title: Sample2_RNA

city: Copenhagen N

first: Kim

middle: B

last: Jensen

address: Belgdamsvej 3B

country: Denmark

institute: University of Copenhagen

description: S2_matrix contains both HTO and RNA counts

library_source: transcriptomic single cell

data_processing:
The demultiplexing and gene counting was done using the functions mkfastq and count from 10x Genomics Cell Ranger 6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files containing both RNA and HTO counts.

source_name: Intestinal epithelia

extract_protocol:
Mouse distal small intestine (2x 3cm) was collected, flushed with ice cold PBS and opened, while villi were scraped with a coverglass. After an additional wash, tissue was incubated in HBSS Ca+Mg+ Free (14175095, ThermoFischer Scientific) containing 5mM EDTA (15575-020, Invitrogen) 10mM HEPES (15630-056, Gibco/Life Technologies ) for 25 min at 37C, vortexing every 5 min. Crypts were shaken out, washed with PBS and then incubated in TrypLE  (12605036, ThermoFisher Scientific) supplemented with 10uM y27632 (Y0503, Sigma-Aldrich), 1mM NAC (A9165, Sigma-Aldrich), 50ug/ml DNaseI (10104159001, Roche) for 21min at 37C and pipetted 50x every 5min to dissociate into single cells. Cells were then pelleted in aDMEM/F12 (12634-028, Gibco/Life Technologies) containing 5% FBS, washed in 0.1% BSA/PBS, strained through 100um cell strainer, washed again in 0.1% BSA/PBS and filtered through blue-capped FACS tubes. Subsequently, cells were stained in 0.1% BSA/PBS, containing following antibodies: EpCAM-APC (AB_1659714, eBioscience, 1:500) CD31 PeCy7 (AB_10612003, BD biosciences, 1:200), CD45 PeCy7 (AB_394489, BD biosciences, 1:200), DAPI 1ug/mL, Hashing Ig (1:100) and transferred to low retention tubes, incubated 15min in the dark on room temperature, washed with 0.1%BSA and resuspended in ultra clean 0.1% BSA/PBS for flow cytometry. Samples were sorted with BD FACS Aria III sorter, 70u nozzle, 1.0 ND filter into an Eppendorf tube with 2uL ultra clean 0.1% BSA/PBS.  Hashing was performed so that each sample contained cells from one mouse and was labelled by a distinct hashing Ig before the sort. This means we had 8 hashed samples from 4 mice that were traced 48h (# 1-4) and 4 mice traced 72h (# 5-8). We sorted GFPhigh clones and GFP- cells from the epithelium as control into 2 eppendorfs so that each contained cells from 48h and 72h clones, as well as the control epithelium, and each contained all 8 hashes. Thus, we had 2 samples for library preparation: Sample 1 contained control epithelium from mice number 1,2,5,6, 48h clones from mice 3,4 and 72h clones from mice 7,8; Sample 2 contained control epithelium from mice number 3,4,7,8, 48h clones from 1,2 and 72h clones from 5,6.
The libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the 10X Genomics protocols v3.1. Maximum 10,000 cells were loaded into 36uL of ultra clean 0.1%BSA/PBS for the formation of Gel Bead-in-Emulsions and followed by reverse transcriptase. cDNA was amplified with 12 polymerase chain reaction (PCR) cycles, while sample-indexing PCR was performed with 14 cycles. The libraries were sequenced on an Illumina NextSeq 2000 platform with a High Output 150 cycles kit.

value: Intestinal epithelia

value: Epithelial

tag: genotype

value: Lgr5-EGFP-IRES- CreERT2;Rosa26-mTmG


title: Sample1_HTO

status: Public on Dec 06 2024

type: SRA

description: S1_matrix contains both HTO and RNA counts

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: hto


title: GBM28, mRNA

city: Houston

first: Briana

middle: Amicarella

last: Burns

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: Library name: GBM28_mRNA

library_source: transcriptomic

data_processing:
Data quality control was performed using fastp to remove adapter sequences and low-quality reads (Q20, Q30).
Clean reads were aligned to the GRCh38 reference genome using HISAT2 v2.0.5.
Gene expression quantification was performed using featureCounts v1.5.0-p3 to generate raw counts and FPKM values.
Assembly: Hg38
Supplementary files format and content: comma separated values include gene-level read counts for each sample for each batch
Supplementary files format and content: comma separated values include normalized gene expression matrix using FPKM values for each batch

molecule: polyA RNA

organism: Homo sapiens

source_name: Human monocyte-derived dendritic cells

growth_protocol: Human monocyte-derived dendritic cells, doubly-loaded with both tumor mRNA and lysate were prepared as described in Decker et al, Vaccine; 2006.

extract_protocol:
Total RNA was extracted from dendritic cell using the Trizol method according to the protocol using the ThermoFisher Trizol protocol
mRNA libraries were prepared using poly-T oligo-attached magnetic beads and sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

value: Human monocyte-derived dendritic cells

tag: batch number

tag: treatment

value: mRNA


title: Sample1_RNA


title: 293T output6-A7

city: shenzhen

first: Guoli

last: Li

address: penfei street

country: China

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description: Library name: 293T output6-A7

data_processing:
bowtie2 aligns sequencing data to the hg38 genome, samtools filters comparison data, and CRADLE software identifies silencer.
Assembly: hg38
Supplementary files format and content: bed file records silencer location and silencer activity

extract_protocol:
293T, K562 and LNCap were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), cell lines are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide. The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.
The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.

tag: cell line


title: GBM16, double loaded

description: Library name: GBM16_2x

value: Double-Loaded


title: GBM22, double loaded

description: Library name: GBM22_2x


title: L236D_CSP

city: Lausanne

first: Shukry

middle: James

last: Habib

address: Rue du Bugnon 7

department: Biomedical Sciences

country: Switzerland

institute: University of Lausanne

description:
Instrument model QC run: MiSeq
10X Genomics
Multiplexed in L236-D

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: hashtag barcode

growth_protocol: Female C57BL/6J mice were group housed under standard conditions until the timepoints: 6 weeks (Young), 23 weeks (Adult), 2 years (Aged).

extract_protocol:
Fresh tissue was dissected and minced on ice, and subjected to Collagenase & DNase1 treatment in HBSS for 30 mins. Cell slurry was strained and stained with TotalSeqA hashtag antibodies and DAPI as live/dead marker. Cells were FACS-sorted and combined in a multiplexed pooled sample, confirmed to be >95% viable at time of submission.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Primers for TotalSeqA hashtag antibody sequences were used during cDNA amplification. Sequencing performed on NextSeq 2000 sequencing on P3 flow cell.

treatment_protocol:
For 10 weeks, Intermittent fasting (IF) mice were given access to food for 4 days/week (Tue, Thu, Sat, Sun) and had food removed on 3 days/week (Mon, Wed, Fri). Ad libitum mice (AL) had access to food 7 days/week.
TotalSeqA antibodies were used to multiplex samples together, resulting in gene expression library (GEX) and cell-surface protein (CSP) barcode data for each cell

value: multiplexed sample:Calvarial Periosteum and Sagittal Suture Mesenchyme

tag: Sex

value: female

tag: age

value: 23 weeks old

tag: strain

value: Wildtype

tag: treatment (diet)

value: Ad libitum


title: L236D_GEX

description:
Total SeqA Hashtag 3 = Periosteum, 23wk, AL
Total SeqA Hashtag 4 = Suture, 23wk, AL
Instrument model QC run: MiSeq
10X Genomics
Multiplexed in L236-D

source_name: total RNA


title: 293T output6-A12

description: Library name: 293T output6-A12


title: L236C_CSP

description:
Total SeqA Hashtag 1 = Periosteum, 2yr, IF
Total SeqA Hashtag 2 = Suture, 2yr, IF
Total SeqA Hashtag 3 = Periosteum, 2yr, AL
Total SeqA Hashtag 4 = Suture, 2yr, AL
Instrument model QC run: MiSeq
10X Genomics
Multiplexed in L236-C

value: 2 years old

value: multiplexed sample:Intermittent Fasting (IF) and Ad libitum (AL)


title: GBM22, mRNA

description: Library name: GBM22_mRNA


title: 293T output1-A6

description: Library name: 293T output1-A6


title: GBM19, double loaded

description: Library name: GBM19_2x


title: L236B_CSP

description:
Total SeqA Hashtag 1 = Periosteum, 23 wk IF
Total SeqA Hashtag 2 = Suture, 23wk IF
Instrument model QC run: MiSeq
10X Genomics
Multiplexed in L236-B

value: Intermittent Fasting


title: L236C_GEX


title: 293T output6-A6

description: Library name: 293T output6-A6


title: cDNA from patient-derived CTCs from BC patient 001 (timepoint 1, exp 1)

