title: LPM_WT and RA receptor mutants_ Cite-Seq Hashtag data

description: 11 samples were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger  (10x Genomics) and  bcl2fastq Conversion  (Illumina)
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

extract_protocol:
Peritoneal exudate cells extracted from each BMC mouse were stained in 100 µL of FACS buffer  (phenol red-free DMEM, 2% FCS, 0.1% azide and 10 mM HEPES, pH 7.9) containing 10 µL FcBlock  (homemade) , CD11b APC  (1 µL, M1/70, BioLegend), and CD115 PE/Cy7  (1 µL, AFS98, BioLegend), 1 µL  (0.5 µg) of a unique hashtag antibody for 10 minutes. Wild-type and four different mutant LPMs, including RARγ mutant, RXRα mutant, RORα mutant, and RXRβ mutant were sorted by their corresponding gRNA-conjugated fluorescence reporter, as live CD11b+CD115+ cells into PBS–BSA 0.1% medium  using the Aria561 cell sorter  (100-µm nozzle). Each NR mutant has two replicates, while three wild-type samples were paired with NR mutant cells from the same BMC. Samples of the same genotype were combined and hashtagged again. The multiple hash-tagged samples  (46,000 cells in total) were then combined into one tube with a final volume of 30 µL PBS-BSA 0.1%.
10x Genomics library prep, 3' v3 chemistry

value: WT, ROR{alpha} mutant, RXR{beta} mutant ,RAR{gamma} mutant and RXR{alpha} mutant

tag: library type

value: HTO

tag: hash id

value: WT-1 (HT12-CTGCAAATATAACGG+HT1-ACCCACCAGTAAGAC); WT-2 (HT12-CTGCAAATATAACGG+HT2- GGTCGAGAGCATTCA);WT-3 (HT12-CTGCAAATATAACGG+HT6- TATGCTGCCACGGTA); RORα mutant-1 (HT8- TATAGAACGCCAGGC +HT4- AAAGCATTCTTCACG); RORα mutant-2  (HT8- TATAGAACGCCAGGC +HT6- TATGCTGCCACGGTA); RARγ mutant-1 (HT8- TATAGAACGCCAGGC +HT1- ACCCACCAGTAAGAC); RARγ mutant-2  (HT8- TATAGAACGCCAGGC +HT2- GGTCGAGAGCATTCA); RXRβ mutant-1 (HT11- GCTTACCGAATTAAC +HT1- ACCCACCAGTAAGAC); RXRβ mutant-2 (HT11- GCTTACCGAATTAAC +HT1- AAAGCATTCTTCACG);RXRα mutant-1 (HT11- GCTTACCGAATTAAC +HT2- GGTCGAGAGCATTCA); RXRα mutant-2 (HT11- GCTTACCGAATTAAC +HT6- TATGCTGCCACGGTA);


title: H_NEG_c [257236337194_2]

status: Public on Dec 16 2024

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression in periodontally healthy EBV-negative gingival tissue sample

hyb_protocol: The labelled cRNAs were hybridized on SurePrint G3 Human Gene Expression v3 8x60K microarrays per manufacturer’s protocol (Agilent Technologies).

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

molecule: total RNA

organism: Homo sapiens

label_protocol: To produce cyanine 3-labeled cRNA, the input of 100 ng total RNA samples were amplified and labeled using the single-color Low Input Quick Amp Labeling kit according to manufacturer’s recommendations (Agilent Technologies).

extract_protocol: The total DNA was extracted using the QIAamp DNA Mini kit (Qiagen) according to manufacturer’s instructions. To isolate the total RNA, the hard gingival tissue was thoroughly homogenized using a gentleMACS dissociator with M tube (Miltenyi) and chemical lysis followed by the extraction using RNeasy Mini kit (Qiagen) per manufacturer’s instructions. The concentration and purity of the extracted total RNA and total DNA were determined using a SimpliNano spectrophotometer. The integrity of RNA was assessed using an Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Healthy gingival tissues were taken as surgical waste produced after surgical processing of maxillary tuberosity harvested for gingival graft and connective tissue graft techniques in periodontally healthy donors. Periodontitis-affected tissue samples were collected as a surgical waste produced during surgical periodontal therapy. The tissue specimens were directly embedded in a transport media consisting of PBS supplemented with antibiotics/antifungals and kept at 4°C before use. The tissue from the same site in each subject was extensively rinsed with transport media and aseptically split into 2 parts of similar size for subsequent DNA and RNA extractions. Extracted DNA was used for testing the presence and quantity of EBV load, while RNA was used for microarray transcriptomic analysis.

tag: tissue

value: Healthy gingiva

tag: ebv status

value: EBV-negative

tag: gender

value: Female

tag: age


title: IAH8R-Cas9-flag-YTHDF2-RNA-MUT-Input

type: SRA

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

library_source: transcriptomic

data_processing:
Reads were mapped to GRCh38 reference genome by vSTAR_2.6.1d. Raw counts for RNA-seq were calculated using Htseq v0.11.2. Peaks calling for RIP-seq and MeRIP-seq was conducted using exomePeak2 with default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Peak files in tab-delimited text format

source_name: Blood lymphoblasts

growth_protocol: Culture the cells with full medium and check the gene knock out or overexpression by western blots

extract_protocol:
Zymo Direct-Zol RNA Microprep Kit for RNA-seq, Zymo Oligo Clean & Concentrator Kit for RIP-seq, Zymo RNA & Concentrator for MeRIP-seq.
For RNA-seq, about 300 ng total RNA of each sample was used for library preparation according to the manufacture’s protocol of KAPA mRNA HyperPrep Kit (Illumina Platforms). 10cycles of PCR amplification were performed. KAPA Pure Beads (Kapa Biosystems) were used for library purification. The quality of each library was verified using a Qubit fluorometer (Thermo Fisher Scientific) and further evaluated by the 2100 Bioanalyzer (Agilent Technologies). For RIP-seq, the libraries were conducted using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) after depletion of ribosome RNA (rRNA). For MeRIP-seq, the libraries were conducted usign the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems).

treatment_protocol: Transfection were conducted at 1200 rpm/min for 2 hours at 32 °C. Drugs were added to the medium directly 24 hours before collection.

value: Blood lymphoblasts

tag: cell line

value: PDX cells (IAH8R)

tag: cell type

value: malignant B cells

tag: genotype

value: RNA-MUT-Input

tag: treatment

value: Transfection of sgRNAs and flag YTHDF2 proteins


title: LPM_GFP_Nr2c2_Mut_2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Mus musculus

source_name: peritoneal exudate

extract_protocol:
The cells were double-sorted directly into 5 μl TCL (Qiagen) buffer containing 1% 2-mercaptoenthonol (Sigma). NR mutant LPMs were sorted by their corresponding gRNA-conjugated fluorescence reporter, as DAPI-CD19-CD3-Ly6C-CD11bhiF4/80hi from BMC mice at 4 weeks after immune reconstitution.   Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

treatment_protocol: Peritoneal exudate were isolated by peritoneal lavage, fluorescent antibodies staining, and flow sorting.

value: peritoneal exudate

value: 4 weeks post reconstitution

tag: Sex

value: Male

tag: strain


title: IAH8R-Cas9-flag-YTHDF2-D-MUT-IP-rep-2

value: D-MUT-IP


title: tumor-case-34.1

type: genomic

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols.

data_processing: Raw data (CEL files) were processed using the R package EaCoN (v0.3.6-2) with SEQUENZA as segmentation algorithm. L2R files in CBS format were used as input for GISTIC (v2.0.22) to identify regions that are significantly amplified or deleted across all samples (confidence level 0.95, focal length cutoff 0.5, q-value threshold 0.1).

label: biotin

molecule: genomic DNA

source_name: tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

value: tumor

value: female

tag: biopsy

value: Punch


title: LPM_WT and RA receptor mutants_ RNA data

value: WT, ROR{alpha} mutant, RXR{beta} mutant ,RAR{gamma} mutant and RXR{alpha} mutant

value: GEX


title: BALF, young mice, D7 post bleomycin

city: Wien

first: Jörg

last: Menche

state: Wien

address: Augasse 2-6,

country: Austria

institute: Ludwig Boltzmann Institute for Network Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, bacoded processing, gene counting and aggregation were performed using Cell Ranger v5.0.1.
Assembly: mm10
Supplementary files format and content: Feature count matrices in h5 format with raw and filtered barcodes.

source_name: BALF

extract_protocol:
Cells were pooled and sorted into PBS with 0.02% BSA to exclude erythrocytes and dead cells. Cell quality was checked, and concentration was adjusted to 800 cells/µl and 10,000 cells were loaded onto the 10x Chromium controller.
Library preparation was performed using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 protocol

treatment_protocol: For single cell RNA-seq, BALF was collected on day 7 post bleomycin challenge from four male, 8-week-old mice, stained for flow cytometry markers for major BALF cell populations and resuspended in PBS 2 % BSA for cell sorting.

value: BALF

value: Lung BALF cells/macrophages

value: C57BL6/J (WT)

value: Bleomycin intratracheal


title: PM,  H_O group, replicate 4

city: Hangzhou

first: Zhida

last: Shen

state: Zhejiang

address: Qingchun East Road 3

department: Department of Cardiology

country: China

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University,

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Analysis of raw counts was performed with DESeq2
Supplementary files format and content: csv file of raw counts for each sample
Assembly: mm10
Supplementary files format and content: tab-delimited csv file includes raw counts

source_name: Peritoneal Macrophages

growth_protocol: Peritoneal macrophages were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (P/S) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using Trizol  (Invitrogen, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells stimulated by high glucose  (33mmol/L) and/or ox-LDL (50 mg/ml) to induce foam cell formation according to the group classification.

