title: HKO_Input

data_processing:
library strategy: meRIP-seq
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
exomePeak R package (version 2.16.0) was used for the m6A peak identification
The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
GO enrichment analysis was implemented by the GOseq R package.
Assembly: mouse reference genome(GRCm38.p6)
Supplementary files format and content: Processed data files; excel; WFF_peaks; WBKO_peaks

growth_protocol: Alkbh5flox/flox and Alkbh5-HKO mice were fed with normal chow for 9 weeks.

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Alkbh5flox/flox and Alkbh5-HKO mice at 9 weeks old. A total of 300 μg RNAs were pooled from three mice each group.
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

value: liver


title: T47D cells, normoxic device, 24 hr, rep2

status: Public on Feb 27 2025

type: SRA

city: Los Angeles

first: JEONG MIN

last: OH

state: California

address: 1042 Downey Way DRB 140

department: Biomedical Engineering

country: USA

institute: University of Southern California

library_source: transcriptomic

data_processing:
Partek Flow Genomic Analysis software version 11.0.24.0328 was used to build the following pipeline:
(i) pre-alignment QA/QC, (ii) trim bases from both ends base on minimum quality level (Phred) of 20 and a minimum read length of 25, (iii) alignment of mRNA-seq reads to the hg38 human genome using STAR, (iv) post-alignment QA/QC, (v) quantification to annotation model (Partek E/M), (vi) noise reduction filter to exclude features where the maximum ≤ 20, (vii) upper-quartile normalization after adding 1.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count for each sample

molecule: total RNA

organism: Homo sapiens

source_name: breast

growth_protocol: Before the device culture, all cell lines were maintained in a humidified incubator at 37 °C with 5% CO2. OAW42, PC9, and LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U mL–1 penicillin and 100 μg mL–1 streptomycin (1% P/S). SKOV3, A549, MCF7, T47D, and PC3 cells were cultured in DMEM supplemented with 10% FBS and 1% P/S

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions.  Quality of the RNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). Only the RNA samples that have passed the QC were used.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were constructed with the NEBNExt Ultra II library kit (New England BioLabs Inc)

treatment_protocol: Each cancer cell type was resuspended in culture medium and injected into the poly-d-lysine coated middle chamber at initial seeding density of 60,000 cells per microdevice. Cells were allowed to attach in a humidified incubator at 37 °C and 5% CO2 for 2 hours. After confirming cell attachment, an additional culture medium was introduced through the side channels of the microdevice for continued incubation.

tag: tissue

value: breast

tag: cell line

tag: cell type

value: cancer cells


title: Aggressive B-cell lymphoma R32D

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

molecule: genomic DNA

source_name: Abdominal mass

label_protocol: Affymetrix OncoScan™ FFPE Assay kit

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: type of sample

value: Aggressive B-cell lymphoma

tag: gender

value: male

value: FFPE


title: Aggressive B-cell lymphoma R27R

source_name: Breast

value: female


title: Liver - LWT_HFD_FASTED - Rep3

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 35083 spots out of 62976 were selected. The mean signal of the 24 first samples and 24 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32437 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Mus musculus

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mouse housing was controlled for temperature (23°C) and light (12-h light/12-h dark). All mice were males.

extract_protocol: Total cellular RNA was extracted with Tri reagent (Molecular Research Center).

treatment_protocol: Following killing by cervical dissociation, livers were removed, weighted and snap-frozen in liquid nitrogen and stored at -80°C.

value: Liver

tag: genotype

value: LWT

tag: diet

value: HFD

tag: nutritional status

value: FASTED

tag: washbatch


title: Liver - LWT_CTRL_FED - Rep6

value: CTRL

value: FED


title: HKO_IP

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

source_name: liver

tag: chip antibody

value: m6A antibody (Merk Millipore)


title: FF_Input


title: T47D cells, µMeRe device (hypoxic), 24 hr, rep1


title: T47D cells, µMeRe device (hypoxic), 24 hr, rep2


title: Aggressive B-cell lymphoma R24D

source_name: Cavum


title: FF_IP


title: Liver - LKO_CTRL_FED - Rep2

value: LKO


title: Aggressive B-cell lymphomaR22D

source_name: Pelvic mass


title: Liver - LKO_HFD_FED - Rep2


title: Liver - LKO_HFD_FASTED - Rep1


title: Liver - LWT_CTRL_FASTED - Rep2


title: Liver - LKO_HFD_FASTED - Rep3


title: MCF7 cells, normoxic device, 24 hr, rep1


title: HKO_3 [Alkbh5-CKO]