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

data_processing:
Trim Galore! (v0.6.6; parameters: –q 20 –length 20)
Mapping using STAR (v 2.5.9a) to human (GRCh38)  with splice junctions from the human GENCODE annotation (release 40)
The gene-level expression counts were computed with featureCounts from the subread package (v.2.0.3; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 40)
Samples were retained for further analyses if they had at least 500’000 reads, at least 5’000 genes with non-zero expression and less than 50% of reads mapping to mitochondrial genes
Assembly: GRCh38 and GENCODE release 40
Supplementary files format and content: counts.txt.gz are tab-delimited files containing raw counts for each library
Supplementary files format and content: processed_counts_matrix.txt.gz is a tab-delimited matrix containing raw counts for all libraries

source_name: CTC

extract_protocol:
Using CellCelector, an automated single-cell picking system (ALS), pools of single CTCs, CTC clusters and CTC–WBC clusters (range of 5–40 cells) were collected and immediately transferred into tubes (Axygen, 321-032-501, Thermofisher AB-0620) containing 10 µl RLT Plus lysis buffer and 1 U SUPERase IN RNase inhibitor (Invitrogen, AM2694). Samples were immediately frozen and kept at −80 °C until further processing. Following a previously published protocol for parallel DNA and RNA sequencing from individual cells (Macaulay, I. C. et al., 2016), genomes and transcriptomes of lysed cells were separated
Amplified cDNA was prepared on-bead according to the Smart-seq2 protocol. Libraries were prepared using Nextera XT (Illumina)

value: CTC

tag: donor

tag: sample type

tag: number of ctcs

tag: number of wbcs attached

tag: timepoint


title: L236A_CSP

description:
Total SeqA Hashtag 1 = Periosteum, 6 wk AL
Total SeqA Hashtag 2 = Suture, 6wk AL
Instrument model QC run: MiSeq
10X Genomics
Multiplexed in L236-A

value: 6 weeks old


title: MF2_CD34

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

description: Library name: 10_MF2_CD34

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: GrCh38
Supplementary files format and content: Comma-separated values of raw counts.

source_name: Sorted CD34+ cells

extract_protocol:
CD34+ cells were enriched with bead purification.Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: Sorted CD34+ cells

tag: disease state

value: Myelofibrosis


title: GBM19, mRNA

description: Library name: GBM19_mRNA


title: Sample2_HTO

value: Intestinal epithelia

value: Epithelial

tag: genotype


title: 293T output7-A11

description: Library name: 293T output7-A11


title: GBM15, double loaded

description: Library name: GBM15_2x

tag: tissue

value: Human monocyte-derived dendritic cells


title: 293T output7-A19

description: Library name: 293T output7-A19


title: 293T output1-A13

description: Library name: 293T output1-A13


title: GBM12, double loaded

description: Library name: GBM12_2x


title: 293T output8-A2

description: Library name: 293T output8-A2


title: 293T output6-A9

description: Library name: 293T output6-A9


title: 293T output6-A8

description: Library name: 293T output6-A8


title: L236B_GEX


title: GBM12, mRNA

description: Library name: GBM12_mRNA

value: mRNA


title: 293T output8-A1

description: Library name: 293T output8-A1


title: 293T output7-A18

description: Library name: 293T output7-A18


title: GBM11, double loaded

description: Library name: GBM11_2x

value: Double-Loaded


title: L236A_GEX

value: multiplexed sample:Calvarial Periosteum and Sagittal Suture Mesenchyme


title: GBM15, mRNA

description: Library name: GBM15_mRNA


title: 293T output7-A14

description: Library name: 293T output7-A14


title: 293T output1-A7

description: Library name: 293T output1-A7


title: GBM11, mRNA

description: Library name: GBM11_mRNA


title: GBM23, double loaded

description: Library name: GBM23_2x


title: 293T output7-A20

description: Library name: 293T output7-A20


title: 293T output7-A13

description: Library name: 293T output7-A13


title: GBM25, double loaded

description: Library name: GBM25_2x


title: PBS replicate 4 (control for Live BHV-1 + Mitomycin C) [re-analysis]

type: RNA

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969682
2R

hyb_protocol: Fragmented sample was hybridized to Affymetrix Clariom S arrays at 45 °C overnight.

scan_protocol: Arrays were imaged using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data was analyzed using the Transcriptome Analysis Console software, Thermo Fischer. Data was processed using SST-RMA, Quantile Normalization, HDF5 output. Please note that files 1M0-12, 2M0-12, and 3M0-12 have 2 separate .chp files. The difference is that the same .CEL file was used on two different analyses (i.e. one .CHP file was produced when generating figure 1, vs the other .CHP file when generating figure 5). Therefore, their normalization outputs would be different even though they came from the same .CEL file, and that is why they have separate .CHP files.

label: Biotin

source_name: B16-C10 subcutaneuos tumour from C57Bl/6 mouse

label_protocol: RNA was normalized to an input amount of 100 ng and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG

growth_protocol: 6- to 8-week-old C57Bl/6 mice were subcutaneously implanted with 5 × 106 B16-C10 cells resuspended in 200 µL PBS into the left flank

extract_protocol: Mice were sacrificed and tumours harvested at day 5. Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purifying using the Qiagen RNA extraction kit (Cat #74004)

treatment_protocol: At 2 weeks post-injection: for Mitomycin C therapy, tumors were treated intratumorally (i.t.) with 100 µg MMC in 50 µL sterile water only at day 1. For BHV-1 therapy, tumors were treated i.t. by injecting 2e7 pfu oBHV in 50 μL PBS beginning at day 2 once daily for 3 consecutive days (days 2, 3 and 4)

value: PBS

value: B16-C10 subcutaneuos tumour


title: hepLPC-2

city: Shanghai

first: Yi

last: Chen

address: No.160 Pujian Road

department: Department of Anesthesiology

institute: Renji Hospital, Jiaotong University School of Medicine

data_processing:
miRNA highthroughput sequencing analysis was performed by Newcore Biotechnology (Shanghai, China). Firstly, fastp software (v0.20.0) was used to trim adaptor and filter low-quality reads to get high-quality clean reads. Then, clean reads from all samples were merged, and miRdeep2 software (v0.1.3) was used to predict novel miRNAs. The clean reads were then aligned to the merged miRNA databases (miRNA from miRbase v22 plus the newly predicted novel miRNAs) using Novoalign software (v3.09.04) with at most one mismatch. The tpm counts were defined as the expression levels of that each miRNA.
Assembly: miRBase v22
Supplementary files format and content: excel file with miRNA tpm

source_name: Hepatocyte-derived liver progenitor-like cells

extract_protocol: Twenty milliliters of cellular supernatant was mixed with RiboTM Exosome Isolation Reagent, and exosome isolation was performed according to the manufacturer’s instructions (RiboBio, China). Exosomal RNA was extracted by a HiPure Liquid miRNA Kit miRNA Kit (Megan, China). The quantity and integrity of exosomal RNA were assessed using Qubit®2.0 (Life Technologies, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA), respectively. Fifty nanograms of exosomal RNA from each sample was used to prepare small RNA libraries with an NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) according to the manufacturer’s instructions. The libraries were sequenced using HiSeq 2500 (Illumina, USA) with a single-end 50-bp sequence by RiboBio Co., Ltd. (RiboBio, China).

tag: cell type


title: GBM23, mRNA

description: Library name: GBM23_mRNA


title: PBS replicate 5 (control for Live BHV-1 + Mitomycin C) [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969683
2RR


title: Live BHV-1 + Mitomycin C replicate 5 [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969693
10RR

value: Live BHV-1 + Mitomycin C


title: UV BHV-1 + Mitomycin C replicate 4

description:
Figure from the paper that the file was used to generate: 4 and 5
6R

value: UV BHV-1 + Mitomycin C


title: UV BHV-1 + Mitomycin C replicate 3

description:
Figure from the paper that the file was used to generate: 4 and 5
6NN


title: Live BHV-1 + Mitomycin C replicate 2 [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969690
10LL


title: Live BHV-1 + Mitomycin C replicate 4 [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969692
10R


title: PBS replicate 1 (control for Live BHV-1 + Mitomycin C) [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969679
2L


title: PBS replicate 2 (control for Live BHV-1 + Mitomycin C) [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969680
2LL


title: UV BHV-1 + Mitomycin C replicate 5

description:
Figure from the paper that the file was used to generate: 4 and 5
6RR


title: PBS replicate 3 (control for Live BHV-1 + Mitomycin C) [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969681
2NN


title: PBS replicate 5 (control for UV BHV-1 + Mitomycin C)

description:
Figure from the paper that the file was used to generate: 4 and 5
1RR


title: Live BHV-1 + Mitomycin C replicate 3 [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969691
10NN


title: 293T output7-A16

description: Library name: 293T output7-A16


title: hepLPC-1

value: Hepatocyte-derived liver progenitor-like cells


title: Live BHV-1 + Mitomycin C replicate 1 [re-analysis]

description:
Figure from the paper that the file was used to generate: 4 and 5
Reanalysis of GSM6969689
10L


title: GBM25, mRNA

description: Library name: GBM25_mRNA


title: hepLPC-3


title: GBM21, double loaded

description: Library name: GBM21_2x


title: UV BHV-1 + Mitomycin C replicate 1

description:
Figure from the paper that the file was used to generate: 4 and 5
6L


title: 293T output7-A12

description: Library name: 293T output7-A12


title: UV BHV-1 + Mitomycin C replicate 2

description:
Figure from the paper that the file was used to generate: 4 and 5
6LL


title: GBM21, mRNA

description: Library name: GBM21_mRNA


title: GBM18, double loaded

description: Library name: GBM18_2x


title: PHH-3

source_name: primary human hepatocytes

value: primary human hepatocytes


title: 293T output7-A15

description: Library name: 293T output7-A15


title: PHH-2


title: 293T output7-A17

description: Library name: 293T output7-A17


title: GBM18, mRNA

description: Library name: GBM18_mRNA


title: 293T output1-A14

description: Library name: 293T output1-A14


title: iBAT_e18.5_mut_rep5

city: Québec

first: Lucie

last: Jeannotte

state: QC

address: 2260, boulevard Henri Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

institute: Université Laval

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
327_5_Null

data_processing:
Reads were trimmed with the software Trim Galore (v0.6.5;https://github.com/FelixKrueger/TrimGalore)
Trimmed reads were mapped to ENSEMB GRCm39 (mm39, release 109) with the software STAR (v2.7.9a) (Dobin et al., Bioinformatics 2013).
Read counts extraction were made with a version manually cured for Hox genes of the mm39 genome (gencode.vM32.chr_patch_hapl_scaff.annotation_manually_cured.gtf)  with FeatureCounts (v2.0.3; Liao et al., Bioinformatics 2014)
Counts were normalized in TPM ( transcripts per million)
Assembly: GRCm39 (109 Ensembl release)
Supplementary files format and content: Tab_delimited text file include raw counts for each Sample
Supplementary files format and content: Tab_delimited text file include TPM for each Sample