value: Peritoneal Macrophages

value: WT

value: high glucose (33mmol/L) and 50 mg/ml ox-LDL for 48h


title: LPM_RFP_Nr2c1_Mut_2


title: IAH8R-Cas9-flag-YTHDF2-D-MUT-Input

value: Blood lymphoblasts

value: PDX cells (IAH8R)

value: malignant B cells

value: D-MUT-Input

value: Transfection of sgRNAs and flag YTHDF2 proteins


title: tumor-case-33.1

value: tumor

value: male

value: Resect


title: LPM_GFP_Nr2c2_Mut_1

value: peritoneal exudate

value: 4 weeks post reconstitution

value: Male


title: LPM_GFP_Nr1h3_Mut_2


title: IAH8R-Cas9-flag-YTHDF2-WT-IP-rep-2

value: WT-IP


title: LPM_RFP_Nr2c1_Mut_1


title: PM,  H_O group, replicate 2


title: IAH8R-Cas9-flag-YTHDF2-WT-IP-rep-1


title: tumor-case-30.1

value: female


title: PM,  H_O group, replicate 3


title: tumor-case-28.1


title: LPM_GFP_Nr1h3_Mut_1


title: H_NEG_b [257236337193_3]

value: Healthy gingiva

value: EBV-negative


title: PM, H_O group, replicate 1

value: Peritoneal Macrophages

value: WT


title: IAH8R-Cas9-flag-YTHDF2-D-MUT-IP-rep-1

value: Blood lymphoblasts

value: D-MUT-IP


title: LPM_BFP_Nr1h2_Mut_2


title: H_NEG_a [257236337192_7]

value: Female


title: tumor-case-27.1


title: tumor-case-31.1

value: Punch


title: LPM_BFP_Nr1h2_Mut_1


title: PM, H_C group, replicate 4

value: high glucose (33mmol/L) for 48h


title: tumor-case-26.1

value: tumor


title: IAH8R-m5C-IP-rep2

molecule: polyA RNA

value: PDX cells (IAH8R)

value: malignant B cells

value: IP with m5C antibody


title: PM, H_C group, replicate 3


title: PM, H_C group, replicate 2


title: tumor-case-24.1


title: IAH8R-Input-rep2 (m5C)

value: Input control


title: LPM_RFP_Nr1d1_Mut_2

value: peritoneal exudate

value: 4 weeks post reconstitution

value: Male


title: tumor-case-25.1

value: male


title: PM, H_C group, replicate 1


title: tumor-case-23.1

value: female


title: LPM_GFP_Nr1d2_Mut_1


title: PM, L_O group, replicate 4

value: Peritoneal Macrophages

value: 50 mg/ml ox-LDL for 48h


title: IAH8R-Input-rep1 (m5C)

value: Blood lymphoblasts


title: tumor-case-22.1


title: IAH8R-Cas9-flag-YTHDF2-WT-Input

value: WT-Input

value: Transfection of sgRNAs and flag YTHDF2 proteins


title: LPM_GFP_Nr1d1_Mut_1


title: PM, L_O group, replicate 3

value: WT


title: IAH8R-m6A-IP-rep2

value: IP with m6A antibody


title: LPM_GFP_Esrra_Mut_2


title: tumor-case-21.1

value: tumor

value: Resect


title: IAH8R-Input-rep2 (m6A)

value: PDX cells (IAH8R)

value: malignant B cells


title: tumor-case-20.1


title: LPM_GFP_Esrra_Mut_1


title: LPM_RFP_Nr1d2_Mut_2


title: IAH8R-m6A-IP-rep1


title: LPM_RFP_Esr1_Mut_2


title: tumor-case-18.1


title: PM, L_O group, replicate 2


title: PM, L_C group, replicate 4

value: mannitol (27.5mM) for 48h


title: IAH8R-m5C-IP-rep1

value: IP with m5C antibody


title: KOPN-8-CCI-38-rep2

value: Inhibited YTHDF2


title: IAH8R-Input-rep1 (m6A)

value: Input control


title: PM, L_C group, replicate 3


title: tumor-case-17.1

value: male

value: Punch


title: LPM_RFP_Esr1_Mut_1

value: peritoneal exudate

value: 4 weeks post reconstitution

value: Male


title: KOPN-8-CCI-38-rep1

value: Blood lymphoblasts


title: PM, L_C group, replicate 2

value: Peritoneal Macrophages


title: LPM_RFP_CTRL_11

value: WT


title: KOPN-8-DMSO-rep2

value: DMSO control

value: DMSO


title: tumor-case-15.1

value: tumor

value: Resect


title: tumor-case-16.1


title: PM, L_C group, replicate 1


title: LPM_RFP_CTRL_12


title: KOPN-8-DMSO-rep1

value: malignant B cells


title: LPM_RFP_CTRL_10


title: IAH8R-shYTHDF2-2-rep2

value: PDX cells (IAH8R)

value: YTHDF2 KD

value: Transfection of shRNAs


title: IAH8R-shPABPC1-2-rep2

value: PABPC1 KD


title: PM, L_O group, replicate 1

value: 50 mg/ml ox-LDL for 48h


title: LPM_GFP_CTRL_9


title: tumor-case-13.1

value: male


title: LPM_GFP_CTRL_8

value: peritoneal exudate


title: IAH8R-shPABPC1-2-rep1


title: IAH8R-shYTHDF2-2-rep1


title: IAH8R-shYTHDF2-1-rep2


title: IAH8R-shPABPC1-1-rep2


title: tumor-case-11.1

value: female


title: tumor-case-09.1


title: IAH8R-shPABPC1-1-rep1


title: IAH8R-shYTHDF2-1-rep1


title: LPM_GFP_CTRL_6

value: 4 weeks post reconstitution

value: Male


title: IAH8R-shNS-rep2 (PABPC1)

value: Blood lymphoblasts

value: non specific control


title: IAH8R-shNS-rep2 (YTHDF2)


title: tumor-case-14.1


title: tumor-case-07.1


title: IAH8R-shNS-rep1 (YTHDF2)


title: LPM_BFP_CTRL_4

value: WT


title: tumor-case-06.1

value: Punch


title: LPM_BFP_CTRL_3


title: tumor-case-05.1

value: tumor


title: U2-NC-3

city: Shanghai

first: YongJie

last: Wang

address: Zhabei District

department: Department of Orthopaedic Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38).
featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile.
Assembly: human hg38
Supplementary files format and content: txt files contain raw mRNA counts

growth_protocol: The base medium for this cell line is ATCC-formulated McCoy's 5a Medium Modified, Catalog No. 30-2007. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

extract_protocol:
mRNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample prepa_x0002_ration kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 151 bp paired end reads.

treatment_protocol: For modulating gene expression, short hairpin RNA (shRNA) constructs were designed to target SQLE (shSQLE), along with non-targeting scramble sequences (shControl). These constructs were cloned into the pGIPZ plasmid (Addgene, Watertown, MA, USA). Verification of all constructs for authenticity was carried out through Sanger sequencing. HEK293T cells (RRID: CVCL_0063) were cultured in 10-cm dishes at 1×107 cells per dish. Transfection was performed using Lipofectamine 3000 (Thermo Fisher Scientific, Waltham, MA, USA) in conjunction with the respective plasmids and packaging plasmid for Lentiviral constructs (Youbio) according to their protocol. The medium was replaced six hours post-transfection, and the viral supernatants were harvested after 48 hours for the subsequent infection of OSA cell lines. Stably transfected cell lines were established through a two-week selection process utilizing puromycin at 2 μg/mL (Thermo Fisher Scientific). Gene knockdown efficacy was verified via quantitative real-time PCR (qRT-PCR) and Western blotting analyses.

value: osteosarcoma

value: scrambled-shRNA


title: U2-NC-2


title: tumor-case-04.1


title: AA_NERVE3

city: Torrance

first: Hayden

last: McSwiggin

address: 1124 W. Carson St.

department: Endocrinology

institute: The Lundquist Institute

description: Lungs and vagal ganglia were dissected, fixed in 4% PFA, then sectioned into 5um slices and placed onto xenium slide. 493 DNA probes were hybridized using 10x Genomic’s Xenium user guide.

hyb_protocol: Probe hybridization was performed at 50°C overnight using the pre-designed, 300-probe Xenium Mouse Mouse Tissue Atlassing in conjunction with a custom 92-probe add-on panel selected based on RNA-seq studies. Next, slides underwent wash steps to remove any unhybridized probes, followed by a 2-hour ligation step at 37°C to anneal probes to their specific mRNA target. The probes were then enzymatically amplified via rolling circle amplification PCR for 2 hours at 37°C. After washing, quenching steps were performed to reduce background autofluorescence, followed by a DAPI nuclear stain. The slide cassettes were subsequently loaded onto the Xenium Analyzer instrument

scan_protocol: Following instrument initialization, slides and consumables were loaded onto the Xenium Analyzer. Once the Xenium Analyzer run begins, slides undergo iterative rounds of image acquisition where probe-specific fluorescent oligos are added, hybridized to the amplified probe sequence, imaged and gently removed. mRNA-specific puncta were decoded into their corresponding gene IDs and assigned a quality score. Using the DAPI nuclear stain, cell boundaries were segmented and transcripts were spatially assigned to cells at a sub-50nm XY localization precision.

data_processing: Xenium In Situ Analyzer performs automated onboard analysis which includes DAPI-based segmentation of nuclei via deep-learning, then expansion of the segmentation masks. A cell-by-gene matrix of segmented nuclei is generated for analysis. Post-processing in R with custom scripts and Seurat

source_name: vagal ganglia asthma

extract_protocol: Lungs were dissected, flushed with PBS and perfused with 4% paraformaldehyde with 20cmH20 pressure for 10 minutes, then further fixed at 4 degrees C for 24 hours. Vagal ganglia were fixed in 4% paraformaldehyde for 2 hours. Tissues were processed according to to recommendations in the Xenium In Situ for FFPE tissue Preparation Guide (10X Genomics) and 5um paraffin slices were situated onto the xenium slide then prossed using Xenium In Situ for FFPE Tissues – Deparaffinization & Decrosslinking guide (10x Genomics).

treatment_protocol: A. alternataextract was purchased from CiteQ 299Laboratories (09.01.26) and dissolved to yield a final concentration of 25μg/ml in PBS. Mice 300were inoculated intranasally with 50μl on days 0, 3, 6, 9 where experiments took place 16 hours later47301.