data_processing:
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing N  base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2  (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate .  padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly  differential expression.
Assembly: mouse reference genome(GRCm38.p6)
Supplementary files format and content: Processed data files; excel; fpkm of each gene

extract_protocol:
Alkbh5flox/flox and Alkbh5-HKO mice were fed with normal chow for 9 weeks.Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to  degrade the RNA. Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends  via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA  fragments, Adaptor with hairpin loop structure were ligated to prepare for  hybridization. In order to select cDNA fragments of preferentially 370~420 bp in  length, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the  effective concentration and the target amount of data off the machine, then being  sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is  generated. The basic principle of sequencing is to synthesize and sequence at the same  time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase  and splice primers were added to the sequenced flowcell and amplified. When the  sequence cluster extends the complementary chain, each dNTP labeled by  fluorescence can release the corresponding fluorescence. The sequencer captures the  fluorescence signal and converts the optical signal into the sequencing peak by  computer software, so as to obtain the sequence information of the fragment to be  tested.


title: Aggressive B-cell lymphomaR21D

source_name: tumor mass not specified


title: HKO_1 [Alkbh5-CKO]


title: HKO_2 [Alkbh5-CKO]


title: Aggressive B-cell lymphomaR10D

source_name: sphenoethmoidal tumor


title: MCF7 cells, µMeRe device (hypoxic), 24 hr, rep1


title: Aggressive B-cell lymphoma R7D

source_name: Mediastinal mass


title: ff_3 [Alkbh5flox/flox]


title: Liver - LWT_HFD_FED - Rep6


title: Aggressive B-cell lymphoma R26R1


title: PC3 cells, normoxic device, 24 hr, rep2

source_name: prostate

value: prostate


title: MCF7 cells, normoxic device, 24 hr, rep2


title: meta_ag_d0

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description:
Library name: Sample_W0073_Rn867
Column name in CountMatrix.txt: Sample_W0073_Rn867

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.5).
Adapter trimming and quality filtering were performed using Trimmomatic (v0.36) with the following parameters: LEADING:3 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36.
The processed reads were aligned to the reference genome (hg19) using TopHat v2.1.1 with Bowtie2.
Gene expression quantification was performed using featureCounts (Subread v1.5.0).
Assembly: hg19
Supplementary files format and content: tab-deliminated txt file includes raw counts for each Sample

source_name: iPS cells

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN).
We prepared sequencing libraries using the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems).

value: iPS cells


title: Liver - LWT_CTRL_FED - Rep3


title: ff_1 [Alkbh5flox/flox]

value: liver


title: meto_ag_d0

description:
Library name: Sample_W0073_Rn868
Column name in CountMatrix.txt: Sample_W0073_Rn868


title: PC3 cells, normoxic device, 24 hr, rep1


title: MCF7 cells, µMeRe device (hypoxic), 24 hr, rep2

value: breast


title: ff_2 [Alkbh5flox/flox]


title: meto_ag_d10

description:
Library name: Sample_W0073_Rn866
Column name in CountMatrix.txt: Sample_W0073_Rn866


title: Liver - LKO_HFD_FED - Rep3


title: KO-2  (Single cells KO vs. WT SMC)

city: New Haven

first: George

last: Tellides

state: CT

address: 10 Amistad st, 337B

department: Surgery

institute: Yale University

description:
KO-2
3,707 cells before, 3,246 cells after filtering

data_processing:
Samples were sequenced on Novaseq 6000
The data from sequencer was processed to obtain the fastq sequences using the "cellranger mkfastq" program provided by the vendor (10X genomics).
The raw reads were aligned to the mouse reference genome (mm10 with added sequences for GFP and tdTomato) and gene expression in cells was quantified using the "cellranger count" program provided by the vendor (10X genomics).
The gene expression data was further processing using the Seurat package (version 4.0), including data filtering, normalization, data dimension reduction, cell clustering, marker identification, cell type identity assignment, and data visualization.
keep cells with all criteria of: eGFP > 1, at least 200 genes detected, UMI between 5000 and 25000, and mitochondria percentage < 10%; keep genes detected in at least 10 cells
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every cell, or under specific clusters/cell types