source_name: interscapular BAT

growth_protocol: Age of embryos was estimated by considering the morning of the day of the vaginal plug as embryonic day (E) 0.5

extract_protocol:
For RNA extraction, embryonic tissues were dissected into ice-cold PBS, and either homogenized immediately in Trizol (Invitrogen), following manufacturer’s instructions or snap-frozen in liquid nitrogen until further processing.
mRNA were isoleted by polyA selection from 500ng to 1000 ng of total RNA. Lbrary were made using Illumina TruSeq RNA prep kit

treatment_protocol: Trachea and diaphragm were collected at E15.5, lungs at E12.5 and E15.5, somites at E10.5 and E12.5, and interscapular brown adipose tissue (iBAT) at E18.5. For somite samples, the C3-T2 trunk segments were removed and dissected away from the neural tube, forelimbs, and thoracic organs. Mouse lines were maintained in the 129/Sv background. The Hoxa5 mutation is described (Jeannotte et al., Genes Dev 1993)

value: interscapular BAT

tag: time


title: GBM10, double loaded

description: Library name: GBM10_2x

tag: batch number


title: 293T output1-A15

description: Library name: 293T output1-A15


title: GBM10, mRNA

description: Library name: GBM10_mRNA

tag: treatment


title: iBAT_e18.5_mut_rep4

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
327_1_Null


title: iBAT_e18.5_mut_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
324_1_Null


title: GBM6, double loaded

description: Library name: GBM6_2x


title: iBAT_e18.5_mut_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
321_1_Null


title: 293T output4-1

description: Library name: 293T output4-1

tag: cell line


title: PHH-1


title: 293T output5-A2

description: Library name: 293T output5-A2


title: GBM6, mRNA

description: Library name: GBM6_mRNA


title: iBAT_e18.5_mut_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
319_1_Null


title: 293T output4-2

description: Library name: 293T output4-2


title: GBM3, double loaded

description: Library name: GBM3_2x


title: iBAT_e18.5_wt_rep5

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
327_4_WT

value: wt


title: PBS replicate 3 (control for UV BHV-1 + Mitomycin C)

description:
Figure from the paper that the file was used to generate: 4 and 5
1NN


title: GBM3, mRNA

description: Library name: GBM3_mRNA


title: 293T output5-A3

description: Library name: 293T output5-A3


title: iBAT_e18.5_wt_rep4

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
327_2_WT


title: PBS replicate 4 (control for UV BHV-1 + Mitomycin C)

description:
Figure from the paper that the file was used to generate: 4 and 5
1R


title: PBS replicate 1 (control for UV BHV-1 + Mitomycin C)

description:
Figure from the paper that the file was used to generate: 4 and 5
1L


title: iBAT_e18.5_wt_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
324_5_WT


title: UV BHV-1 12hr biological rep 3

description:
Figure from the paper that the file was used to generate: 1
3U0-12

source_name: B-16 C10 cells from cell culture

growth_protocol: B-16 C10 cells were seeded a 12-well plate and grown to ~90% confludency before treatment

extract_protocol: RNA from cells were purified using the Qiagen RNA extraction kit (Cat #74004)

treatment_protocol: Cells were mock infected or infected with MOI 10 live BHV-1 or equivalent volume of UV BHV-1. Samples with Mitomycin C received recovery media containing 20µg/mL (Sigma Cat#M5353)

value: UV BHV-1 harvested at 12hpi

value: B16-C10 cells from cell culture


title: 293T output3-A13

description: Library name: 293T output3-A13


title: 293T output5-A15

description: Library name: 293T output5-A15


title: PBS replicate 2 (control for UV BHV-1 + Mitomycin C)

description:
Figure from the paper that the file was used to generate: 4 and 5
1LL


title: Mock 12hr biological rep 3_analysis 1

description:
Figure from the paper that the file was used to generate: 1
3M0-12 1

value: Mock-infected harvested at 12hpi


title: 293T output5-A4

description: Library name: 293T output5-A4


title: UV BHV-1 + Mitomycin C 12hr biological rep 3

description:
Figure from the paper that the file was used to generate: 5
3UM-12

value: UV BHV-1+mito harvested at 12hpi


title: iBAT_e18.5_wt_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
319_2_WT


title: Myotube Rep2

city: Evanston

first: vadim

last: backman

state: IL

address: 2170 Campus Drive, Silverman Hall 3627

department: Bioengineering

institute: Northwestern University

description: Library name: MT_B14

library_source: genomic

data_processing:
Myoblast and myotube samples were aligned to hg38 and processed using the Next Flow Core Hi-C pipeline (https://github.com/nf-core/hic/tree/2.1.0). Coolers were generated at 5kb and 80kb resolutions from the Hi-C Pro output. Contacts were dumped using Cooltools (https://github.com/open2c/cooltools)(91) and used for downstream analysis. Contact maps were visualized using GENOVA.
Assembly: hg38
Supplementary files format and content: compressed binarized .mcool files

molecule: genomic DNA

source_name: Myotube

growth_protocol: Cell lines were obtained from ATCC and experiments were performed in cells at low passage number. Primary human myoblasts were cultured and maintained in Mesenchymal stem cell media (ATCC) with the addition of the contents of the primary human skeletal muscle growth kit (ATCC) and 1% PS. Myotubes were generated by having myoblasts reach confluency, and then cultured for 96 h in differentiation tool media (ATCC) with the addition of 1% PS.

extract_protocol:
To wash the nuclei, samples were thawed and resuspended in 50 µL ice cold PB, followed by the addition of 150 µL ice-cold RNase-free water. 50 µL of Buffer C1 (Qiagen Epitect Hi-C Kit, #59971) was added to each sample and mixed. Samples were then centrifuged at 2500 x g and 4 ˚ C for 5 minutes. The supernatant was aspirated and the nuclear pellet was resuspended in 500 µL of RNase-free water, before being centrifuged again at 2500 x g and 4 ˚ C for 5 minutes. Library generation and subsequent steps used proprietary reagents from Qiagen’s Epitect Hi-C Kit. Washed nuclei were digested with according to the Epitect Hi-C protocol using a proprietary enzyme cocktail that cut at the GATC motif. Nuclei were end-labeled with biotin followed by ligation for 2 hours at 16 ˚C. Ligated chromatin was then de-crosslinked using 20 µL of Proteinase K solution at 56 ˚C for 30 minutes and then heated to 80 ˚C for 90 minutes. Ligated, decrosslinked DNA was purified using a Qiagen column kit (Qiagen Epitect Hi-C Kit, #59971).  and resuspended in 130 µL EB. Hi-C library samples were fragmented to a median size of between 400 and 600 bp using a Covaris E220 sonicator with a sample size of 130 µL. Samples were purified for fragments between 400 and 500 bp using a Qiagen bead purification size exclusion kit .
Reagents used in Hi-C library generation were supplied with Qiagen Epitect Hi-C Kit unless otherwise noted.  Hi-C samples were streptavidin-purified to enrich for properly ligated contact pairs using streptavidin beads and a magnetic bead rack. Beads were first washed in 100 µL of bead wash buffer, resuspended in 50 µL of bead resuspension buffer, and then mixed with 50 µL of Hi-C sample. The mixture was then incubated at room temperature for 15 minutes in a thermal mixer at 1000 RPM. Enriched bead-bound DNA was then end-repaired, phosphorylated, and poly-A tailed using a combined ER/A-tailing solution. The samples were incubated for 15 minutes at 20 ˚C followed by incubation at 65 ˚C for 15 minutes. Beads were then washed once with 100 µL of bead wash buffer, washed again with 95 µL of adapter ligation buffer, and resuspended in adapter ligation buffer in preparation for ligation of Illumina adapter sequences. Each sample was mixed with 5 µL of one of 6 Illumina adapter sequences (specified in the Qiagen protocol appendix) and 2 µL of ultralow input ligase. These samples were then incubated for 45 minutes. Following adapter ligation, each sample was washed three times before adding 400 µL of library amplification mixture to the beads. Samples were then distributed equally across 8 wells of a 96-well PCR plate and cycled using the following parameters on an Eppendorf Mastercycler x50s thermocycler

value: Myotube

value: human muscle

value: WT

value: differentiation media


title: Live BHV-1 + Mitomycin C 12hr biological rep 3

description:
Figure from the paper that the file was used to generate: 5
3LM-12

value: Live BHV+mito harvested at 12hpi


title: Myotube Rep1

description: Library name: MT_A13

treatment_protocol: Myotubes were generated by having myoblasts reach confluency, and then cultured for 96 h in differentiation tool media (ATCC) with the addition of 1% PS.