value: Vagal Ganglia

tag: developmental stage

value: Adult


title: output

city: Bloomington

first: Ankur

last: Dalia

state: IN

address: 1001 E Third St. BB469A

institute: Indiana University

description: Library name: TND1801 ChIP output

library_source: genomic

data_processing:
Analysis was then performed using the open-source web-based platform Galaxy. Demultiplexed paired-end fastq files were aligned to V. cholerae reference genome (Vibrio cholerae O1 biovar El Tor str. N16961, NCBI RefSeq assembly: GCF_000006745.1) using the built-in tool bowtie2 with default parameters for paired-end data. Output BAM file was converted to a bigWig file for peak visualization using the built-in tool bamCoverage. Bin size was set to 50 bp and coverage was normalized to 1x. Effective genome size was user-specified at 4,033,464. The tool bigwigCompare was then used to visualize enrichment of output over input bigWig files. Output file was set as the “treatment file” and input was set as “bigwig file” and the option “compute the ratio signals” was used to generate output/input signal. To account for regions of zero coverage, a pseudocount of 0.01 was added to each binned region. The output bigWig file was then visualized on Integrated Genome Viewer 2.8.4.
Assembly: NC_002505 and NC_002506
Supplementary files format and content: bigwig file of the normalized ChIP output / normalized ChIP input

organism: Vibrio cholerae

source_name: Strain TND1801

extract_protocol:
V. cholerae strains were initiated from freezer stocks and incubated at 30°C in LB broth rolling for ∼16 hours. The following day, cultures were subcultured into fresh LB to an OD600 of 0.08 and incubated rolling for 6 hours at 30°C. Cells were incubated with 1% paraformaldehyde at room temperature for 20 minutes shaking to crosslink DNA and proteins. A 1.2 molar excess of Tris (10 minutes, room temperature, shaking) was used to quench residual paraformaldehyde. Crosslinked cells were washed twice with TBS (25 mM Tris HCl, pH 7.5 and 125 mM NaCl) and then frozen at -80°C. Cells were then resuspended in lysis buffer (1x FastBreak cell lysis reagent (Promega), 50 μg/mL lysozyme, 1% Triton X-100, 1 mM PMSF, and 1x protease inhibitor cocktail; 100x inhibitor cocktail contained the following: 0.07 mg/mL phosphoramidon (Santa Cruz), 0.006 mg/mL bestatin (MPbiomedicals/Fisher Scientific), 1.67 mg/mL AEBSF (Gold Bio), 0.07 mg/mL pepstatin A (DOT Scientific), 0.07 mg/mL E64 (Gold Bio) suspended in DMSO) to an OD600 of 50.0. These resuspensions were incubated rocking at room temperature for 20 minutes to permit cell lysis. Lysates were then sonicated to shear DNA into 200-300bp fragments (sonication was performed with a Fisherbrand Model 705 Sonic Dismembrator 6 times for 10 seconds at 1% amplitude, resting on ice for at least 30 seconds between each sonication). The sonicated lysates were then clarified by centrifugation and diluted 1:5 in Immunoprecipitation (IP) Buffer (50 mM HEPES NaOH pH 7.5, 150 mM NaCl, 1 mM EDTA, and 1% Triton X-100). An “input DNA” sample was collected from this diluted lysate. 1 mL of this diluted lysate was then added to Pierce anti-DYKDDDDK magnetic agarose equilibrated in IP buffer and then incubated at room temperature with end-over-end mixing. After two hours of incubation, a magnetic separation rack was used to facilitate removal of the supernatant. The agarose was washed twice with IP Buffer for 1 minute, once with Wash Buffer 1 (50 mM HEPES NaOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 500 mM NaCl, and 0.1% SDS) for 5 minutes, once with Wash Buffer 2 (10 mM Tris HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 1% Triton X-100) for 5 minutes, and once with Buffer TE (10 mM tris pH 8.0 and 1 mM EDTA) for 1 minute. SDS elution buffer (50 mM Tris HCl pH 7.5, 10 mM EDTA, and 1% SDS) was used to elute protein and DNA off the magnetic agarose (30 minutes at 65°C). Supernatant was collected and digested for 2 hours with 20 μg Proteinase K in SDS Elution Buffer at 42°C. 6 hours of incubation at 65°C was then used to reverse crosslinking. Both the input and the output samples were then purified via silica spin columns to remove non-DNA components.
Libraries were prepared using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina protocol (catalog no. E7645L) and analyzed by Agilent 4200 TapeStation. Libraries were pooled and loaded on a NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 flow cell (catalog no. 20046811) configured to generate 2x61 nt paired end reads. Demultiplexing was performed with bcl2fastq, version 2.20.0.

value: Strain TND1801


title: input

description: Library name: TND1801 ChIP input


title: LPM_BFP_CTRL_1


title: tumor-case-12.1


title: tumor-case-03.1

value: Resect


title: U2-NC-1


title: LPM_BFP_CTRL_2


title: AA_NERVE1


title: LPM_GFP_CTRL_7


title: AA_NERVE2


title: tumor-case-02.1


title: U2-sh-3

value: SQLE-shRNA


title: LPM_BFP_CTRL_5


title: U2-sh-2


title: cftr+- larvae

city: Chengdu

first: Huaqin

last: Sun

address: Renmin Nanlu

institute: Sichuan University

description: Library name: Sample 2

data_processing:
We performed alignment to this amended reference using 10x Cell Ranger v7.0 , which employs the STAR sequence aligner. The reference genome was the human genome GRCh38 or the mouse genome mm10. Overall, 36,000 cells passed the quality control. To remove the cells with low quality, cells with gene number over 500 and the ratio of mitochondria lower than 0.20 were maintained, and genes with at least one feature count in more than three cells were used for the following analysis. We determined gene expression counts using unique molecular identifiers (UMIs) for each cell barcode-gene combination. Following alignment, we filtered cell barcodes to identify those which contain cells using the approach implemented in Cell Ranger v7.0 , and only these barcodes were considered for downstream analysis including clustering and cell type identification, differential expression analysis by Seurat(v4.0.1).
Assembly: To enable unsupervised clustering and cell type identification, we perform dimensionality reduction with principal component analysis (PCA) on the combined set of samples for each tissue.To visualize the data, we further reduced the dimensionality of all 26,231 cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes: 1)Using the LogNormalize method of the "Normalization" function of the Seurat software to calculated the expression value of genes; 2)PCA (Principal component analysis) analysis was performed using the normalized expression value, Within all the PCs, the top 50 PCs were used to do clustering and t-SNE analysis；3)To find clusters, selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method. Marker genes for each cluster were identified by the "bimod"（Likelihood-ratio test）with default parameters via the FindAllMarkers function in Seurat(4.0.1). Filter Fold Change>1.5 and FDR<0.1 from the calculation results of findmarker, and then sort to top10 gene as the marker gene.
Supplementary files format and content: We used the Monocle 2 (v2.18.0) to place cells onto pseudotime trajectories ( https://github.com/cole-trapnell-lab/monocle-release), which applies reversed graph embedding (RGE) , a recently developed machine learning strategy, to accurately reconstruct complex single-cell trajectories. Monocle 2 requires the genes without a priori information that characterize the biological process, the number of cell fates or branch points in the trajectory, or the design of the experiment. Monocle 2 outperforms not only its previous version but also more recently developed methods, producing more accurate, robust trajectories. The Monocle2 analysis is based on the following three steps: 1) Genetic screening :Monocle looks for genes that change in "interesting" (not just noisy) ways, and uses those genes to construct the data; 2) Lower dimensions: Once the genes for cell sequencing are selected, Monocle reduces the dimensions of the data; 3) Pseudotime cell analysis: By projecting expression data into a lower dimensional space, the differentiation locus between cells was constructed.

organism: Danio rerio

source_name: whole larvae

extract_protocol:
The tissue samples was obtained from healthly donors and patients or mouse, the obtained tissue samples were washed 2-3 times in 4-degree precooled 1×PBS on ice, transferred to a sterile RNase-free culture dish , and cut into small pieces ( about 0.5mm2) with 10cm surgical scissors，the tissues were washed with 1×PBS, and remove as many non-purpose tissues as possible such as blood stains, fatty layers and connective tissue. The tissue samples were incubated in a constant temperature water bath or shaker at 37℃ with the self-prepared hydrolysate or the hydrolysate kit (MACS Human Tumor Dissociation kit DS_130-095-929/ MACS Mouse Tumor Dissociation kit DS_ 130-096-73 0). Generally, the incubation was terminated when the digestive juice was turbid and the tissue mass disappeared. Then Use 40µm cell sieve to filter, or use 100µm/70µm cell filter if the tissue mass is large. Generally, the cell suspension was centrifuged at 300r at 4℃ for 5min (Adjust centrifugal force and time according to cell size and number). Discard the supernatant and add 1mL of re-suspension to the centrifuge tube to re-suspend the cells, add 3mL of pre-cooled erythrocytes lysis liquid in tube (Solarbio), blowing and suction evenly. Incubate at 4℃ for 5-10min, centrifuge at 300r at 4℃ for 5min immediately after completion and remove the supernatant and add 1mL of re-suspension( Precooled 1X PBS) to fully re-suspend the cells. Test with cell counter（Countstar Rigel S2）, adjust the concentration according to the test result, the target concentration is 700-1200 cell/µL, the Cell activity is greater than 85%, and the agglomeration is less than 15%. Once the final cell concentration and activity were reached, the cells were placed on ice and 10x Genomics single cell transcriptome chip on-board experiment was carried out within 30 minutes.
We prepared single cell RNA-seq libraries with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 on the Chromium Controller(10× Genomics).We prepared single cell suspensions from cultured cell lines and single cells were suspended in PBS containing 0.04% BSA.The cell suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsion(GEMs) according to the manufacturer’s recommendation.captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol .The quality of libraries was assessed by Qubit 4.0 and the Agilent 2100. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per cell and 150 bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).

value: whole larvae

value: body cell

value: cftr+-

value: 7 dpf


title: AA_LUNG

source_name: lung asthma

value: Male

value: Lung


title: tumor-case-01.1

value: female


title: WT larvae

description: Library name: Sample 1

value: WT


title: IAH8R-shNS-rep1 (PABPC1)

value: Blood lymphoblasts

value: PDX cells (IAH8R)

value: malignant B cells

value: non specific control

value: Transfection of shRNAs


title: U2-sh-1

value: osteosarcoma


title: DLD-1 cell,KI-TAZ-ALFA-tag,anti-TAZ(Af-CUT&Tag)

status: Public on Dec 15 2024

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

description: Library name: DLD1_TAZ-ALFA-tag_anti-TAZ-CUT_Tag

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Following cell or nucleus counting, permeabilization is performed without the addition of antibodies. The permeabilized samples are incubated with LgBiT-Tn5 or NbALFA-Tn5, and unbound proteins are subsequently removed. A transposition activation reaction is then conducted to fragment intracellular DNA, which is extracted for downstream library preparation. Indexed libraries are generated using universal i5 primers and unique barcoded i7 primers, with each sample assigned a distinct barcode. The libraries are amplified through 15 cycles of PCR, and the resulting DNA is purified for high-throughput sequencing.

