Brain, WNV, 7 dpi, m8


title: Brain, WNV, 7 dpi, m5


title: CN1043V2

value: vehicle


title: Hi-C_ETPDMSOCon48h


title: CN1043F2

value: 7 days treatment with drug renew daily


title: Brain, WNV, 7 dpi, m4

value: Brain


title: CN1030V2


title: CN1030V1


title: Brain, Mock, 10 dpi, m1

value: Day 10


title: Hi-C_DMSOCon_91374012

value: DMSO


title: CN1030L2


title: Hi-C_CK-p25_Step2Replicate2