title: 293T output2-A16

description: Library name: 293T output2-A16


title: Mock 12hr biological rep 3_analysis 2

description:
Figure from the paper that the file was used to generate: 5
3M0-12 2


title: Live BHV-1 + Mitomycin C 12hr biological rep 2

description:
Figure from the paper that the file was used to generate: 5
2LM-12


title: Somites_E12.5_mut_rep4

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM24

source_name: Somites

value: Somites


title: UV BHV-1 12hr biological rep 2

description:
Figure from the paper that the file was used to generate: 1
2U0-12


title: UV BHV-1 + Mitomycin C 12hr biological rep 2

description:
Figure from the paper that the file was used to generate: 5
2UM-12


title: iBAT_e18.5_wt_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
321_5_WT


title: KMS34_Input

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

country: Japan

institute: Jichi  Medical  University

description: Library name: KMS34_Input

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Assembly: hg38
Supplementary files format and content: bigWig,narrow Peak(except for Input sample)

source_name: Hematopoietic cells

growth_protocol: We cultured KMS34 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with anti-H3K36me2 antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: We fixed KMS34 cells  in 1% formaldehyde at room temperature  for 10 min and isolated  chromatin fractions using enzymatic shearing

value: Hematopoietic cells

value: Multiple Myeloma

tag: chip antibody


title: Live BHV-1 12hr biological rep 3

description:
Figure from the paper that the file was used to generate: 1
3L0-12

value: Live BHV-1 harvested at 12hpi


title: 293T output5-A14

description: Library name: 293T output5-A14


title: 293T output1-A5

description: Library name: 293T output1-A5


title: Myoblast Rep1

description: Library name: MB_A11

source_name: Myoblast

value: Myoblast


title: Somites_E12.5_mut_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM23


title: Myoblast Rep2

description: Library name: MB_B12


title: Mock 12hr biological rep 2_analysis 2

description:
Figure from the paper that the file was used to generate: 5
2M0-12 2


title: 293T output5-A16

description: Library name: 293T output5-A16


title: Somites_E12.5_mut_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM22


title: KMS34_H3K36me2_RK552  ChIPSeq

description: Library name: KMS34_H3K36me2_RK552_Millipore


title: 293T output2-A17

description: Library name: 293T output2-A17


title: Live BHV-1 12hr biological rep 2

description:
Figure from the paper that the file was used to generate: 1
2L0-12


title: KMS34_H3K36me2_DMSO  ChIPSeq

description: Library name: KMS34_H3K36me2_DMSO_Millipore


title: 293T output2-A18

description: Library name: 293T output2-A18


title: Somites_E12.5_mut_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM21


title: Somites_E12.5_wt_rep4

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM20


title: Somites_E12.5_wt_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM19


title: 293T output1-A2

description: Library name: 293T output1-A2


title: 293T output3-A11

description: Library name: 293T output3-A11


title: Somites_E12.5_wt_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM17


title: Somites_E12.5_wt_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM18


title: Brain, VAD, Rep3

city: New Haven

first: Sebastian

last: Diaz

state: Connecticut

address: 300 George St

department: Immunobiology

institute: Yale University

description: 10X Genomics

data_processing:
Barcoded processing, gene counting and aggregation were made using CellRanger v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated value and matrix files

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Nuclei from postmortem periventricular white matter were extracted via dounce homogenizing and sucrose ultracentrifugation.
Library was performed according to the manufacturer's instructions (Single Cell 3' v3 Protocol, 10X Genomics).

value: Brain

value: Astrocytes, microglia, oligodendrocytes, OPCs, neurons, endothelial cells


title: Brain, Control, Rep4

description: 10X Genomics


title: Brain, VAD, Rep1

description: 10X Genomics


title: Brain, VAD, Rep4

description: 10X Genomics


title: Brain, VAD, Rep2

description: 10X Genomics


title: Somites_E10.5_mut_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM08


title: UV BHV-1 12hr biological rep 1

description:
Figure from the paper that the file was used to generate: 1
1U0-12


title: 293T output3-A12

description: Library name: 293T output3-A12


title: Mock 12hr biological rep 1_analysis 2

description:
Figure from the paper that the file was used to generate: 5
1M0-12 2


title: Live BHV-1 + Mitomycin C 12hr biological rep 1

description:
Figure from the paper that the file was used to generate: 5
1LM-12


title: Brain, Control, Rep2

description: 10X Genomics


title: Mock 12hr biological rep 2_analysis 1

description:
Figure from the paper that the file was used to generate: 1
2M0-12 1


title: 293T output4-10

description: Library name: 293T output4-10


title: Brain, Control, Rep3

description: 10X Genomics


title: UV BHV-1 + Mitomycin C 12hr biological rep 1

description:
Figure from the paper that the file was used to generate: 5
1UM-12


title: 293T output4-9

description: Library name: 293T output4-9


title: 293T output2-A19

description: Library name: 293T output2-A19


title: Brain, Control, Rep1

description: 10X Genomics


title: Live BHV-1 6hr biological rep 3

description:
Figure from the paper that the file was used to generate: 1
3L0-6

value: Live BHV-1 harvested at 6hpi


title: Somites_E10.5_mut_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM06


title: Live BHV-1 12hr biological rep 1

description:
Figure from the paper that the file was used to generate: 1
1L0-12


title: Somites_E10.5_wt_rep4

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM05

value: wt


title: Mr1-/- + PD, rep2

first: Yuxiang

last: Sun

state: Texas

address: One Baylor Plaza, Houston, TX, 77030, United States

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: peritoneum

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer  (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: peritoneum

value: intraperitoneal injection of 4.25% PD fluid


title: Somites_E10.5_wt_rep3

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM04


title: A_BG4_CPS1MUT_2

first: Yanhao

last: Yu

address: Yueyang Street

institute: Center of Excellence in Molecular Cell Science

data_processing:
The CUT&Tag reads were mapped to the human genome (UCSC hg38) with Bowtie2. The duplicated reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per genome coverage, RPGC) with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigwig files for BG4/H3K4me3 enrichment
Library strategy: CUT&Tag

source_name: cell line

growth_protocol: A549 cell lines were cultured in DMEM (Gibco, 11965-118) media supplemented with 10% FBS (ExCell, FSP500). H1944 cell line was cultured in RPMI1640 (Gibco, 11875-119) supplemented with 10% FBS and 1 mM sodium pyruvate (Gibco, 11360070). All media were supplemented with penicillin and streptomycin (Gibco, 15140-122). Cells were cultured at 37°C with 5% CO2, and were periodically tested and shown to be mycoplasma negative.

extract_protocol:
WT, G4 sequences mutated and APE1 KO A549/H1944 cells (1 × 106) were used for the CUT&Tag experiment, and cell counting was performed using a Luna II (Logos Biosystems, Korea).
CUT&Tag was performed essentially as described (68), with minor modifications according to the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).

value: cell line

value: Melanoma


title: Somites_E10.5_mut_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM07


title: Mr1-/- + PBS, rep2

value: intraperitoneal injection of PBS


title: A_BG4_CPS1MUT_1


title: Mr1-/- + PD, rep1


title: Somites_E10.5_wt_rep2

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM02


title: A_BG4_ARG2MUT_2


title: Somites_E10.5_wt_rep1

description:
150 pd
Raw_counts_iBAT_somites.txt
TPM_iBAT_somites.txt
JM01


title: Mr1-/- + PBS, rep1


title: Mock 6hr biological rep 3

description:
Figure from the paper that the file was used to generate: 1
3M0-6

value: Mock-infected harvested at 6hpi

value: B16-C10 cells from cell culture


title: A_BG4_ARG2MUT_1


title: Diaphragm_E15.5_mut_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ048_S32

source_name: Diaphragm

value: Diaphragm


title: D15-100uM-FR3

city: Oslo

first: Thomas

last: Sæther

state: Oslo

address: Sognsvannsveien 9

department: Dept. of Molecular Medicine

country: Norway

institute: University of Oslo

data_processing:
RNA-seq reads were filtered to remove low-quality reads using fastp (v 0.23.2).
Filtered reads were aligned to hg38 genome with STAR v2.7.10a using Ensembl GRCh38.p13 release 104 reference annotation
Transcript abundance was estimated using --featureCounts in Subread v2.0.1. DESeq2 v1.36.0, as implemented in SARTools, was used for raw count normalization and differential gene expression analysis. Differentially expressed genes (DEGs) were filtered based on log2 fold-change (strictly below the third quartile for downregulated genes, and strictly above the first quartile for upregulated genes). Reads per kilobase of transcript per million (RPKM) mapped reads were calculated for each transcript.
Assembly: hg38
Supplementary files format and content: gene count table

source_name: Human primary adipose stem cells

extract_protocol:
RNeasy Micro kit (Cat. 74004, Qiagen)
TruSeq Stranded mRNA library kit from Illumina

value: Human primary adipose stem cells

value: Day 15

tag: replicate


title: UV BHV-1 6hr biological rep 3

description:
Figure from the paper that the file was used to generate: 1
3U0-6

tag: strain

value: UV BHV-1 harvested at 6hpi


title: UV BHV-1 6hr biological rep 2

description:
Figure from the paper that the file was used to generate: 1
2U0-6


title: Mock 12hr biological rep 1_analysis 1

description:
Figure from the paper that the file was used to generate: 1
1M0-12 1

value: Mock-infected harvested at 12hpi


title: Live BHV-1 6hr biological rep 2

description:
Figure from the paper that the file was used to generate: 1
2L0-6


title: Mock 6hr biological rep 2

description:
Figure from the paper that the file was used to generate: 1
2M0-6


title: UV BHV-1 6hr biological rep 1

description:
Figure from the paper that the file was used to generate: 1
1U0-6


title: D9-100uM-FR3

value: Day 9


title: Diaphragm_E15.5_mut_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ046_S30


title: iMGL, OGD

description: 10X Genomics

source_name: Human iPSC-derived microglia

extract_protocol:
iMGL were resuspended in cold 1X PBS prior to loading.
Library was performed according to the manufacturer's instructions (Single Cell 3' v3 Protocol, 10X Genomics).