value: colon

value: epithelial

value: KI-TAZ-ALFA-tag

value: anti-TAZ


title: DLD-1 cell,KI-TAZ-ALFA-tag,NbALFA-Tn5(Af-CUT&Tag)

description: Library name: DLD1_TAZ-ALFA-tag_Af-CUT_Tag


title: SW480 cell,KI-CTCF-HiBiT,anti-HiBiT(CUT&Tag)

description: Library name: SW480_CTCF-HiBiT_anti-HiBiT_CUT_Tag

value: KI-CTCF-HiBiT

value: anti-HiBiT


title: DLD-1 cell,control,NbALFA-Tn5(Af-CUT&Tag)

description: Library name: DLD1_WT-NbALFA-Tn5


title: SW480 cell,KI-RPB1-HiBiT,5000_cells,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_RPB1_HiBiT_5000_cells


title: SW480 cell,KI-RPB1-HiBiT,500_cells,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_RPB1_HiBiT_500_cells


title: DLD-1 cell,KI-YAP1-HiBiT,anti-YAP1(CUT&Tag)

description: Library name: DLD1_YAP1-HiBiT_anti-YAP1


title: cdca7ab_2, H2A.W.6_7, rep1

city: WIEN

first: Pierre

last: Bourguet

address: Dr. Bohr Gasse 3

institute: GMI

description:
Library name: ChIP_cdca7ab_2_H2A.W.6_7_rep1
score file normalized to depth and log2 normalized to H3

library_source: other

data_processing:
The data were analyzed using the nfcore/chipseq pipeline v2.0.0 (https://nf-co.re/chipseq/2.0.0/) (Ewels et al., 2020) with Nextflow (v22.10.7). We used custom arguments for read length (150 bp), fragment size (275), and blacklisted mitochondrial and chloroplast genomes. To get the average value for each annotation, we used the bigWigAverageOverBed script from UCSC tools (https://github.com/ucscGenomeBrowser/kent-core/tree/master). We further analyzed the data with deepTools v3.3.1 (Ramírez et al., 2016). To normalize by H3 or by the WT, we used bigwigCompare with a bin size of 10 bp, ignoring non-covered regions with skipNonCoveredRegions. To produce average profile plots (metaplots), annotations were scaled to an arbitrary size of 1000 bp and the enrichment value was calculated by 50 bp bins, using computeMatrix scale-regions.
Assembly: TAIR10
Supplementary files format and content: Enrichment score provided as BigWig files. Input and H3 are normalized to depth and use variable steps. H2A.W, H2A.Z, H3K9me2 and H3K27me1 are normalized to depth, log2 normalized to H3, and use a fixed 10bp step.

molecule: other

organism: Arabidopsis thaliana

source_name: 31-day-old rosette leaves

growth_protocol: grown in soil in long days at 21°C in a climatic chamber

extract_protocol:
Tissues were frozen in liquid nitrogen and ground in a 5-ml grinding jar on a Retsch Mixer Mill MM 200 at 30 Hz for 45 s. Tubes were kept at room temperature until the powder showed signs of thawing. We added 35 ml of nuclei isolation buffer (NIB, 10 mM MES-KOH pH 5.3, 250 mM sucrose, 10 mM NaCl, 10 mM KCl, 2.5 mM EDTA, 0.1 mM spermine, 0.1 mM spermidine, 2.5 mM ß-mercaptoethanol, 0.3% Triton X-100 and protease inhibitors) (Lorkovic 2004 MBC), followed by vortexing until homogeneous. The extract was filtered through two layers of Miracloth, which were washed with 10 ml of NIB and spun at 3,400 rpm at 4°C for 5 min. Pellets were resuspended in 25 ml of NIB, vortexed and incubated for 10 min on ice to fully dissolve chlorophyll content. Tubes were spun as above and pellets were carefully washed with 5 ml of shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitors) without resuspending and spun again. This washing step was repeated and pellets were resuspended in 0.9 ml of shearing buffer. One ml of the extracted chromatin was transferred to Covaris glass tubes and sonication was conducted at 4°C for 900 seconds per sample (peak power 140.0; duty factor: 5.0; Cycles/Burst: 200). Sheared chromatin was spun for 5 min at 4°C at 15,000 rpm. The supernatant was collected and spun again, and the supernatant was transferred to a 5 ml tube. Fifteen µl of chromatin were kept to control for sonication efficiency. Chromatin was diluted to 3.5 ml to reduce SDS concentration with a ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS and protease inhibitors). For preclearing, 200 µl of Dynabeads protein A (Thermofisher, reference 1001D) were added to the chromatin and rotated 1 h at 4°C. Beads were discarded by collecting supernatants after two centrifugations at maximum speed for 30 s. A hundred µl of pre-cleared chromatin was kept at -20°C for input control, and the remaining chromatin was aliquoted with 500 µl per immunoprecipitation (IP) and incubated with 5 µg of anti-H3 (Abcam, ab1791), anti-H2A.W.6/7, anti-H2A.Z.9/11, anti-H3K27me1 (Millipore, 17-643) or anti-H3K9me2 (Abcam, ab1220) antibodies at 4 °C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A magnetic beads, rotated at 4°C for 3 h, and washed two times with a low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630 and 0.1% deoxycholic acid) and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Elution was done with 200 µl of 0.1 M NaHCO3 and 1% SDS, incubated at 65°C for 15 min. We added 20.4 µl of reverse cross-link buffer (0.4 M Tris-HCl pH 8.0, 2 M NaCl, 10 mM EDTA, 0.6 mg ml−1 proteinase K (Thermo Fisher Scientific)) and incubated at 45°C for 3 h and 65°C for 16 h. RNA was subsequently degraded for 30 min at room temperature with 10 µg of RNase A (Thermo Fisher Scientific), and DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo, reference D5205).
Libraries were prepared with the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs), following the manufacturer's instructions. Fragment size distribution was analyzed on a 5200 Fragment Analyzer System (Agilent), and size selection with SPRI beads (Molecular Biology Services, IMP, Vienna, Austria) was applied to remove large fragments and self-ligated adapters, when necessary. To maximize comparability, if only one sample had undesired fragments, we size-selected all samples for a given antibody. For size selection, briefly, DNA was diluted to 100 µl, we mixed in 60 µl of magnetic SPRI beads, collected the supernatant, and added 40 µl of magnetic SPRI beads, washed two times with 80% ethanol, and eluted DNA. Sequencing was carried out on a NovaSeq 6000 instrument using an S4 flow cell to generate paired-end 150 bp reads with around 25 million reads per sample.

treatment_protocol: 1.5 g of rosette leaves from 31-d-old plants were fixed in 37 ml 1% formaldehyde in PBS by vacuum-infiltration for 10 min. The cross-linking reaction was quenched by adding glycine to a final concentration of 125 mM.

value: 31-day-old rosette leaves

tag: chip antibody

tag: batch

value: C


title: DLD-1 cell,KI-RPB1-ALFA-tag,anti-RPB1(nano-CUT&Tag),Rep1

description: Library name: DLD1_RPB1-ALFA-tag_anti-RPB1-Rep1


title: DLD-1 cell,KI-YAP1-HiBiT,IgG

description: Library name: DLD1_YAP1-HiBiT_anti-IgG

value: anti-IgG


title: SW480 cell,KI-RPB1-HiBiT,Nano-Tn5(nano-CUT&Tag),Rep2

description: Library name: SW480_RPB1-HiBiT_Nano-Tn5-Rep2


title: DLD-1 cell,KI-YAP1-HiBiT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: DLD1_YAP1-HiBiT_LgBiT-Tn5


title: SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_CTCF-HiBiT_LgBiT-Tn5_Af-CUT_Tag


title: DLD-1 cell,KI-RPB1-ALFA-tag,NbALFA-Tn5(Af-CUT&Tag),Rep2

description: Library name: DLD1_RPB1-ALFA-tag_NbALFA-Tn5-Rep2


title: SW480 cell,KI-RPB1-HiBiT,50000_cells,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_RPB1_HiBiT_50000_cells


title: RKO cell,KI-TAZ-HiBiT,anti-IgG(CUT&Tag)

description: Library name: RKO_TAZ-HiBiT_anti-IgG

value: RKO

value: KI-TAZ-HiBiT


title: RKO cell,KI-TAZ-HiBiT,LgBiT-Tn5(Af-CUT&Tagg)

description: Library name: RKO_TAZ-HiBiT_LgBiT-Tn5


title: SW480 cell,control,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_WT_LgBiT-Tn5

value: WT


title: SW480 cell,KI-RPB1-HiBiT,LgBiT-Tn5(Af-CUT&Tag),Rep2

description: Library name: SW480_RPB1-HiBiT_LgBiT-Tn5-Rep2


title: SW480 cell,KI-CTCF-HiBiT,IgG(nano-CUT&Tag)

description: Library name: SW480_CTCF-HiBiT_anti-IgG


title: DLD-1 cell,KI-RPB1-ALFA-tag,anti-RPB1(nano-CUT&Tag),Rep2

description: Library name: DLD1_RPB1-ALFA-tag_anti-RPB1-Rep2


title: SW480 cell,KI-RPB1-HiBiT,IgG(nano-CUT&Tag)

description: Library name: SW480_RPB1-HiBiT_IgG


title: SW480 cell,KI-RPB1-HiBiT,anti-RPB1(CUT&Tag),Rep1

description: Library name: SW480_RPB1-HiBiT_anti-RPB1-Rep1


title: DLD-1 cell,KI-RPB1-ALFA-tag,NbALFA-Tn5(Af-CUT&Tag),Rep1

description: Library name: DLD1_RPB1-ALFA-tag_NbALFA-Tn5-Rep1


title: SW480 cell,KI-RPB1-HiBiT,Nano-Tn5(nano-CUT&Tag),Rep1

description: Library name: SW480_RPB1-HiBiT_Nano-Tn5-Rep1


title: RKO cell,KI-TAZ-HiBiT,anti-TAZ(CUT&Tag)

description: Library name: RKO_TAZ-HiBiT_anti-TAZ


title: SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(scAf-CUT&Tag)

description: Library name: SW480-CTCF-HiBiT_scAf-CUT_Tag

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
genome coverage bedGraph files are generated using bamCoverage (v3.3.1) and bedtools map (v2.30)
PCA and UMAP are applied for dimensionality reduction, followed by KMeans clustering to identify sample clusters.
Assembly: mm10,hg19
Supplementary files format and content: barcode-list.txt