source_name: aortic SMC

growth_protocol: Mice were bred and housed under standard conditions

extract_protocol:
Ascending aorta/aortic arch segments were enzymatically digested under cold conditions, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye), GFP+ SMCs were sorted into buffer with 0.04% BSA, and between 2,000 to 4,000 cells from individual aortic segments were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

treatment_protocol: GFPiSMC (WT) and Tgfbr1/2iSMCKO (KO) mice were administered tamoxifen for 5 days at a dose of 1 or 2 mg/d i.p. at 4 or 11 weeks of age, respectively, and the ascending aorta/aortic arch segments were analyzed at 12 weeks of age

tag: strain

value: ascending aorta/aortic arch

tag: age


title: PC3 cells, µMeRe device (hypoxic), 24 hr, rep2

value: cancer cells


title: PC3 cells, µMeRe device (hypoxic), 24 hr, rep1


title: KO-1  (Single cells KO vs. WT SMC)

description:
KO-1
4,376 cells before, 4,031 cells after filtering


title: meta_ag_d10

description:
Library name: Sample_W0073_Rn865
Column name in CountMatrix.txt: Sample_W0073_Rn865


title: Liver - LWT_CTRL_FASTED - Rep6


title: Liver - LKO_CTRL_FASTED - Rep4


title: Liver - LWT_HFD_FASTED - Rep5


title: meso_SIX2_Sort

description:
Library name: Sample_W0073_Rn864
Column name in CountMatrix.txt: Sample_W0073_Rn864


title: LNCaP cells, normoxic device, 24 hr, rep2

value: LNCaP


title: WT-2  (Single cells KO vs. WT SMC)

description:
WT-2
3,420 cells before, 3,000 cells after filtering

value: GFPiSMC


title: meso_SIX2_Bulk

description:
Library name: Sample_W0073_Rn863
Column name in CountMatrix.txt: Sample_W0073_Rn863


title: LNCaP cells, normoxic device, 24 hr, rep1


title: Liver - LKO_CTRL_FED - Rep5


title: Liver - LKO_CTRL_FED - Rep4


title: LNCaP cells, µMeRe device (hypoxic), 24 hr, rep2


title: Liver - LWT_CTRL_FASTED - Rep5


title: WT-1  (Single cells KO vs. WT SMC)

description:
WT-1
2,597 cells before, 2,151 cells after filtering


title: LNCaP cells, µMeRe device (hypoxic), 24 hr, rep1


title: OSR1_Sort

description:
Library name: Sample_W0073_Rn861
Column name in CountMatrix.txt: Sample_W0073_Rn861


title: MSP-1 specific MBCs, 3H3, scATAC-seq

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

description: Library name: MSP1_3H3

library_source: genomic single cell

data_processing:
scATAC-seq data was processed using Cell Ranger ATAC (v.2.1.0).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: peaks.bed, singlecell.csv, fragments.tsv.gz

source_name: Spleen

extract_protocol:
Memory B cells were flow sorted, nuclei were isolated and run on the 10X Chromium (10X Genomics).
Library preparation was performed according to the manufacturer’s protocol for Chromium Next GEM Single Cell 5’ Reagent Kit v2 with Feature Barcode technology and V(D)J amplification for mouse B cells (10X Genomics).

value: Spleen

value: Memory B cells

tag: cell subset

value: MSP-1 specific MBCs

value: WT

tag: treatment


title: meso_PS

description:
Library name: Sample_W0073_Rn862
Column name in CountMatrix.txt: Sample_W0073_Rn862


title: Liver - LKO_HFD_FED - Rep6

value: Liver

value: HFD


title: MSP-1 specific MBCs, rIgG, scATAC-seq

description: Library name: MSP1_rIgG

value: rIgG


title: Liver - LKO_CTRL_FASTED - Rep5

value: CTRL

value: FASTED


title: PC9 cells, normoxic device, 24 hr, rep2

source_name: lung

value: lung


title: Polyclonal MBCs, 3H3, scATAC-seq

description: Library name: Polyclonal_3H3

value: Polyclonal MBCs


title: OSR1_Bulk

description:
Library name: Sample_W0073_Rn860
Column name in CountMatrix.txt: Sample_W0073_Rn860