value: Human iPSC-derived microglia


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry+, single-nuclei multi-ome (atac)

city: Los Angeles

first: Patricia

last: Nano

state: CA

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

description: 10x multi-ome

library_source: genomic single cell

data_processing:
For PIP-sequencing: FASTQ files were aligned to a custom reference containing the human genome (GRCh38), genomes of four common mycoplasma species, and either the mCherry sequence, GFP sequence, or both, as dictated by the sorted population (PIPseeker, v3). To maximize our ability to call single-cell droplets in each capture, sensitivity was set to 5 and the resulting count matrices were used as inputs for CellBender (remove-background function, v0.3.2, 37550580). These counts matrices were then used to generate Seurat objects for each capture (Seurat, v5, min.cells = 3), and doublets were excluded using DoubletFinder (v2.0.4, 30954475). All samples were then merged into one Seurat object using rigorous quality control standards as detailed above (omitting cells with < 500 genes detected and/or > 5% of UMIs mapping to mitochondrial genes). To annotate cell types in the chimeroid data, label transfer pipeline described for Seurat v5 (FindTransferAnchors and MapQuery functions) were used to transfer cell subtypes from our developmental meta-atlas onto the chimeroid dataset.   For 10x multi-ome: FASTQ files were aligned to a custom reference containing the human genome (GRCh38), genomes of four common mycoplasma species, and either the mCherry sequence, GFP sequence, or both, as dictated by the sorted population (cellranger-arc, version 2.2.0). These counts matrices were then used to generate Seurat objects for each capture using rigorous quality control standards as detailed above (omitting cells with < 500 genes detected and/or > 5% of UMIs mapping to mitochondrial genes). Seurat objects across all experimental conditions were merged and cell type labels were transferred from the developmental meta-atlas as described above. Chromatin accessibility was analyzed by generating chromatin assays and Seurat objects for each sample using the counts from the Peaks assay (min. cells = 100, min.features = 200). Gene annotations were then extracted from EnsDb and added to the object. Quality control (QC) metrics (nucleosome signal scores, transcription start site (TSS) enrichment scores, fraction of counts in blacklist regions, fraction of reads in peaks) were then calculated using the built-in functions in Signac (v1.14). Cells with nCount_peaks < 3000 and > 150,000, nucleosome signal scores > 2, TSS enrichment scores < 1, fraction of counts in blacklist regions > 0.015, and fraction of reads in peaks < 0.5 were omitted. Individual Seurat objects were then merged using the Merge function in Seurat. To evaluate the effects of FEZF2 and TSHZ3 shRNAs on promoter chromatin accessibility, a gene activity matrix was created using the Signac GeneActivity function on the merged Seurat object. The resulting matrix was added to the Seurat object as a new assay (GeneActivity) and normalized using LogNormalize, with the median nCount_GeneActivity as the scale factor.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files, and comma-seprated values files

source_name: Mixture of UCLA1, UCLA6, and KOLF

growth_protocol: Human embryonic stem cells used for this study were between passage 7 – 25

extract_protocol:
For PIP-sequencing: Chimeroids were harvested at week 8 for single-cell sequencing using the PIPseq™ T2 3’ Single Cell RNA Kit v4.0PLUS (Fluent Biosciences). Three chimeroids from the single-shRNA conditions and 33 chimeroids from the double knock-down conditions were prepared for flow-assisted cell sorting as described above for the organoid knock-down experiments. Target populations were sorted on a FACSAria (BD Biosciences) configured with a 561-nm laser, 595LP dichroic mirror, and 605/40-nm bandpass filter for mCherry detection; a 481-nm laser, 505LP dichroic mirror, and a 530/30-nm bandpass filter for GFP detection; and a 355-nm laser, 450 LP dichroic mirror, and 515/30-nm bandpass filter for DAPI detection. Sorted samples were pelleted and resuspended in 2% FBS in PBS to obtain an estimated 5,000 cells / µL. This enabled the targeting of ∼ 25,000 cells for capture. To maximize our ability to obtain high-quality single-cell profiles, we conducted at least two PIP captures for each sorted cell population. For 10x multi-ome: Chimeroids were harvested at week 10 for single-cell multi-omic profiling using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit CG000338 Rev F (10X Genomics). Eight chimeroids from the FEZF2-shRNA and nine chimeroids TSHZ3-shRNA conditions were prepared for flow-assisted cell sorting as described above, with over 100,000 cells obtained per sort. Nuclei were extracted as per the 10X Nuclei Isolation Protocol (CG000365), using a 3-minute incubation in lysis buffer and 3, 1-mL washes with Wash Buffer.
For PIP-sequencing: Sequencing libraries were obtained from cells according to PIPseq T2 instructions, using 16 cycles for cDNA amplification and 8 – 12 cycles for library amplification depending on the amount of DNA. For 10x multi-ome: Sequencing libraries were obtained from cells according to manufacturer instructions, using 7-9 cycles for ATAC library amplification; 6-9 cycles for cDNA amplification; and 14 – 16 cycles for gene expression library amplification depending on the amount of DNA. All libraries were quantified on an Agilent 2100 Bioanalyzer, and sequenced as per manufacturer recommendation on a NovaSeq X Plus flow cell.
scRNA-seq; single-nuclei multi-ome (gene expression and ATAC)

treatment_protocol: After a maximum of two passages, each cell line was used to generate and maintain cortical organoids using protocols based on Kadoshima et al., 2013 (PMID: 24277810) and Bhaduri et al., 2020 (PMID: 31996853).  At day 19, all organoids were dissociated and re-aggregated to generate cortical chimeroids using protocols based on Anton-Bolanos et al., 2024 (PMID: 38926573), at which time cells were also incubated with diluted lentiviral supernatants. After 20 hours, 100 µL of media on the re-aggregating chimeroids was replaced with 100 µL of DMEM/F12-GlutaMAX media (Cat. # 10565-018, Life Technologies) supplemented with 1X N2 (Cat. # 17502-048, Life Technologies), 1X CD Lipid Concentrate (Cat. # 11905-031, Life Technologies), and 1X penicillin-streptomycin to resume organoid maturation. Media was changed again the next day, and, at 23 days, organoids were transferred onto six-well ultra-low adhesion plates (Cat. # 07-200-601, Corning) and placed onto an orbital shaker rotating at 100 rpm.

value: Mixture of UCLA1, UCLA6, and KOLF


title: Mr1+/+ + PD, rep3


title: iMGL, Hypoxia

description: 10X Genomics


title: Diaphragm_E15.5_wt_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ044_S28


title: D0-100uM-FR3

value: Day 0


title: Mr1+/+ + PD, rep2


title: D15-DMEM2-FR3

value: LG


title: Diaphragm_E15.5_mut_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ047_S31


title: Mr1+/+ + PD, rep1

value: peritoneum


title: Live BHV-1 6hr biological rep 1

description:
Figure from the paper that the file was used to generate: 1
1L0-6

value: Live BHV-1 harvested at 6hpi


title: Mr1+/+ + PBS, rep3


title: Mock 6hr biological rep 1

description:
Figure from the paper that the file was used to generate: 1
1M0-6


title: D9-DMEM2-FR3


title: Diaphragm_E15.5_mut_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ045_S29


title: iMGL, Normoxia

description: 10X Genomics


title: Diaphragm_E15.5_wt_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ043_S27

value: wt


title: Mr1+/+ + PBS, rep2


title: Diaphragm_E15.5_wt_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ042_S26


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry-, single-nuclei multi-ome (atac)

description: 10x multi-ome


title: Diaphragm_E15.5_wt_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ041_S25


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP-, single-nuclei multi-ome (atac)

description: 10x multi-ome


title: Mr1+/+ + PBS, rep1


title: PM_LPS5

city: St Louis

first: Erik

last: Musiek

address: 4370 Duncan Ave

department: Neurology

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned and quantitated with Illumina DRAGEN version 4.0.3-8 Bio-IT platform
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts and TPM in tab-delimitted text format

source_name: cortex

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit, 1ug of total RNA was used for construction of  sequencing libraries
KAPA RiboErase

treatment_protocol: 2-month-old C57Bl6 male mice were treated with i.p. LPS [2mg/kg] or PBS at ZT1 or ZT13 for two consecutive days and harvested on the third

value: cortex

value: WT

value: PBS


title: PM_LPS4


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP+, single-nuclei multi-ome (atac)

description: 10x multi-ome


title: Donor10-D0-100uM


title: Donor10-D0-DMEM2


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry+, single-nuclei multi-ome (gene expression)

description: 10x multi-ome


title: Lung_E15.5_mut_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ040_S24

source_name: Lung

value: Lung


title: PM_LPS2

value: LPS


title: D0-DMEM2-FR3

value: Human primary adipose stem cells


title: Donor8-D0-100uM


title: Lung_E15.5_mut_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ039_S23


title: PM_LPS3


title: Donor10-D0-Normal

value: NF


title: Lung_E15.5_mut_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ038_S22


title: Donor8-D0-DMEM2


title: PM_PBS2


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP+, single-nuclei multi-ome (gene expression)

description: 10x multi-ome


title: Chimeroid cells, FEZF2 and TSHZ3 shRNA-treated and mCherry–;EGFP–, scRNAseq, tube 2

description: PIP-seq


title: D15-100uM-FR5

value: Day 15


title: D15-Normal-FR3


title: Lung_E15.5_wt_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ034_S18


title: PM_PBS1


title: PM_LPS1


title: PM_PBS3


title: Lung_E15.5_mut_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ037_S21


title: D9-100uM-FR5


title: Chimeroid cells, FEZF2 and TSHZ3 shRNA-treated and mCherry–;EGFP–, scRNAseq, tube 1

description: PIP-seq


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP-, single-nuclei multi-ome (gene expression)

description: 10x multi-ome


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry+, scRNAseq, tube 2

description: PIP-seq


title: Chimeroid cells, FEZF2 and TSHZ3 shRNA-treated and mCherry+;EGFP+, scRNAseq, tube 1

description: PIP-seq


title: Lung_E15.5_wt_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ036_S20


title: Lung_E15.5_wt_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ035_S19


title: Trachea_E15.5_mut_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ032_S16

source_name: Trachea

value: Trachea


title: AM_LPS5


title: D0-100uM-FR5


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry-, single-nuclei multi-ome (gene expression)