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
The LgBiT-Tn5 complex was prepared in 192-well PCR strip tubes, each containing 1.5 μL of 26 μM recombinant LgBiT-Tnp protein, 0.75 μL of 50 μM 5′ barcode, 0.75 μL of 50 μM 3′ barcode, and 4 μL of dialysis buffer, and incubated at 25°C for 60 minutes. HiBiT-tagged cells or nuclei (2 million) were washed, permeabilized, resuspended in antibody buffer with NanoLuciferase, and distributed into 192 wells (10,000 cells/nuclei per 50 μL). Each well received 1 μL of the LgBiT-Tnp complex, followed by incubation (room temperature for 60 minutes or overnight at 4°C). After centrifugation at 300×g for 3 minutes, the solution was mostly discarded, and the wells were washed three times with 100 μL Dig-300 buffer. The cells/nuclei were pooled, centrifuged at 600×g for 3 minutes, resuspended in 400 μL Dig-300 buffer, and filtered. Using FACS, 200 cells/nuclei were distributed into 96 wells, where tagmentation was initiated by adding 25 μL of tagmentation buffer, incubating at 37°C for 60 minutes, and stopping the reaction for DNA extraction. For library preparation, each well received 18 μL DNA, 1.25 μL of 10 μM 5′ library index barcode, 1.25 μL of 10 μM universal 5′ barcode, 0.5 μL TAE, and 5 μL of 5×TAB. PCR amplification was performed for 20 cycles.


title: SW480 cell,KI-RPB1-HiBiT,LgBiT-Tn5(Af-CUT&Tag),Rep1

description: Library name: SW480_RPB1-HiBiT_LgBiT-Tn5-Rep1


title: 3C_Tac_rep2

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Kyoto University

data_processing:
*library strategy: 3C-seq
Data were processed using HiC-Pro version 3.0.0 (Servant et al., 2015). Normalized contact matrices were generated with MAX_ITER = 500. LOW_COUNT_PERC was set to 0.006 for Thermococcus kodakarensis.
Assembly: GCA_000009965.1, GCA_000195915.1
Supplementary files format and content: Tab-delimited tables. The first and second columns indicate genomic bins. The third column indicate normalized interaction frequencies between the bins.

organism: Thermoplasma acidophilum

extract_protocol:
Cells were crosslinked, permeabilized, and treated with AluI and HaeIII to digest genomic DNA. The insoluble fraction was collected and used for proximity ligation. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol, precipitated in ethanol, and sonicated.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.

value: Wild type


title: SW480 cell,KI-RPB1-HiBiT,ATAC

description: Library name: SW480_RPB1-HiBiT_ATAC_seq

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Harvest cells by centrifuging at 600×g for 5 minutes, discard the supernatant, and resuspend in PBS. Centrifuge a single-cell suspension containing the desired number of target cells at 600×g for 5 minutes, discard the supernatant, and resuspend in 50 µL of pre-cooled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.02% digitonin, 0.1% Tween-20). Allow the cells to lyse by placing them on ice for 5 minutes. Centrifuge at 500×g for 10 minutes at 4°C to collect the cell nuclei and immediately continue to transposition reaction. To make the transposition reaction mix, combine the following: 10 μL 5×TD Buffer (50 mM Tris pH 7.5, 25 mM MgCl2, and 50% dimethylformamide), 16.5 µL PBS, 0.5 µL 10% Tween-20, 0.5 µL 1% digitonin 18.5 ddH2O and 4 µL LgBiT/NbALFA-Tn5 Transposase (~1 µM). Resuspend nuclei in the transposition reaction mix and incubate the transposition reaction at 37°C for 30 min. PCR mix (Vazyme#TD601) and adapters (VazymeTD#202) were used for library amplification, the total volume is 50 µL. The fragmented DNA library was initially incubated with a 0.55× (27.5 µL) volume of DNA purification magnetic beads (Vazyme#N411). After discarding the magnetic beads, the supernatant was retained, and a 1.2× (60 µL) volume of DNA magnetic beads was added to further purify the DNA fragment library.


title: DLD-1 cell,KI-RPB1-ALFA-tag,ATAC

description: Library name: DLD1_RPB1-ALFA-tag_ATAC-seq


title: SW480 cell,KI-CTCF-HiBiT,anti-CTCF(CUT&Tag)

description: Library name: SW480_CTCF-HiBiT_anti-CTCF_CUT_Tag

value: anti-CTCF


title: ChIP_XerA_IP_xerA_rep1

data_processing:
Data were mapped using Bowtie 2 version 2.3.5.1 (Langmead & Salzberg, 2012). Low-quality alignments (MAPQ < 30) were removed using SAMtools version 1.9 (Li et al., 2009). Generated BAM files were processed using the bamCoverage function (version 3.5.1) of deepTools (Ramirez et al., 2016) to calculate Reads Per Kilobase region per Million mapped reads (RPKM) for genomic bins. Mapped data were processed for peak calling using MACS v3.0.0a6 with the following setting: --fe-cutoff 3, --keep-dup all, --call-summits, -m 1 50.
Assembly: GCA_000009965.1
Supplementary files format and content: bedgraph
Supplementary files format and content: bed

organism: Thermococcus kodakarensis

extract_protocol:
Crosslinked cells were lysed by sonication, and the extract was clarified by centrifugation. Protein-DNA complexes were purified from the extract with antisera. After reversal of crosslinks, the DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated in ethanol.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads.

value: xerA deletion

value: XerA (custom)


title: ChIP_XerA_input_xerA_rep1


title: ChIP_TrmBL2_IP_trmBL2_rep1

data_processing:
Data were mapped using Bowtie 2 version 2.3.5.1 (Langmead & Salzberg, 2012). Low-quality alignments (MAPQ < 30) were removed using SAMtools version 1.9 (Li et al., 2009). Generated BAM files were processed using the bamCoverage function (version 3.5.1) of deepTools (Ramirez et al., 2016) to calculate Reads Per Kilobase region per Million mapped reads (RPKM) for genomic bins.
Assembly: GCA_000009965.1
Supplementary files format and content: bedgraph

value: trmBL2 deletion

value: TrmBL2 (custom)


title: 3C_Tac_rep1


title: ChIP_TrmBL2_input_trmBL2_rep2


title: ChIP_TrmBL2_IP_KU216_rep2

value: Parental strain KU216


title: ChIP_XerA_IP_KU216_rep1


title: ChIP_TrmBL2_IP_KU216_rep1


title: ChIP_TrmBL2_IP_trmBL2_rep2


title: SW480 cell,KI-RPB1-HiBiT,anti-RPB1(CUT&Tag),Rep2

description: Library name: SW480_RPB1-HiBiT_anti-RPB1-Rep2

value: colon

value: epithelial


title: ESC4

city: Valencia

first: Francisco

last: Domínguez

state: SPAIN

address: Avenida Fernando Abril Martorell, 106

country: Spain

institute: IVI Foundation

data_processing:
FastQC was used for checking the quality of the raw sequence data. Those fragments that did not meet quality requirements were trimmed using Trimmomatic.
Assembly: Alignment and quantification was performed using the Salmon algorithm (reference genome GRCh38).
Supplementary files format and content: Tab-delimited text file includes raw counts, and PRKM values for each Sample and scramble vs iPGRMC1 comparation statistic data.

source_name: Endometrium

growth_protocol: Human Endometrial Stromal Cells (hEnSCs) were mantained in phenol red-free DMEM F12 supplemented with 10% fetal bovine serum (FBS), antibiotics and antifungals in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using a SMART-Seq V4 Ultra-Low Input RNA Sequencing kit (Clontech, CA, USA) that uses oligo(dT) priming.
cDNA was synthesized with 3′SMART-Seq CDS primer II (Clontech, CA, USA) and PCR amplified (17 cycles) from 10 pg of RNA following manufacturer’s instructions. Amplified cDNA was purified using AMPure XP magnetic beads (Illumina, CA, USA). cDNA integrity was checked with a 2100 Bioanalyzer (Agilent Technologies, CA, USA), then 1 ng of cDNA per sample was fragmented, and libraries were constructed using NexteraXT DNA sample preparation (Illumina, CA, USA) according to manufacturer’s instructions. Samples were quantified using a 2100 Bioanalyzer (Agilent Technologies, CA, USA). An RNA pool was generated using equal concentration (5 nM) of RNA per sample. Barcodes and adapters were included in the library to sequence and identify all samples.

treatment_protocol:
PGRMC2 silencing was induced with a pool of 3 different siRNAs specific to PGRMC2 (100 nM/well) transfected into cells using Lipofectamine 3000 Transfection Reagent (Invitrogen, USA) for 24 h. As a control, trilencer-27 Universal Scrambled Negative Control siRNA Duplex (Origene, USA) was transfected into cells using Lipofectamine 3000 Transfection Reagent (Invitrogen, USA) for 24 h.
Decidualization was induced by 4 days treatment of 80-90% confluent cells with 0.5 mM stable cyclic adenosine 3′:5′ monophosphate analog bromo-cAMP and 1 μM medroxyprogesterone 17-acetate progestin.

value: Endometrium

value: hEnSC

value: PGRMC2 inhibited

value: Decidualization


title: ESC8


title: ChIP_TrmBL2_input_KU216_rep1


title: ChIP_XerA_input_KU216_rep1


title: ChIP_TrmBL2_input_KU216_rep2


title: ESC3

value: Scramble


title: ESC7


title: ESC2


title: ESC5


title: 3C_Tko_xerA_rep1


title: SARS-Cov-2 S protein treatment of HAEC cells 2

city: Changchun

first: xizi

last: luo

state: jilin

address: 126 Xinmin Street, Changchun, Jilin, China

institute: Jilin University

description: Library name: s2

data_processing:
Remove reads containing adapters. Remove reads containing N ratio greater than 10%. Remove reads that are all A bases.Remove low-quality reads (bases with quality value Q≤20 account for more than 50% of the entire read).Base quality analysis, ribosome alignment, gene type statistics, gene expression statistics
Assembly: Ensembl_release109
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Tab-separated values files include RPKM values for each sample

source_name: cell line

growth_protocol: HAEC cells were cultured in DMEM medium containing 10% FBS and 1% double antibody in a cell culture incubator at 37°C and 5% CO2.