value: iPS cells


title: Liver - LKO_HFD_FASTED - Rep6

value: LKO


title: NPC_S-O-

description:
Library name: Sample_W0073_Rn849
Column name in CountMatrix.txt: Sample_W0073_Rn849


title: PC9 cells, normoxic device, 24 hr, rep1


title: PC9 cells, µMeRe device (hypoxic), 24 hr, rep2


title: MSP-1 specific MBCs, 3H3, ADT

description:
Library name: MSP1_3H3_ADT
MSP1_3H3_sample_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
scRNA-seq, CITE-seq and V(D)J-seq were processed using Cell Ranger Multi v7.1.0
V, D and J genes were assigned using IgBLAST.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: sample_filtered_feature_bc_matrix.h5
Supplementary files format and content: IgBLAST output: BCR_data_sequences_igblast_db-pass.tsv
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Memory B cells were flow sorted and run on the 10X Chromium (10X Genomics).
Library preparation was performed according to the manufacturer’s protocol for Chromium Next GEM Single Cell 5’ Reagent Kit v2 with Feature Barcode technology and V(D)J amplification for mouse B cells (10X Genomics).


title: Polyclonal MBCs, rIgG, scATAC-seq

description: Library name: Polyclonal_rIgG


title: NPC_S-O+

description:
Library name: Sample_W0073_Rn848
Column name in CountMatrix.txt: Sample_W0073_Rn848


title: PC9 cells, µMeRe device (hypoxic), 24 hr, rep1


title: NPC_S+O+

description:
Library name: Sample_W0073_Rn847
Column name in CountMatrix.txt: Sample_W0073_Rn847


title: MSP-1 specific MBCs, 3H3, VDJ

description:
Library name: MSP1_3H3_VDJ
BCR_data_sequences_MSP13H3_igblast_db-pass.tsv

data_processing:
scRNA-seq, CITE-seq and V(D)J-seq were processed using Cell Ranger Multi v7.1.0
V, D and J genes were assigned using IgBLAST.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: sample_filtered_feature_bc_matrix.h5
Supplementary files format and content: IgBLAST output: BCR_data_sequences_igblast_db-pass.tsv
Library strategy: scBCR-Seq

molecule: polyA RNA


title: A549 cells, normoxic device, 24 hr, rep2


title: NPC_Bulk

description:
Library name: Sample_W0073_Rn846
Column name in CountMatrix.txt: Sample_W0073_Rn846


title: Liver - LWT_HFD_FED - Rep5

value: LWT

value: FED


title: MSP-1 specific MBCs, 3H3, GEX

description:
Library name: MSP1_3H3_GEX
MSP1_3H3_sample_filtered_feature_bc_matrix.h5


title: A549 cells, normoxic device, 24 hr, rep1

value: cancer cells


title: Liver - LWT_HFD_FASTED - Rep4


title: Liver - LWT_CTRL_FASTED - Rep3


title: MSP-1 specific MBCs, rIgG, ADT

description:
Library name: MSP1_rIgG_ADT
MSP1_rIgG_sample_filtered_feature_bc_matrix.h5


title: Late_PS_OSR1+

description:
Library name: Sample_W0073_Rn844
Column name in CountMatrix.txt: Sample_W0073_Rn844


title: A549 cells, µMeRe device (hypoxic), 24 hr, rep2


title: MSP-1 specific MBCs, rIgG, VDJ

description:
Library name: MSP1_rIgG_VDJ
BCR_data_sequences_MSP1rIgG_igblast_db-pass.tsv


title: Liver - LKO_HFD_FASTED - Rep2


title: Late_PS_Bulk

description:
Library name: Sample_W0073_Rn843
Column name in CountMatrix.txt: Sample_W0073_Rn843


title: MSP-1 specific MBCs, rIgG, GEX

description:
Library name: MSP1_rIgG_GEX
MSP1_rIgG_sample_filtered_feature_bc_matrix.h5