description: 10x multi-ome


title: Trachea_E15.5_mut_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ031_S15


title: Donor8-D0-Normal


title: AM_LPS2


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry+, scRNAseq, tube 1

description: PIP-seq


title: Chimeroid cells, FEZF2 and TSHZ3 shRNA-treated and mCherry+;EGFP+, scRNAseq, tube 2

description: PIP-seq


title: AM_PBS3


title: AM_PBS2


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP+, scRNAseq, tube 3

description: PIP-seq


title: AM_LPS4


title: D0-DMEM2-FR5


title: D15-Normal-FR5


title: Lung_E15.5_wt_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ033_S17


title: AM_LPS3


title: Trachea_E15.5_wt_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ027_S11


title: D15-DMEM2-FR5


title: D9-DMEM2-FR5

value: Day 9


title: RV, Volume overload, P21, scRNA-seq, rep2

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

data_processing:
Reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version GRCm38, using the STAR algorithm. Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.Then we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat_3.0.2 R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package.
To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression.
Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package.Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method after computing a shared nearest neighbor graph.
For sub-clustering, we applied the same procedure of scaled, dimensionality reduction, and clustering to the specific set of data (usually restricted to one type of cell.) For each cluster, we used the Wilcoxon Rank-Sum Test to find significant deferentially expressed genes comparing the remaining clusters. SingleR and known marker genes were used to identify cell type.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: right ventricle

growth_protocol: Mice live with their mother under 19-22℃ with free access to food and water

extract_protocol:
Right ventricular tissue of mouse pups on postnatal day 21 were rapidly removed from executed mouse and flash frozen in -80℃ refrigerator. Nucleus was isolated using Shbio Nuclei Isolation Kit (SHBIO,#52009-10, China). Nuclei were counted with a cell counter (Thermo Fisher, America).
Using a Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10X Genomics),nuclei were immediately loaded onto a Chromium Single Cell Processor(10X Genomics) for barcoding of RNA from single nuclei. Sequencing libraries were constructed according to the manufacturer’s instructions (10× Genomics) and then sequenced in a NovaSeq 6000 sequencing system (Illumina, 20012866).

value: right ventricle

value: VO

value: volume overload


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP–, scRNAseq, tube 3

description: PIP-seq

value: Mixture of UCLA1, UCLA6, and KOLF


title: D0-Normal-FR5

value: Day 0


title: RV, Volume overload, P21, scRNA-seq, rep1

description: 10X Genomics


title: AM_LPS1


title: Trachea_E15.5_mut_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ030_S14


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry–, scRNAseq, tube 2

description: PIP-seq


title: Lung_E12.5_mut_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ024_S8


title: Chimeroid cells, TSHZ3 shRNA-treated and mCherry–, scRNAseq, tube 1

description: PIP-seq


title: Trachea_E15.5_mut_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ029_S13


title: Trachea_E15.5_wt_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ028_S12


title: Chimeroid cells, scram shRNA-treated and mCherry+, scRNAseq, tube 2

description: PIP-seq


title: D9-Normal-FR5


title: Lung_E12.5_mut_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ022_S6


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP+, scRNAseq, tube 2

description: PIP-seq


title: D9-Normal-FR3


title: Trachea_E15.5_wt_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ026_S10


title: nestin-cKO_lymphnode_EAE_1

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

data_processing:
The paired-end, 150-bp raw sequencing reads for each sample were aligned to the mouse reference genome and transcriptome (GRCm39) using STAR (v 2.7.10)
The expected read counts of each gene were estimated by RSEM (v1.3.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes the raw read count for each sample

source_name: lymph node

growth_protocol: non

extract_protocol:
Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen; Cat# 74104) and its concentration was determined using a Nanodrop 2000 spectrophotometer and a Qubit fluorometer (both from ThermoFisher Scientific). The quality of the extracted RNA was evaluated using a 2100 Bioanalyzer (Agilent).
For bulk transcriptomics of EAE-affected spinal cords, library preparation was performed using the SureSelect Strand-Specific RNA Library Prep System (Agilent; Cat# G9691) following the manufacturer’s protocols. These samples were sequenced on the NovaSeq 6000 System (Illumina), achieving a sequencing depth of over 30 million 2x150bp paired-end reads.

treatment_protocol: Hooke Kits™ for EAE Induction in C57BL/6 Mice with MOG35-55/CFA emulsion and pertussis toxin was purchased from Hook laboratory (Cat# EK-2110). 9 to 13 weeks old female and male mice were used for immunization and EAE development.

value: lymph node

value: bulk

value: nestin-cKO

value: EAE


title: D9-DMEM2-FR4

value: LG


title: Trachea_E15.5_wt_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ025_S9

value: wt


title: D15-100uM-FR4


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP–, scRNAseq, tube 2

description: PIP-seq


title: D0-DMEM2-FR4


title: RV, sham-operated, P21, scRNA-seq, rep2

description: 10X Genomics

value: Sham

value: WT

value: sham-operated


title: Lung_E12.5_mut_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ023_S7

value: Lung


title: Chimeroid cells, scram shRNA-treated and mCherry–, scRNAseq, tube 1

description: PIP-seq


title: D9-100uM-FR4

value: Human primary adipose stem cells


title: AM_PBS1

value: cortex

value: LPS


title: RV, sham-operated, P21, scRNA-seq, rep1

description: 10X Genomics

value: right ventricle


title: Lung_E12.5_wt_rep3

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ019_S3


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP–, scRNAseq, tube 1

description: PIP-seq


title: D0-100uM-FR4


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 1000µM biol. Repl. 3

city: Braunschweig

first: Florian

last: Engelhardt

address: Inhoffenstraße 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Centre for Infection Research

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx1000_3

data_processing:
Initial quality assessment of the sequencing data was conducted using FastQC (v0.11.9). Subsequently, reads were trimmed and aligned to the PA14 reference genome (NC 008463.1) using bowtie2 (v1.3.1) (Langmead & Salzberg, 2012), with only uniquely mapped reads retained for further analysis. Genomic features were annotated using featureCounts (v2.0.1) (Liao et al., 2014). Differential expression analysis between samples was performed using the R package edgeR with the glmQLFit function (Chen et al., 2017). The package employed the Benjamini-Hochberg procedure to correct the p-values for multiple testing. Genes were deemed significantly regulated if their adjusted p-value was ≥ 0.05.
Assembly: NC_008463.1
Supplementary files format and content: tab-delimited text file contains reads per gene

organism: Pseudomonas aeruginosa

source_name: wildtype

growth_protocol: P. aeruginosa PA14 was streaked from a glycerol stock onto lysogeny broth (LB; composed of 5 g yeast extract, 7.5 g NaCl, and 10 g tryptone per liter) agar, forming single colonies. After an overnight incubation at 37°C, a single colony was used to inoculate 10 mL of LB liquid medium in a 50 mL flask, which was then cultured for approximately 16 hours at 37°C with agitation at 180 revolutions per minute (r.p.m.). The bacterial cells from the overnight culture were harvested by centrifugation at 10000xg for 5 minutes, washed twice in PBS, and resuspended in PBS. The suspension's cell density was determined by measuring its optical density using a spectrophotometer (Libra S22; ID 80-2115-20, Biochrom). Next, 20 mL of M9 minimal medium (M9 MM; containing 1 mM MgSO4, 0.1 mM CaCl2, 8.6 mM NaCl, 18.7 mM NH4Cl, 22 mM KH2PO4, 42.2 mM Na2HPO4, 0.01 mM FeSO4, and 20 mM Glucose) in a 100 mL flask was adjusted with the bacterial suspension to an OD600 of 0.1 and then incubated at 37°C with agitation at 180 r.p.m. When the OD600 reached 0.5±0.1 for the main cultures, the appropriate volume of an aqueous DL-serine hydroxamate (SHX; ID S4503, Merck) solution was added to the flasks to induce stringent response. After a 30-minute incubation at 37°C with agitation at 180 r.p.m., the cells were harvested for further processing.

extract_protocol:
To initiate cell lysis, the thawed samples underwent centrifugation at 8000 revolutions per minute for 5 minutes at room temperature, after which the supernatant was discarded. Following this, 100 microliters of TE buffer containing 800 micrograms per milliliter of lysozyme were introduced to the samples and vigorously vortexed for 30 seconds. The mixture was then allowed to incubate for 10 minutes at room temperature with intermittent brief vortexing. Subsequently, 350 microliters of RLT buffer (from the RNeasy Mini Kit; ID 74106, Qiagen), supplemented with 1% β-mercaptoethanol, were added to the samples. After gently inverting the samples several times, they were incubated at -80°C for 1 hour. The thawed mixture was then loaded into a QIAshredder column (ID 79656, Qiagen) and centrifuged for 2 minutes at 14000 revolutions per minute. Total RNA isolation from the resulting flow-through was performed using the RNeasy Mini Kit (ID 74106, Qiagen) according to the manufacturer’s instructions. Any remaining DNA in the extracted RNA samples was eliminated by treatment with the DNA-free DNA Removal kit (ID AM1906, Invitrogen) following the manufacturer’s protocol.
Library preparation from total RNA followed the methods outlined by Bhattacharyya et al., (2019) and Shishkin et al., (2015). Initially, 1 microgram of total RNA was combined with 10x FastAP buffer (ID EF0651, ThermoFisher Scientific) and subjected to a 90-second incubation at 94°C to induce fragmentation (resulting in fragment sizes of 100 – 300 base pairs). Any residual DNA was eliminated through DNAse treatment using TurboDNAse (ID AM1907, Invitrogen) followed by purification using magnetic beads (RNAClean XP; ID A63987, Beckman Coulter). To ligate 5’ phosphorylated barcode oligonucleotides to the dephosphorylated 3’ end of RNA fragments, ligation mixes were incubated for 2 minutes at 70°C employing T4 RNA Ligase 1 (ID M0437M, NEB). Subsequently, individual samples were pooled into a single library preparation mixture and purified using the RNA Clean & Concentrator Kit (ID R1017, Zymo Research). Ribosomal RNA was depleted from the pooled samples using RiboZero (ID RZMB12324, Illumina), followed by bead purification as previously described. RNA fragments were transcribed into cDNA using SMARTScribe Reverse Transcriptase (ID 639536, Takara) with incubation at 42°C for 60 minutes followed by 70°C for 10 minutes. After exonuclease treatment (Exonuclease I; ID M0293L, NEB) and bead purification, Illumina index barcode P5 and library-specific primer X01 were introduced during PCR enrichment utilizing AccuPrime Taq DNA Polymerase (ID 12346-086, Invitrogen). Following a final bead purification step, library preparation was concluded. Post-pooling of individual samples and final bead purification, the fragment size profile was assessed using the Fragment Analyzer system (Agilent), and nucleic acid concentration was determined via fluorometric measurement using the Qubit 2.0 system (Thermo Fisher Scientific). Upon successful quality assessment, the final sequencing library underwent paired-end 50 base pair Illumina sequencing at the Genome Analytics Facility (HZI) utilizing a NovaSeq 6000 system.