extract_protocol:
After extracting the total RNA of the sample, rRNA is removed using a conventional kit and mRNA is enriched.
After enriching eukaryotic mRNA with polyA tails by magnetic beads with Oligo (dT), the mRNA was sheared with buffer. Using the fragmented mRNA as a template and random oligonucleotides as primers, the first cDNA chain was synthesized in the M-MuLV reverse transcriptase system, and then the RNA chain was degraded with RNaseH, and the second cDNA chain was synthesized with dNTPs as raw materials under the DNA polymerase I system. The purified double-stranded cDNA was repaired at the end, A-tailed and connected to the sequencing adapter, and the cDNA of about 200bp was screened with AMPure XP beads, PCR amplification was performed, and the PCR product was purified again using AMPure XP beads to finally obtain the library.

treatment_protocol: 10nm SARS-CoV-2 S protein stimulates HAEC for 24 hours

value: cell line

value: HAEC

value: Human amniotic epithelial cells

value: S

value: 10NM SARS-CoV-2 S protein stimulation


title: SARS-Cov-2 S protein treatment of HAEC cells 1

description: Library name: s1


title: Untreated HAEC cells 2

description: Library name: hc2

value: WT

value: Unprocessed


title: Untreated HAEC cells 1

description: Library name: hc1


title: ChIP_TrmBL2_input_trmBL2_rep1

value: trmBL2 deletion


title: Untreated HAEC cells 3

description: Library name: hc3


title: SARS-Cov-2 S protein treatment of HAEC cells 3

description: Library name: s3


title: ESC6


title: 50CA4

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Bowtie2 version 2.1.0 with the reference genome and the annotation GTF file downloaded from ENSEMBL (release 79, GRCH38), and the gene expression level was estimated using RSEM v1.2.15.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (74106, Qiagen) following the manufacturer's instructions and RNA integrity was checked by using an Agilent Bioanalyzer 2100.
Total RNA sample preparation and sequencing were performed using the VAHTS Total RNA‐Seq Library PrepKit for Illumina.

value: Hippocampus

tag: subfield

tag: group

value: AD+CAA


title: 50EC

value: EC


title: 50CA3


title: ESC1


title: 50CA1


title: 50CA2


title: 49CA1


title: 49CA2


title: 49EC


title: 48EC


title: 49CA3


title: 49CA4


title: 48CA4


title: 48CA2


title: 48CA1


title: 47EC


title: 46CA4


title: 46EC


title: 47CA4


title: 47CA3


title: 45CA4


title: 46CA2


title: 46CA3


title: 48CA3


title: 46CA1


title: 47CA1


title: 45CA3


title: 45CA2


title: 44CA4


title: 44CA3


title: 44CA2


title: 44EC


title: 43EC


title: 44CA1


title: 43CA3


title: 42EC


title: 43CA4


title: 42CA3


title: 42CA4


title: 45EC


title: 42CA2


title: 42CA1


title: 41CA4


title: 41CA3


title: 41EC


title: 41CA1


title: 40EC


title: 40CA4


title: 40CA2


title: 41CA2


title: 40CA3


title: 39EC


title: 45CA1


title: 40CA1


title: 39CA4


title: 39CA2


title: 38EC


title: 39CA3


title: 38CA4


title: 43CA1


title: 38CA3


title: 37EC


title: 47CA2


title: 38CA2


title: 37CA3


title: 37CA1


title: 36EC


title: 36CA4


title: 37CA4


title: 36CA3


title: 36CA1


title: 35CA3


title: 35CA1


title: 35CA4


title: 37CA2


title: 34CA3

value: CAA


title: 34CA4


title: 34EC


title: 35CA2


title: 34CA2


title: 39CA1


title: 34CA1


title: 38CA1


title: 33CA4


title: 33CA3


title: 33CA1


title: 33EC


title: 33CA2


title: 32CA3


title: 32EC


title: 32CA4


title: 32CA2


title: 32CA1


title: 36CA2


title: 31CA3


title: 31CA1


title: 31CA4


title: 35EC


title: 43CA2


title: 31EC


title: 30CA4


title: 30CA1


title: 30CA3


title: 30CA2


title: 29EC


title: 29CA2


title: 29CA1


title: 28CA4

value: AD


title: 28CA3


title: 28EC


title: 28CA1


title: 28CA2


title: 27CA4


title: 27EC


title: 31CA2


title: 27CA1


title: 26CA4


title: 26CA2


title: 30EC


title: 25CA4


title: 26EC


title: 25CA3


title: 29CA4


title: 25CA2


title: 26CA1


title: 27CA3


title: 26CA3


title: 24CA3


title: 24CA4


title: 25CA1


title: 24EC


title: 24CA2


title: 29CA3


title: 24CA1


title: 23CA4


title: 27CA2


title: 23EC


title: 23CA2


title: 23CA1


title: 22CA4


title: 22CA2


title: 22CA3


title: 22CA1


title: 25EC


title: 23CA3


title: 20CA4


title: 21CA3


title: 21CA1


title: 20CA1


title: 19EC


title: 19CA4


title: 20EC


title: 19CA2


title: 21CA2


title: 21CA4


title: 19CA1


title: 18EC


title: 19CA3


title: 18CA4


title: 18CA3


title: 18CA2


title: 17EC


title: 17CA3


title: 18CA1


title: 17CA4


title: 17CA2


title: 21EC


title: 20CA2


title: 17CA1


title: 16CA4


title: 20CA3


title: 16EC


title: 16CA1


title: 16CA3


title: 16CA2


title: 15EC


title: mouse,post-hepatectomy,anti-H3K27Ac(nano-CUT&Tag)

description: Library name: post-hepatectomy_anti-H3K27Ac

source_name: liver

value: liver


title: 15CA4


title: pre-hepatectomy,KI-mYap1-HiBiT,anti-HiBiT(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-pre_anti-HiBiT

value: anti-HiBiT


title: mouse,pre-hepatectomy,anti-H3K27Ac(nano-CUT&Tag)

description: Library name: pre-hepatectomy_anti-H3K27Ac


title: post-hepatectomy,KI-mYap1-HiBiT,anti-TAZ(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-post_anti-YAP1


title: 15CA3


title: 15CA2


title: pre-hepatectomy,KI-mYap1-HiBiT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: mYap1-HiBiT-pre_LgBiT-Tn5


title: 14EC

value: NC


title: post-hepatectomy,KI-mYap1-HiBiT,anti-HiBiT(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-post_anti-HiBiT


title: pre-hepatectomy,KI-mYap1-HiBiT,anti-TAZ(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-pre_anti-YAP1


title: 14CA4


title: 14CA2


title: control,KI-mYap1-HiBiT,IgG(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-IgG

value: anti-IgG


title: 14CA3


title: 13EC


title: E.coli Null

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

description: ONT is using .bam files as a platform to store basecalled reads which have been demultiplexed. This file includes all aligned and unaligned reads post basecalling. pod5 could be included, but they are not demultiplexed, and would need to be compressed.

data_processing:
pod5 files generated by MinKNOW (via guppy) were re-basecalled using dorado 0.5.3 and the super-accuracy basecaller model (dna_r10.4.1_e8.2_400bps_sup@v4.3.0) on two NVIDIA RTX A4000 GPUs (dorado basecaller -batchsize 200 --modified-bases 6mA 5mC_5hmC --kit-name SQK-NBD114-96) (Oxford Nanopore Technologies, 2024a). Basecalled reads were demultiplex using dorado (dorado demux –no-classify). Reads were subsequently aligned to either the N. gaditana (accession #) or E. coli (accession #) genomes using the dorado implementation of minimap2 (dorado align {REFGENOME} {UBAM}) (Li, 2018). Aligned reads were subsequently passed to ModKit v0.6.2 to parse and count methylated bases (5mC, 5hmC and 6mA) (Modkit pileup --sampling-frac 1.0 –reference and Modkit summary –sampling-frac 1.0). Modified bed files were then split by base modification (5mC, 5hmC, or 6mA) and coerced into methylKit compatible files for methylKit analysis of differential methylation. ONT Modkit differential methylation analysis was performed at a base-pair resolution and gene resolution (modkit dmr pair -a -b –ref -o –base or modkit dmr multi -s –ref -o –base –regions). Hypermethylated adenines shared between all six replicates (light and dark) were combined, and motif analysis performed using MEME Suite (settings minimum width 4, maximum 6).
Raw fastq files were trimmed of adapters and poor-quality ends by trim galore v0.6.10. Reads were aligned using bismark v0.24.1 (to either the N. salina or N. gaditana genomes retrieved from JGI, accession #CCMP1776 and # CCMP1894 respectively) (Krueger and Andrews, 2011). Reads were deduplicated using Bismark (deduplicate_bismark). Aligned reads were parsed and methylated bases counted by methylDackel v0.3.0 (MethylDackel extract –methylKit –minDepth X –CHH, --CHG) (Ryan, 2024). Counts were taken as input for methylKit v1.28.0 analysis of differentially methylated bases (methylKit:: getMethylDiff()) (Akalin et al., 2012). Several permutations of statistical cutoffs were employed, with a linear regression model and SLIM multiple testing correction for statistical testing.
Assembly: E. coli genome was retrieved from genbank accession #U00096.3.   N. salina or N. gaditana genomes retrieved from JGI, accession #CCMP1776 and # CCMP1894 respectively
Supplementary files format and content: Data files are either methylDackel output for methylKit, or modKit calls for methylation.