title: H143Desc

description: 640 cells before, 344 cells after filtering

library_source: transcriptomic single cell

data_processing:
Samples were sequenced on Novaseq 6000
The data from sequencer was processed to obtain the fastq sequences using the "cellranger mkfastq" program provided by the vendor (10X genomics).
The raw reads were aligned to the human reference genome (Genome Reference Consortium Human Build 38, GRCh38) and gene expression in cells was quantified using the "cellranger count" program provided by the vendor (10X genomics).
The gene expression data was further processing using the Seurat package (version 4.3), including data filtering, normalization, data dimension reduction, cell clustering, marker identification, cell type identity assignment, and data visualization.
keep cells with all criteria of: genes between 1000 and 5000, UMI between 1500 and 25000, and mitochondria percentage < 15%; keep genes detected in at least 10 cells
Assembly: GRCh38
Supplementary files format and content: filtered matrix, barcodes and features from Cellranger by 10x

source_name: Human aortic desc media

extract_protocol:
Human ascending aorta/aortic arch segments were enzymatically digested, stained with CD45 and CD235a, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye), and CD45 negative, CD235a negative cells were sorted into buffer with 0.04% BSA, and between 600 to 2700 cells from individual aortic segments were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: Human aortic desc media

value: aortic cells


title: A549 cells, µMeRe device (hypoxic), 24 hr, rep1


title: Liver - LKO_HFD_FED - Rep4


title: Liver - LWT_CTRL_FED - Rep1


title: H143Arch

description: 1157 cells before, 593 cells after filtering

source_name: Human aortic arch media

value: Human aortic arch media


title: Polyclonal MBCS, 3H3, VDJ

description:
Library name: Polyclonal_3H3_VDJ
BCR_data_sequences_Polyclonal3H3_igblast_db-pass.tsv

value: Spleen

value: Memory B cells

value: Polyclonal MBCS


title: Middle_PS

description:
Library name: Sample_W0073_Rn842
Column name in CountMatrix.txt: Sample_W0073_Rn842


title: Polyclonal MBCS, 3H3, ADT

description:
Library name: Polyclonal_3H3_ADT
Polyclonal_3H3_sample_filtered_feature_bc_matrix.h5

value: WT


title: Early_PS

description:
Library name: Sample_W0073_Rn841
Column name in CountMatrix.txt: Sample_W0073_Rn841


title: H143Asc

description: 1394 cells before, 943 cells after filtering

source_name: Human ascending aorta media

value: Human ascending aorta media


title: Liver - LWT_HFD_FED - Rep1

value: Liver

value: HFD


title: Liver - LKO_CTRL_FED - Rep1

value: CTRL


title: Polyclonal MBCS, 3H3, GEX

description:
Library name: Polyclonal_3H3_GEX
Polyclonal_3H3_sample_filtered_feature_bc_matrix.h5


title: Late_PS_OSR1-

description:
Library name: Sample_W0073_Rn845
Column name in CountMatrix.txt: Sample_W0073_Rn845


title: Liver - LWT_HFD_FASTED - Rep1

value: FASTED


title: Liver - LKO_CTRL_FASTED - Rep1


title: Control G21 T1

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
Library name: G21T1
Ribo and Globin depleted library

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Assembly: GRCh38
Supplementary files format and content: excel file including raw counts for each sample (columns) across 58096 genes (rows) [counts matrix]

source_name: Whole Blood

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1,T2 and T3 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

value: Whole Blood

tag: Sex

value: Male

tag: patient

tag: timepoint


title: H137Arch

description: 2020 cells before, 1768 cells after filtering

data_processing:
Samples were sequenced on Novaseq 6000
The data from sequencer was processed to obtain the fastq sequences using the "cellranger mkfastq" program provided by the vendor (10X genomics).
The raw reads were aligned to the human reference genome (Genome Reference Consortium Human Build 38, GRCh38) and gene expression in cells was quantified using the "cellranger count" program provided by the vendor (10X genomics).
The gene expression data was further processing using the Seurat package (version 4.3), including data filtering, normalization, data dimension reduction, cell clustering, marker identification, cell type identity assignment, and data visualization.
keep cells with all criteria of: genes between 500 and 4000, UMI between 1000 and 20000, and mitochondria percentage < 15%; keep genes detected in at least 10 cells
Assembly: GRCh38
Supplementary files format and content: filtered matrix, barcodes and features from Cellranger by 10x

source_name: Human aortic arch

extract_protocol:
Human root/ascending aorta/aortic arch segments were enzymatically digested, single (based on SSC-W vs SSC-H and FSC-W vs FSC-H gating), viable (based on exclusion of viability dye) cells were sorted into buffer with 0.04% BSA, and between 1,000 to 3,100 cells from individual aortic segments were analyzed for each sample
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