treatment_protocol: 1 milliliter of the primary culture was combined with an equal volume of RNAprotect Bacteria Reagent (ID 76506, Qiagen) and allowed to incubate for 5 minutes at room temperature. After incubation, the cells were harvested by centrifugation at 17000xg for 10 minutes. The supernatant was then removed, and the samples were stored at -80 °C until needed.

value: wildtype

value: treated with  1000µM SHX


title: nestin-cKO_lymphnode_EAE_2


title: cx3cr1-cKO_lymphnode_EAE_2


title: D15-DMEM2-FR4

value: Day 15


title: Chimeroid cells, scram shRNA-treated and mCherry+, scRNAseq, tube 1

description: PIP-seq

value: Mixture of UCLA1, UCLA6, and KOLF


title: Chimeroid cells, scram shRNA-treated and mCherry–, scRNAseq, tube 2

description: PIP-seq


title: Lung_E12.5_wt_rep4

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ020_S4


title: Lung_E12.5_mut_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ021_S5


title: D0-Normal-FR4

value: NF

value: Day 0


title: cx3cr1-cKO_lymphnode_EAE_1

value: lymph node

value: bulk

value: EAE


title: nestin-control_lymphnode_EAE_2

value: nestin-control


title: Lung_E12.5_wt_rep1

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ017_S1

value: wt


title: cx3cr1-cKO_lymphnode_EAE_3


title: Lung_E12.5_wt_rep2

description:
100 pd
Raw_counts_respiratory_system.txt
TPM_respiratory_system.txt
JJ018_S2


title: D9-Normal-FR4

value: Day 9


title: cx3cr1-control_lymphnode_EAE


title: D0-Normal-FR3


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 500µM biol. Repl. 2

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx500_2

value: treated with  500µM SHX


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 500µM biol. Repl. 3

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx500_3


title: rTMS-MSCs-4

city: Guang Zhou

first: Shimei

state: Guang Dong

address: Guang Zhou, Guang Dong, China

department: Department of Rehabilitation Medicine

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

data_processing:
After quality control, reads were mapped to rat genome reference (version Rattus_norvegicus.mRatBN7.2) using Hisat2 (version 2.1.0). The Htseq-count(version 0.11.2) were used to generate the gene count matrix. DESeq2(version 1.40.1) were used to perform differential gene analysis. A P value <0.05 and absolute log2FoldChange value above 1 was considered statistically significant. The online database genemania (https://genemania.org/) and of trrust (and https://www.grnpedia.org/trrust/) were used to analyze protein-protein interaction (PPI) networks.
Assembly: RatBN7.2
Supplementary files format and content: processed data.count

organism: Rattus norvegicus

source_name: PC12 cells

extract_protocol:
total RNA was extracted from  the PC12 cells  in each group using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, USA).
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: PC12 cells


title: A_H3K4me3_AKO_2

value: Melanoma

value: APE1 knockout


title: D15-Normal-FR4

value: Human primary adipose stem cells


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 1000µM biol. Repl. 2

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx1000_2

value: wildtype


title: pdgfra-cKO_lymphnode_EAE_3

value: pdgfra-cKO


title: A_H3K4me3_AKO_1


title: rTMS-MSCs-2


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 100µM biol. Repl. 3

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx100_3

value: treated with  100µM SHX


title: Chimeroid cells, FEZF2 shRNA-treated and EGFP+, scRNAseq, tube 1

description: PIP-seq

value: Mixture of UCLA1, UCLA6, and KOLF


title: MSCs-4


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 500µM biol. Repl. 1

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx500_1


title: MSCs-3


title: pdgfra-cKO_lymphnode_EAE_2


title: A_H3K4me3_WT_1

value: WT


title: rTMS-MSCs-3


title: A_H3K4me3_WT__2


title: MSCs-2


title: cspg4-cKO_lymphnode_EAE_2


title: pdgfra-cKO_lymphnode_EAE_1


title: cspg4-cKO_lymphnode_EAE_3


title: H_BG4_AKO_1


title: control_lymphnode_EAE

value: control


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 1000µM biol. Repl. 1

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx1000_1

value: treated with  1000µM SHX


title: cspg4-control_lymphnode_EAE

value: lymph node

value: bulk


title: control_lymphnode_non-EAE

value: W/O EAE


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 0µM biol. Repl. 3

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx0_3


title: MSCs-1


title: H_BG4_WT_1


title: ATAC_AKO_2

data_processing:
The ATAC-seq reads were mapped to the human genome (UCSC hg38) with Bowtie2. The duplicated reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per genome coverage, RPGC) with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigwig files for enrichment

growth_protocol: A549 cell lines were cultured in DMEM (Gibco, 11965-118) media supplemented with 10% FBS (ExCell, FSP500). All media were supplemented with penicillin and streptomycin (Gibco, 15140-122). Cells were cultured at 37°C with 5% CO2, and were periodically tested and shown to be mycoplasma negative.

extract_protocol:
WT and APE1 KO A549 cells (1 × 106) were used for the ATAC-seq experiment, and cell counting was performed using a Luna II (Logos Biosystems, Korea).
ATAC-seq was performed  according to the TruePrepTM DNA Library Prep Kit V2 for Illumina protocol (Vazyme, Nanjing, China).


title: OGDR-4


title: ATAC_WT__2


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 100µM biol. Repl. 2

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx100_2

value: treated with 100µM SHX


title: nestin-cKO_spinalcord_EAE_3

source_name: spinal cord

value: spinal cord

value: nestin-cKO

value: EAE


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 0µM biol. Repl. 1

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx0_1


title: OGDR-3

value: PC12 cells


title: LX-2 cells siAURKA-3

city: guangzhou

first: Guan qi

last: Dai

state: guangdong

address: shiliugang Road 13 courtyard

department: Integrated Hospital of Traditional Chinese Medicine

institute: southern medical university

data_processing:
Total RNAs from LX2 cells transfected with siAURKA and siNC were isolated by TRIzol reagent.
The quality and quantity of the total RNA that was used to construct the transcriptome RNA-seq library met the following standards: OD260/280 = 1.8~2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0 and >10 μg.
High-quality RNA from each sample was sent to for RNA-seq on the Illumina HiSeq Xten platform.
The clean reads were then aligned to the human genome (version GRCh38) using the HISAT2.
STRING TIE was used to count genes
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts values for each Sample

source_name: liver

growth_protocol: LX2 cells are activated human hepatic stellate cells; they were maintained in DMEM with 10% FCS containing penicillin and streptomycin.  Cells were plated onto 100 mm plastic petri dishes at 1000,000 cells/plate

extract_protocol:
RNA were extracted using Trizol regent
Total RNAs from LX2 cells transfected with siAURKA and siNC were isolated by TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with siAURKA or siNC for 48 hours.

value: liver

value: Non parenchymal cell

value: AURKA knockdown

value: siAURKA transfected


title: nestin-cKO_spinalcord_EAE_2


title: nestin-cKO_spinalcord_EAE_1


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 100µM biol. Repl. 1

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx100_1

value: wildtype


title: rTMS-MSCs-1


title: CD45+ cells, ADT & HTO

city: Boston

first: Yufei

last: Wang

state: MA

address: 450, Brookline Ave

institute: Dana-Farber Cancer Institute

description: ADT & HTO: R1: R1 contains barcode and UMI, R2 contains  ADT or HTO tag

data_processing:
CellRanger v6.1.1 was used for read alignment, filtering, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

molecule: protein

source_name: Kidney & lung

extract_protocol:
Tumor samples were dissociated into single cells by a semi-automated combined mechanical/enzymatic process. The tumor tissue was cut into pieces of (2-3mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes H, R and A (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was accomplished by performing a program (37C_h_TDK_1) on the gentleMAC Octo Dissociator with Heaters (Miltenyi Biotech). Single cell suspensions generated from ccRCC tumor samples were FACS sorted on a SONY MA900 sorter (SONY) for viable human TILs (Zombie- mCD45- hCD45+, BioLegend).
Sorted cells were stained with a distinct barcoded antibody (Cell-Hashing antibody, TotalSeq-C, Biolegend). After washing, the stained cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μL, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5′ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and protein (hashtags) library sequenced to an average of 15,000 reads per cell, all using Illumina Novaseq.