organism: Escherichia coli

extract_protocol:
Whole genome bisulfite sequencing was performed as previously described (Steadman 2020). Genomic DNA from N. salina and N. gaditana was isolated from three sets of cultures: nitrogen replete (full nutrients three days prior to nitrogen starvation), nitrogen starvation (the day nitrogen was not detectable in the media), and nitrogen depletion (three days after nitrogen starvation occurred). One ug of gNDA was digested with 1 unit of dsDNA Shearase Plus (Zymo catalog #E2018-50). Fragments were end-blunted, 3’-terminal-A extended, and purified using DNA Clean & Concentrator kit (Zymo catalog #D4003). Fragments were ligated to pre-annealed adapters containing methylated (5’-methyl) cytosine, filled in, and treated with sodium bisulfite using the EZ DNA Methylation-Lightning kit (Zymo catalog #D5003) . Illumina TruSeq indices were used for PCR; bisulfite treated fragment size and concentration were determined using an Agilent 2200 TapeStation (Agilent catalog #G2991BA). Fragments were sequenced on an Illumina HiSeq 2500.2x108 N. gaditana cells were processed using the Qiagen HW MagAttract kit (Qiagen catalog #67563 ) following the protocol for “gram (-) bacteria”. Prior to processing, cells were resuspended in buffer ATL and lysed by eight freeze thaw cycles -- 5 minutes on dry ice (-37c), followed by 5 minutes in a heat block at (37c) . DNA was eluted in 190uL ddH20 to prevent carryover of PCR inhibitors. To remove remaining RNA not removed by the kit, 400ug (4uL: 10mg/mL) RNASE A (ThermoFisher catalog #EN0531) was added with incubation at 37c for 1hr. Subsequently, to reduce polysaccharide contamination, 200uL 2X CTAB buffer was added to DNA solution (1.4 M NaCl, 20mM EDTA: pH 8.0, 2% CTAB w/v, 0.2% v/v β- mercaptoethanol, 100 mM Tris-Cl: pH 8.0), 400uL 25:24:1 Phenol:Chloroform:Isoamyl Alcohol buffered to pH 8.0 (Sigma Aldrich catalog #P2069) added, solution inverted 40X and phases separated by 5 minutes of centrifugation at 5000g. The aqueous phase was retained, taking care to avoid carryover of lipids or polysaccharides in the interphase. DNA was precipitated at -80c for 1hr by addition of 1/10 volume of NaACOH and ice-cold Ethanol (200 proof) (Thermo Fisher catalog #T036181000) to a final concentration of 75%, pelleted by centrifugation for 15 minutes at 7500g, washed with ice cold 75% ethanol, repelleted by 15 minutes centrifugation at 7500g, and air dried in the hood. DNA was resuspended in nuclease-free ddH20 and quantified using the Qubit 3.0 fluorometer and gDNA tapestation kit (Agilent catalog #5067-5366).
WBGS libraries were prepared using zymo kit #D5003. ONT libraries were constructed by: Libraries were prepared using the Native Barcoding DNA Ligation Kit K14 from nanopore (ONT catalog # SQK-NBD114.96). An E. coli DNA methylation null control was also prepared using the above ONT kit (Zymo catalog #D5016). Libraries were loaded onto a V11.4 Promethion flow cell (ONT catalog #FLO-PRO114M) with light shield (ONT catalog #SPR-FLS001P) and sequenced using MinKNOW with real-time basecalling set to fast and minimum length set to 200bp.
Bisulfite-seq and Oxford nanopore

value: {delta}DAM,  {delta}DCM,


title: pre-hepatectomy,KI-mTaz-HiBiT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: mTaz-HiBiT-pre_LgBiT-Tn5


title: 13CA4


title: post-hepatectomy,KI-mYap1-HiBiT,LgBiT-Tn5(nano-CUT&Tag)

description: Library name: mYap1-HiBiT-post_LgBiT-Tn5


title: pre-hepatectomy,KI-mTaz-HiBiT,anti-TAZ(nano-CUT&Tag)

description: Library name: mTaz-HiBiT-pre_anti-TAZ

value: anti-TAZ


title: pre-hepatectomy,KI-mTaz-HiBiT,anti-HiBiT(nano-CUT&Tagg)

description: Library name: mTaz-HiBiT-pre_anti-HiBiT


title: 22EC


title: 13CA3


title: 15CA1


title: 13CA1


title: 12EC


title: 12CA4


title: post-hepatectomy,KI-mTaz-HiBiT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: mTaz-HiBiT-post_LgBiT-Tn5


title: mouse,pre-hepatectomy,ATAC

description: Library name: pre-hepatectomy_ATAC


title: mouse,post-hepatectomy,ATAC

description: Library name: post-hepatectomy_ATAC


title: 12CA2


title: post-hepatectomy,KI-mTaz-HiBiT,anti-HiBiT(nano-CUT&Tag)

description: Library name: mTaz-HiBiT-post_anti-HiBiT


title: post-hepatectomy,KI-mTaz-HiBiT,anti-TAZ(nano-CUT&Tagg)

description: Library name: mTaz-HiBiT-post_anti-TAZ


title: mouse,mYAP1-HiBiT,post-hepatectomy,LgBiT-Tn5(scAf-CUT&Tag)

description: Library name: mYAP1-HiBiT_post-hepatectomy-scAf-CUT_Tag

value: partial hepatectomy


title: 11EC


title: 12CA1


title: 11CA4


title: N_gaditana_Deplete_3

organism: Nannochloropsis gaditana

value: Deplete


title: 11CA2


title: 13CA2


title: N_gaditana_Starved_3

value: Starved


title: N_gaditana_Starved_2


title: N_gaditana_Deplete_1


title: 11CA1


title: N_gaditana_Starved_1


title: 10EC


title: N_gaditana_Replete_3

value: Replete


title: 10CA4


title: N_gaditana_Replete_2


title: 12CA3


title: 10CA3


title: N_gaditana_Replete_1


title: 10CA2


title: 09CA4


title: 09CA3


title: mouse,mYAP1-HiBiT,pre-hepatectomy,LgBiT-Tn5(scAf-CUT&Tag)

description: Library name: mYAP1-HiBiT_pre-hepatectomy-scAf-CUT_Tag


title: 11CA3


title: 09CA2


title: 08EC


title: 2-cell embryo TRPS1 Repeat1

city: Fuzhou

first: sun

middle: jian

last: dong

address: 1 North Road, Xuefu

institute: Fujian medical university

description: Library name: 2-cell embryo TRPS1 Repeat1

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (v 0.20.0). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem -k 32 -T 30 -t 4 -M. These reads were then filtered for high quality (MAPQ ≥ 13), Only uniquely mapped reads were used for further analysis.
All peak calling was performed with MACS2 (v 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call- summits --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets. Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER (v 4.9.1) software with‘-len 8,10,12,14 -gc -size given -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein andgene. ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of peak related genes in KEGG pathways.
bigWig files were generated using the genomicRanges R package.Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse 2-cell embryo

extract_protocol:
We performed chromatin analysis using CUT&Tag according to its standard protocol using Hyperactive® Universal CUT&Tag Assay Kit for Illumina (Vazyme, China). Briefly, 200 2-cell embryos per group were incubated with ConA beads for 10 minutes at room temperature. Then, the ConA beads-embryos complex was incubated overnight with anti-TRPS1 or normal rabbit lgG control at 4°C，followed by incubation secondary antibodies (Goat Anti-Rabbit IgG, 1:100 dilution) for 60 minutes at room temperature and subsequent incubation of pG-Tn5 transposase for 60 minutes at room temperature. pG-Tn5 transposase identified the target proteins through specific antibody and finished DNA sequences cleavage. The DNA sequences were tagmented with adapters and further sent to Beijing Nuohe Zhiyuan Technology Co., Ltd. for library construction and sequencing.
The DNA sequences were tagmented with adapters and further sent to Beijing Nuohe Zhiyuan Technology Co., Ltd. for library construction and sequencing. library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina)according to the manufacturer’s instructions. The library preparations weresequenced on Illumina Novaseq platform at Tianjin Novogene Bioinformatic Technology Co., Ltd.(Beijing, China)and 150 bp paired-end reads were generated

value: mouse 2-cell embryo


title: 2-cell embryo lgG Repeat2

description: Library name: 2-cell embryo lgG Repeat2


title: 2-cell embryo TRPS1 Repeat2

description: Library name: 2-cell embryo TRPS1 Repeat2


title: 2-cell embryo lgG Repeat1

description: Library name: 2-cell embryo lgG Repeat1


title: BMMs of SLC11A2cKO, RANKL 48h, rep3

first: Siyue

last: Tao

state: Please Select

address: 3rd, Qingchun Road, Shangcheng district

department: Orthopedics department

institute: Sir run run shaw hospital affiliated to zhejiang university

description: Library name: slcoc_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Eight-week-old mice were euthanized, and hindlimb bones were harvested and flushed with PBS. Bone marrow was filtered through a 0.4 μm mesh, centrifuged, and resuspended in α-MEM containing 10 ng/mL MCSF and 10% FBS, then plated in 10 cm dishes. After 2-4 days, cells were passaged and cultured in media supplemented with 30 ng/mL MCSF and 50 ng/mL RANKL.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Primary bone marrow derived macrophages

value: 50ng/mL RANKL, 48h


title: BMMs of SLC11A2cKO, RANKL 48h, rep2

description: Library name: slcoc_2


title: 10CA1

value: Hippocampus


title: 08CA4


title: BMMs of SLC11A2cKO, RANKL 48h, rep1

description: Library name: slcoc_1


title: 09EC

value: EC


title: 08CA2


title: 08CA3


title: BMMs of SLC11A2f/f, RANKL 48h, rep3

description: Library name: ctrloc_3


title: 08CA1


title: dKI, replicate 3, snRNA-seq

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 base paired-end mode.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

extract_protocol:
Sinlge nucleus droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 3' Reagent Kits v3 User Guide.
single-nucleus RNA-seq

value: DAPI positive cell nuclei

value: AppNL-G-F/MAPT double knock-in

value: No tau administration


title: 09CA1


title: 07EC


title: BMMs of SLC11A2f/f, RANKL 48h, rep2

description: Library name: ctrloc_2


title: Tau-dKI, replicate 2, snRNA-seq

value: Tau administration


title: BMMs of SLC11A2f/f, RANKL 48h, rep1

description: Library name: ctrloc_1


title: 07CA3

value: NC


title: 07CA4


title: Tau-dKI, replicate 3, snRNA-seq


title: 07CA2


title: dKI, replicate 2, snRNA-seq


title: N_gaditana_Dark_3

value: Dark


title: dKI, replicate 1, snRNA-seq

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Generated reads were input into the cellranger pipeline (Cell Ranger v.4.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A_premrna
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected


title: 07CA1


title: Tau-dKI, replicate 1, snRNA-seq


title: 06EC


title: Tau-dKI, injected, replicate 2, Visium

description: Injected side

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 28+120-base paired-end mode.
Raw sequencing data for the sample was converted to a matrix of expression using Space Ranger version: 1.0.0 (10X Genomics).
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: Brain

extract_protocol:
The gene expressions of mouse brain slide were detected by following Visium Spatial Gene Expression Reagent Kits User Guide.
RNA libraries were prepared by using 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit.
OTHER: Spatial Transcriptomics

value: Brain


title: N_gaditana_Dark_1


title: N_gaditana_Dark_2


title: Tau-dKI, uninjected, replicate 2, Visium

description: Uninjected side


title: Tau-dKI, uninjected, replicate 1, Visium

description: Uninjected side


title: 06CA4


title: Tau-dKI, injected, replicate 1, Visium

description: Injected side


title: SS mice, salivary gland draining lymph node, PD-1+Tigit+CD11+T cells_6 [dLN6]

city: Guangzhou

first: Jin-Fen

last: Ma

address: 382 East Central Road, University Town

institute: South China University of Technology

data_processing:
The mouse reference genome (mm10) was used for alignment with STAR software. Read counts for each gene were converted into reads per kilobase million (RPKM) values and count values for subsequent analysis using an R script.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
For RNA-seq, submandibular glands of mice were harvested for liquid nitrogen storage. Mouse submandibular gland draining lymph nodes were dissected to isolate cells. Isolated cells were filtered through 70 μm nylon mesh and stained with TCRβ (H57-597, Biolegend), NK1.1 (PK136, Biolegend), CD8a (53-6.7, BD Biosciences), TIGIT(1G9, Biolegend), PD-1(29F.1A12, Biolegend). PD-1+Tigit+CD8+ immune cells were collected by fluorescence-activated cell sorting using BD Aria III (BD Biosciences).
Total RNA was extracted from  tissues and  cells using the Trizol (Takara) method. VAHTS mRNA Capture Beads (Vazyme, China) were used to select mRNA, and VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) was used to construct sequencing libraries. The NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) platform was used for sequencing with 150 bp paired-end reads.