tag: tissue

value: Human aortic arch


title: Liver - LWT_CTRL_FED - Rep4

source_name: Liver

value: LWT

value: FED


title: Control G13 T2

description:
Library name: G13T2
Ribo and Globin depleted library

value: Female


title: Liver - LWT_HFD_FASTED - Rep6


title: Polyclonal MBCs, rIgG, VDJ

description:
Library name: Polyclonal_rIgG_VDJ
BCR_data_sequences_PolyclonalrIgG_igblast_db-pass.tsv

value: Polyclonal MBCs

value: rIgG


title: Liver - LWT_CTRL_FED - Rep2


title: Polyclonal MBCs, rIgG, GEX

description:
Library name: Polyclonal_rIgG_GEX
Polyclonal_rIgG_sample_filtered_feature_bc_matrix.h5

value: Spleen


title: H137Root

description: 1212 cells before, 1084 cells after filtering

source_name: Human aortic root

value: Human aortic root

value: aortic cells


title: Control G13 T1

description:
Library name: G13T1
Ribo and Globin depleted library


title: Control E39 T2

description:
Library name: E39T2
Ribo and Globin depleted library


title: TPKP_ENZ-B_RNA-seq

city: shanghai

first: jiacheng

last: guo

address: yueyang road 320

institute: Shanghai Institute of Nutrition and Health

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The read length was 2×150 bp. The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per million mapped reads) using Perl. Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package in R between different groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM  values for each sample

extract_protocol:
RNA was extracted using Trizol purification from prostate epithelial cells or organoids, 1µg total RNA was used for the construction of sequencing libraries
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina) following manufacturer's protocols

value: prostate organoid

value: prostate

value: ENZ


title: Ascending_C46

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0)
Gene expression levels were quantified using StringTie (v1.3.3b) with gene models (v27) from the GENCODE project
Differentially expressed genes were identified using DESeq2 (v 1.22.1)
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

source_name: Ascending aorta

extract_protocol:
Human aortas were procured and total RNA was extracted via RNeasy Mini Kit from QIAGEN (cat. 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols with rRNA depletion

value: Ascending aorta


title: TPKP_ENZ-A_RNA-seq


title: Control E39 T1

description:
Library name: E39T1
Ribo and Globin depleted library


title: H143Root

description: 2692 cells before, 1971 cells after filtering

source_name: Human aortic root media

value: Human aortic root media


title: Polyclonal MBCs, rIgG, ADT

description:
Library name: Polyclonal_rIgG_ADT
Polyclonal_rIgG_sample_filtered_feature_bc_matrix.h5

value: Memory B cells

value: WT


title: H137Asc

description: 3148 cells before, 2464 cells after filtering

source_name: Human ascending aorta

value: Human ascending aorta


title: Liver - LWT_CTRL_FASTED - Rep1

value: Liver

value: CTRL

value: FASTED


title: Root_C45

source_name: Aortic root

value: Aortic root


title: TPK_ENZ-B_RNA-seq


title: Control E23 T2

description:
Library name: E23T2
Ribo and Globin depleted library

value: Whole Blood

value: Male


title: Control G21 T2

description:
Library name: G21T2
Ribo and Globin depleted library


title: TPK_ENZ-A_RNA-seq


title: Control E23 T1

description:
Library name: E23T1
Ribo and Globin depleted library


title: Liver - LWT_HFD_FED - Rep2

value: LWT

value: HFD

value: FED


title: Descending_C30

source_name: Descending aorta

value: Descending aorta

value: aortic cells


title: Control E01 T2

description:
Library name: E01T2
Ribo and Globin depleted library

value: Female


title: TP_ENZ-B_RNA-seq

source_name: prostate

value: prostate organoid

value: prostate

value: Tmprss2CreERT2; Ptenflox/flox

value: ENZ


title: Liver - LKO_CTRL_FASTED - Rep6

value: LKO


title: Arch_C29

source_name: Aortic arch

value: Aortic arch


title: Liver - LKO_HFD_FASTED - Rep5

value: Liver


title: Liver - LKO_CTRL_FED - Rep6

value: CTRL


title: Control E01 T1

description:
Library name: E01T1
Ribo and Globin depleted library


title: Root_C52

value: Aortic root


title: Liver - LKO_HFD_FED - Rep1


title: Ascending_C28

value: Ascending aorta


title: TP_ENZ-A_RNA-seq


title: PAH,rep3

city: Jining

first: Hongwei

last: Fu

state: Shandong

address: No. 45 Jianshe South Road, Rencheng District

country: Singapore

institute: Jining Medical University

description: Library name: SAMPLE 12

data_processing:
Data filtering
Comparative analysis
Expression analysis
Functional analysis
Selective shear analysis
Assembly: rn7
Supplementary files format and content: tab-delimited text file includes raw counts for each example