value: Kidney & lung


title: P.aeruginosa PA14, exponential phase, 30 minutes, SHX 0µM biol. Repl. 2

description: Library name: fen17_RNASeq_20201129_PA14_t1_shx0_2


title: OGDR-2


title: LX-2 cells siAURKA-2


title: nestin-control_spinalcord_EAE_1

value: nestin-control


title: LX-2 cells, siNC-3

value: WT

value: siNC transfected


title: Decompensated RV-2,SD rats, 8w SuHx

city: London

first: Lan

last: Zhao

address: Du Cane road

department: NHLI

country: United Kingdom

institute: Imperial College London

description: CountMatrix.txt column name: FG2015_34 (Decompensated RV)

data_processing:
Salmon (version 0.14.1)
Reads mapping and couning, quantification of the reads/abundance
Normalization of the expression matrix
Computation of differential expressing genes (DEGs)
Assembly: The transcriptome index used for reads mapping was built with the mice genome, transcriptome and annotation files (GRCm38.p6). DEGs between groups were computed using the built-in Wald statistic of the DESeq2 R package (version 1.24.0). Benjamini-Hochberg procedure was applied to control the false discovery rate (FDR) and to offer the p values with adjustment. The adjusted p value < 0.01 and the fold change > 2 were set as the criteria of DEGs. The annotation of the DEGs and the pathway enrichment were performed using clusterProfiler R package (version 3.12.0).
Supplementary files format and content: tab-delimited xlsx file include normalised counts for each sample

source_name: Right ventricle

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). The tissues (no more than 30mg) were homogenized in 500µL Buffer RLT (containing 0.01% ß-mercaptoethanol). The homogenate was then mixed with 1 volume of 70% ethanol and was transferred to RNeasy Mini spin column and centrifuged. Next, the on-column DNase digestion was performed following the manufacture instruction. Following the DNase digesting steps, the column was washed with 700µL Buffer RW1 for once and 500 µL Buffer RPE for twice sequentially. Then the spin column was transferred to RNA collection tubes, and the RNA was eluted in 30µL RNase-free water. RNA concentration and quality were estimated using a NanoDrop Spectrophotometer.
The sequencing library was constructed from the total RNA using the TruSeq RNA Sample Preparation Kit (Illumina) following the product manual.

value: Right ventricle

value: 8 weeks

tag: Sex

value: male

value: Sprague-Dawley

value: SuHx


title: ATAC_AKO_1

value: Melanoma

value: APE1 knockout


title: LX-2 cells siAURKA-1


title: nestin-control_spinalcord_EAE_2

value: spinal cord

value: bulk

value: EAE


title: Myocardian fibroblast, cultured, subject tp410, PF supernatant and TGFbR1i treated

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

data_processing:
Bulk-RNA sequencing (RNASeq) reads were pseudo-mapped to NCBI RefSeq human transcript models using Kallisto 0.42.4
Assembly: GRCh38
Supplementary files format and content: The tab-delimited processed counts file for each sample contains two columns: the NCBI RefSeq transcript accession, and the Transcripts Per Million normalized read count for that transcript.

source_name: myocardial fibroblast

growth_protocol: Fibroblasts isolated from the right atrial appendage were minced into 0.5-1mm fragments and suspended in Iscove’s Modified Dulbecco’s Medium (IMDM; Lonza, Walkersville, MD) supplemented with 10% fetal bovine serum (Gibco by Life Technologies, Burlington, Canada) and 50,000 units of penicillin-streptomycin (Life Technologies, Burlington, Canada). Tissue suspensions were plated and cultured at 37°C in 5% CO2. Passages 1-4 were used for experiments. All cells were serum starved for 24-hours prior to mRNA isolation.

extract_protocol:
RNeasy kit (Qiagen) per the manufacturer’s protocol
NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Isolation Module

value: myocardial fibroblast

tag: individual

value: subject tp410

value: percardial fluid supernatant + TGFbR1i


title: LX-2 cells, siNC-1

value: liver

value: Non parenchymal cell


title: cx3cr1-cKO_spinalcord_EAE_3


title: Myocardian fibroblast, cultured, subject tp410, PF supernatant treated

value: percardial fluid supernatant


title: OGDR-1

value: PC12 cells


title: Decompensated RV-1, SD rats, 8w SuHx

value: Right ventricle


title: cx3cr1-cKO_spinalcord_EAE_2


title: Myocardian fibroblast, cultured, subject tp410


title: ControlRV2, SD rats, day0

description: CountMatrix.txt column name: FG2015_32 (Control RV)


title: ControlRV3, SD rats, day0

description: CountMatrix.txt column name: FG2015_33 (Control RV)


title: ATAC_WT_1

value: WT


title: cx3cr1-control_spinalcord_EAE_1


title: NC14Interphase.2_1

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

data_processing:
Micro-C data for D. melanogaster were aligned to the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly with BWA-MEM 82 using parameters -S -P -5 -M.
The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.
The resultant files were indexed with pairix (https://github.com/4dn-dcic/pairix).
The pairs files for individual replicates were merged with pairtools, and then used to generate contact matrices at 100bp resolution with Cooler.
Finally, balancing and mcool file generation was performed using Cooler’s zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool
Library strategy: Micro-C

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
Embryos were collected on yeasted apple juice plates in population cages. For nc1-8 embryos, plates were changed every 30 mins, and subjected to immediate fixation. For nc14 embryos, plates were laid for 1 hour, then collected, incubated for 2 hours at 25℃, and subjected to fixation. For stage 10-12 embryos, plates were laid for 2 hours, incubated for 6 hours at 25C, and subjected to fixation.
Micro-C libraries were prepared as previously described in Batut…Levine 2022.

value: embryo

value: wt

tag: Stage


title: Decompensated RV-3,SD rats, 8w-SuHx

value: 8 weeks

value: male

value: Sprague-Dawley

value: SuHx


title: CD45+ cells, GEX

description: GEX (5' mRNA): R1 contains barcodes and UMI, R2 contains transcript

value: Kidney & lung


title: Myocardian fibroblast, cultured, subject tp393, PF supernatant treated

value: subject tp393


title: Myocardian fibroblast, cultured, subject tp393, PF supernatant and TGFbR1i treated

value: myocardial fibroblast


title: control_spinalcord_EAE

value: spinal cord

value: bulk

value: control

value: EAE


title: NC14Interphase.1_2


title: Myocardian fibroblast, cultured, subject tp393


title: NC12m.2_2


title: ring1a1b_RNAseq_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 11-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000, paired-end 150bp).

value: Arabidopsis seedlings

value: ring1a-/- ring1b-/-


title: ring1a1b_RNAseq_rep2


title: LX-2 cells, siNC-2

value: liver

value: Non parenchymal cell

value: siNC transfected


title: cx3cr1-cKO_spinalcord_non-EAE

value: W/O EAE


title: NC14Interphase.1_1

value: embryo

value: wt


title: NC14Interphase.2_2


title: pdgfra-cKO_spinalcord_EAE_3

value: pdgfra-cKO


title: ring1a1b_RNAseq_rep1


title: NC12m.2_1


title: al24567_RNAseq_rep3


title: pdgfra-cKO_spinalcord_EAE_2


title: cx3cr1-cKO_spinalcord_EAE_1


title: al24567_RNAseq_rep1


title: Myocardian fibroblast, cultured, subject tp321, PF supernatant treated

value: subject tp321

value: percardial fluid supernatant


title: ControlRV1, SD rats, day0

description: CountMatrix.txt column name: FG2015_31 (Control RV)

value: Right ventricle

value: male

value: Sprague-Dawley


title: pdgfra-cKO_spinalcord_EAE_1

value: spinal cord

value: bulk


title: Myocardian fibroblast, cultured, subject tp323, PF supernatant and TGFbR1i treated

value: myocardial fibroblast

value: subject tp323

value: percardial fluid supernatant + TGFbR1i


title: cspg4-cKO_spinalcord_EAE_3

value: EAE


title: NC12m.1_1


title: al24567_RNAseq_rep2

value: Arabidopsis seedlings


title: Myocardian fibroblast, cultured, subject tp323, PF supernatant treated


title: Myocardian fibroblast, cultured, subject tp323


title: Col-0_RNAseq_rep2

value: wild type


title: cspg4-control_spinalcord_EAE_1


title: S10-12.1_1


title: S10-12.2_1


title: Myocardian fibroblast, cultured, subject tp321


title: cspg4-cKO_spinalcord_EAE_1


title: Col-0_RNAseq_rep1


title: NC12m.1_2


title: NC14.2_2


title: al24567_H3K4me3_rep1

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)


title: Myocardian fibroblast, cultured, subject tp320, PF supernatant treated

value: subject tp320


title: NC14.2_1

value: embryo


title: S10-12.2_2

value: wt


title: Col-0_H3K4me3_rep2


title: NC14.1_2


title: Myocardian fibroblast, cultured, subject tp307

value: subject tp307


title: Col-0_H3K4me3_rep1


title: al24567_H3K4me3_rep2


title: Myocardian fibroblast, cultured, subject tp320


title: cspg4-control_spinalcord_EAE_2


title: Myocardian fibroblast, cultured, subject tp307, PF supernatant and TGFbR1i treated


title: control_spinalcord_non-EAE

value: control

value: W/O EAE


title: Col-0_RNAseq_rep3


title: sdg2_H2Aub_rep1


title: Myocardian fibroblast, cultured, subject tp300, PF supernatant treated

value: subject tp300

value: percardial fluid supernatant


title: NC1-8.2_1


title: S10-12.1_2


title: KD3

first: Junling

last: Fu

address: 北京市长椿街45号

institute: 首都医科大学宣武医院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchword
Assembly: mm10
Supplementary files format and content: counts, FPKM

source_name: brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain

value: male

value: db/db

value: ketogenic diet (KD)


title: Col-0_H2Aub_rep6


title: NC1-8.1_1


title: NC14.1_1


title: Myocardian fibroblast, cultured, subject tp308, PF supernatant treated

value: myocardial fibroblast

value: subject tp308