value: lymph node


title: SS mice, salivary gland draining lymph node, PD-1+Tigit+CD11+T cells_4 [dLN4]


title: SS mice, salivary gland draining lymph node, PD-1+Tigit+CD11+T cells_5 [dLN5]


title: N_gaditana_Deplete_2


title: N_gaditana_Light_2

value: Light


title: 06CA2


title: 06CA1


title: 06CA3


title: SS mice, salivary gland draining lymph node, PD-1-Tigit-CD8+T cells_3 [dLN3]


title: N_gaditana_Light_1


title: SS mice, salivary gland draining lymph node, PD-1-Tigit-CD8+T cells_1 [dLN1 ]


title: 3C_Tko_ectopicBoundary1_rep1

data_processing:
Data were processed using HiC-Pro version 3.0.0 (Servant et al., 2015). Normalized contact matrices were generated with MAX_ITER = 500. LOW_COUNT_PERC was set to 0.006 for Thermococcus kodakarensis.
Assembly: GCA_000009965.1, GCA_000195915.1
Supplementary files format and content: Tab-delimited tables. The first and second columns indicate genomic bins. The third column indicate normalized interaction frequencies between the bins.
Library strategy: 3C-seq

value: Strain possessing both endogenouis and ectopic boundary 1


title: CAR-T cell treated SS mice, salivary gland_2 [SG6]

source_name: submandibular gland

value: submandibular gland

value: CAR-T cell treated


title: 05EC


title: 3C_Tko_ectopicBoundary1_rep2


title: SS mice, salivary gland draining lymph node, PD-1-Tigit-CD8+T cells_2 [dLN2]


title: CAR-T cell treated SS mice, salivary gland_1 [SG5]


title: Control T cell treated SS mice, salivary gland_2 [SG4]

value: Control T cell treated


title: Control T cell treated SS mice, salivary gland_1 [SG3]


title: 3C_Tko_boundary1delta_ectopicBoundary1_rep2

value: Strain possessing ectopic boundary 1 instead of endogenous boundary 1


title: 05CA4


title: N_gaditana_Light_3


title: 05CA3


title: control mice, salivary gland_2 [SG2]

value: P40-/-CD25+/- (control mice)


title: 3C_Tko_boundary1delta_ectopicBoundary1_rep1


title: control mice, salivary gland_1 [SG1]


title: control mice, salivary gland-draining lymph nodes, immune cells, TCR

data_processing:
Raw scRNA-seq data were processed by Cell Ranger (version 6.1.2). Cell Ranger multi was run with default parameters, using STAR (version 2.7.10a) for alignment on the mouse genome (mm10) reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: submandibular gland-draining lymph nodes

extract_protocol:
For scRNA-seq, mouse submandibular glands were cut into small pieces and digested with RPMI 1640 (Gibco) containing 1mg/ml collagenase type II (Sigma) in a shaking incubator at 180 rpm at 37°C for 20min. After digestion, PBS containing 2% BSA was added to the submandibular gland cells to terminate digestion. Draining lymph nodes were triturated to separate cells.The isolated cells were filtered through 70-μm nylon mesh and stained with CD45.2 (104, BD Biosciences). CD45+ immune cells were collected by fluorescence-activated cell sorting using BD Aria III (BD Biosciences).
Single-cell library preparation was carried out according to the BD Rhapsody™ Single-Cell Whole transcriptome analysis alpha protocol (https://www.bdbiosciences.com/) and ST library were constructed according to the 10x protocol (CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevA)

value: control


title: SS mice, salivary gland-draining lymph nodes, immune cells, TCR

value: submandibular gland-draining lymph nodes

value: SS


title: 05CA2

value: Hippocampus


title: 05CA1


title: control mice, salivary gland, immune cells, TCR


title: 3C_Tko_boundary1delta_rep1

value: boundary 1 deletion


title: SS mice, salivary gland, immune cells, TCR


title: 04EC

value: EC


title: control mice, salivary gland, immune cells, GEX


title: ChIP_XerA_input_xerA_rep2

value: xerA deletion


title: Brain, CAAHS1

first: Huipeng

last: Huang

address: 600 Tianhe Road

institute: the Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts.
Obtain clean data by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data
Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes FPKMs for each Sample

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared usilg Illumina Kit following manufacturer's protocols.

tag: disease state

value: CAA

value: Chronic restraint stress


title: SS mice, salivary gland, immune cells, GEX

tag: tissue


title: SS mice, salivary gland-draining lymph nodes, immune cells, GEX


title: 04CA4

value: NC


title: ChIP_XerA_IP_KU216_rep2

value: Parental strain KU216

value: XerA (custom)


title: Brain, CAACtrl1

value: Brain

value: Mock


title: Brain, CAAHS2


title: Brain, CAACtrl2


title: Brain, WTHS1

value: WT


title: 04CA1


title: RNA_Tko_scpB_rep3

data_processing:
Reads were counted using Salmon version 1.9.0 (Patro et al., 2017). Differentially expressed genes were identified using edgeR version 3.40.2 (Robinson et al., 2010).
Assembly: GCA_000009965.1
Supplementary files format and content: Tab-delimited tables showing Transcripts Per Million (TPM) values for each gene.

extract_protocol:
Cells were grown to mid-to-late log phase and used for RNA extraction. 23S, 16S, and 5S rRNAs were removed using complementary DNA oligos and Rnase H.
Libraries were constructed NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: scpB deletion


title: ChIP_XerA_input_KU216_rep2


title: ChIP_XerA_IP_xerA_rep2


title: 04CA3


title: 04CA2


title: 3C_Tko_boundary1delta_rep2


title: Brain, WTCtrl1


title: 03EC


title: Brain, WTCtrl2


title: Bone marrow derived neutrophils, Aβ40 2

source_name: Bone marrow derived neutrophils

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 6 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared usilg Illumina Kit following manufacturer's protocols.

value: Bone marrow derived neutrophils


title: RNA_Tko_scpB_rep2


title: Brain, WTHS2


title: control mice, salivary gland-draining lymph nodes, immune cells, GEX

value: control


title: 03CA4


title: Bone marrow derived neutrophils, Aβ40 1


title: Bone marrow derived neutrophils, Ctrl2

value: DMSO


title: RNA_Tko_scpB_rep1


title: 03CA3


title: Bone marrow derived neutrophils, Ctrl1


title: RNA_Tko_scpA_rep3

value: scpA deletion


title: Proximal and periurethral region

city: New York

first: Michael

last: Shen

state: NY

address: 1130 St. Nicholas Avenue

institute: Columbia University Irving Medical Center

description: single cell

data_processing:
Reads were aligned to the mouse mm10 reference genome, and quantified with the Cell Ranger Single-Cell Software Suite (cellranger-7.0.0, 10x Genomics).
Assembly: mm10
Supplementary files format and content: mtx

source_name: prostate

extract_protocol: Prostate tissue was minced with scissors, and incubated in Papain (20 units/ml) /DNaseI (200 units/ml) solution (Worthington, LK003150) at 37°C with gentle agitation. After 45 minutes, tissue fragments were gently triturated by manual pipetting, and incubated for further 45 minutes. Upon addition of an equal volume Ovomucoid (1 mg/ml)/Bovine Serum Albumin (1 mg/ml) solution (Worthington, LK003150) to inactivate papain, samples were passed through a 70 mm cell strainer (PluriSelect, 43-10070-70), followed by centrifugation at 150g for 5 minutes. Afterwards, samples were incubated in TrypLE Express (Gibco 12605-010)/DNaseI (200 units/ml) solution for 4 minutes at 37°C with gentle agitation. Upon addition of Fetal Bovine Serum (final conc. 10% v/v) to inactivate TrypLE, samples were gently resuspended by manual pipetting, passed through a 40 mm cell strainer (PluriSelect, 43-10040-70), washed in PBS/EDTA (1mM) solution, and spun down. Samples were resuspended in PBS/Bovine Serum Albumin (BSA, 0.04% w/v), passed through a 20 mm cell strainer (PluriSelect, 43-10020-70), automatically counted and spun down. At this point, samples were resuspended at 1 x 10E6 cells per ml, approximately, in PBS/BSA and were ready for single-cell RNAseq library preparation. Before preparing single-cell RNA-seq libraries, samples were assessed for viability using the Countess™ II FL Automated Cell Counter (Thermo Fisher). Only samples with >85% single, live cells were used. We targeted 5000 cells for single-cell sequencing using a Chromium Controller (10x Genomics). ML003 Single-cell RNA-Seq libraries were generated using the Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics) and ML008 Single-cell RNA-Seq libraries were generated using the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) according to manufacturer’s instructions. We used 12 cycles for cDNA amplification and 12 cycles for library construction. Sequencing was performed on a NovaSeq 6000 (r1 = 26, i1 = 8, r2 = 91). Single-cell RNA-seq (10x Genomics)

value: prostate

value: male


title: 03CA2

value: Hippocampus


title: RNA_Tko_scpA_rep2


title: ventral prostate lobes

description: single cell


title: RNA_Tko_scpA_rep1


title: 02CA4


title: 02CA3


title: RNA_Tko_smc_rep3

value: smc deletion


title: RNA_Tko_smc_rep2


title: 02CA2