organism: Rattus norvegicus

source_name: Pulmonary artery

extract_protocol:
Sample purity detected by Nanof Hortomel ® spectrophotometer (Thermofischer Semerfiche); Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA) was used to test RNA samples Integrity and concentration of the product.
The 3' end of eukaryotic mRNA had a polyA tail structure, and magnetic beads with Oligo(dT) were used for enrichment and purification. Fragmentation Buffer is added to the purified mRNA to make the fragments short. Then, the fragmented RNA was used as a template, and the first strand of cDNA was synthesized by random primers for reverse transcription, and the second strand of cDNA was synthesized by adding 2nd Strand Marking Buffer and 2nd Strand/End Repair Enzyme Mix. After end repair, base A was added, sequencing adapter was added, the target fragment was recovered by magnetic bead screening, and PCR amplification was carried out to complete the entire library preparation.

value: Pulmonary artery

value: H


title: PPK_ADT-B_RNA-seq

value: prostate epithelium

value: PtenPC-/-; Kmt2cPC-/-

value: ADT


title: Arch_C23

value: aortic cells


title: PPK_ADT-A_RNA-seq


title: Ascending_C22


title: PAH,rep1

description: Library name: SAMPLE 10


title: PP_ADT-B_RNA-seq

value: PtenPC-/-


title: Root_C21


title: PAC,rep4

description: Library name: SAMPLE 9

value: C


title: Liver - LKO_CTRL_FED - Rep3

value: FED


title: PPK-B_RNA-seq

value: prostate

value: sham


title: PP_ADT-A_RNA-seq


title: PAC,rep2

description: Library name: SAMPLE 8


title: Descending_C18

value: Descending aorta


title: PPK-A_RNA-seq


title: Root_C27


title: PAC,rep1

description: Library name: SAMPLE 7


title: Ascending_C16


title: MAH,rep3

description: Library name: SAMPLE 6

source_name: Mesenteric artery

value: Mesenteric artery


title: PP-B_RNA-seq


title: PAH,rep2

description: Library name: SAMPLE 11


title: HFFF cells infected with HSV-1 WT strain 17, histone H2A.Z, replicate 3

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

library_source: genomic

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Assembly: GRCh37/hg19
Supplementary files format and content: bedGraph

source_name: foreskin

growth_protocol: HFFFs were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected with WT HSV-1 strain 17 at an MOI of 10.

extract_protocol:
Samples were processed according to the ChIPmentation protocol with few adjustments indicated in Materials and Methods (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015)
See Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015, Oct;12(10):963-965. doi: 10.1038/nmeth.3542. Epub 2015 Aug 17. PMID: 26280331; PMCID: PMC4589892.

treatment_protocol: Cells were infected with WT HSV-1 for 15 min using an MOI of 10. Samples were crosslinked and collected at 8 h p.i. and afterwards processed according to the ChIPmentation protocol.

value: foreskin

tag: cell line

value: Human fetal foreskin fibroblasts

value: HSV-1 WT, strain 17, infection

tag: time post_infection

value: 8 h p.i.

value: anti-H2A.Z (Diagenode, #C15410201)


title: Liver - LKO_CTRL_FASTED - Rep2

value: Liver

value: LKO

value: CTRL

value: FASTED


title: PP-A_RNA-seq

tag: cell type

value: prostate epithelium


title: HFFF cells mock infected, histone H2A.Z, replicate 3

value: mock infection

value: no infection


title: Liver - LKO_HFD_FASTED - Rep4

value: HFD


title: Liver - LWT_HFD_FASTED - Rep2

value: LWT


title: Liver - LWT_CTRL_FED - Rep5

value: FED


title: Root_C15

value: Aortic root

value: aortic cells


title: Group C colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 21 passages

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

hyb_protocol: Bisulphite converted DNA was amplified,fragmented and hybridized to human Infinium Methylation EPIC v2.0 BeadChip using standard lllumina protocol

scan_protocol: Arrays were imaged using illumina iscan scanner and standard recommended Illumina scanner setting

data_processing: The data is analyzed using GenomeStudio software (illumina)

label: Cy3 and Cy5

label_protocol: Standard lllumina Protocol

growth_protocol: HT-29 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium, supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100μg/mL)

extract_protocol: DNA was extracted from cell pellet using TIANamp Genomic DNA Kit (TIANGEN)

treatment_protocol: Control group was treated with DMSO and experimental group was treated with MG132 (0.2 µM)

value: colorectal cancer cells


title: Ascending_C14

value: Ascending aorta


title: HFFF cells infected with HSV-1 WT  strain 17, histone H2A.Z, replicate 2

value: foreskin

value: Human fetal foreskin fibroblasts

value: HSV-1 WT, strain 17, infection


title: Liver - LWT_HFD_FED - Rep4

value: Liver


title: Liver - LKO_HFD_FED - Rep5

value: LKO


title: MAC,rep3

description: Library name: SAMPLE 3

value: Mesenteric artery

value: C


title: Liver - LWT_CTRL_FASTED - Rep4

value: CTRL

value: FASTED


title: HFFF cells mock infected, histone H2A.Z, replicate 2

value: mock infection

value: no infection

value: anti-H2A.Z (Diagenode, #C15410201)


title: TP-AR_restore-KMT2C_CUT&Tag

description: Library name: Sample 24

data_processing:
Cuttag-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2 and an initial threshold q-value of 0.01 as cutoff.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Assembly: mm10
Supplementary files format and content: Bigwig file of annotated prostate tumor organoid sequencing results
Library strategy: CUT&Tag

extract_protocol:
Extract the organoids or sorted cells according to the instructions of Vazyme's Cuttag-Kit.
Follow the instructions of Vazyme's Cuttag-Kit to build the library.

value: prostate organoid

value: prostate

value: Tmprss2CreERT2; Ptenflox/flox


title: Arch_C17

value: Aortic arch

value: aortic cells


title: Group A colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 21 passages

value: colorectal cancer cells


title: MAH,rep2

description: Library name: SAMPLE 5

value: H


title: HFFF cells infected with HSV-1 WT  strain 17, histone H2A.Z, replicate 1

value: foreskin

value: Human fetal foreskin fibroblasts

value: HSV-1 WT, strain 17, infection

value: 8 h p.i.


title: MAC,rep1

description: Library name: SAMPLE 1

value: Mesenteric artery

value: C


title: Group C colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 14 passages


title: TP-AR_restore-AR_CUT&Tag

description: Library name: Sample 23


title: TPK-ENZ_ATAC

description: Library name: Sample 4

data_processing:
ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2 and an initial threshold q-value of 0.01 as cutoff.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Assembly: mm10
Supplementary files format and content: Bigwig file of annotated prostate tumor organoid sequencing results

extract_protocol:
Extract organoids or sort cells according to the instructions of the Novoprotein ATAC-Kit.
Build the library according to the instructions of Novoprotein ATAC-Kit

value: ENZ


title: HFFF cells mock infected, histone H2A.Z, replicate 1

value: mock infection


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq3_S9

city: Paris

first: Yimin

last: SHEN

state: Val-de-Marne

address: 27 Rue Juliette Dodu

institute: Fondation Jean Dausset-CEPH

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq3_S9
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt

data_processing:
analyzed with different types of second and third generation sequencing protocols (see workflow of the different bioinformatic analyses ), then analyzed using the same microsatellite identification method based on the recognition of the 4 consecutive regions: (i), (ii), (iii) and (iv)
Assembly: other sequences
Supplementary files format and content: microsatellite profil text files

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Plasmid preparation
Illumina sequencing: QIAseq 1-Step Amplicon Library Kit (Qiagen), QIAseq FX DNA Library Kit (Qiagen), and xGen Prism DNA Library Prep Kit (Integrated DNA Technologies). PacBio sequencing: SMRTbell prep kit 3.0 (PacificBiosciences) and SMRTbell binding kit 2.0 (Pacific Biosciences). Nanopore sequencing : Native Barcoding Kit 96 V14 (Oxford Nanopore Technologies (ONT)) together with NEBNext® Ultra II End Repair / dA-tailing Module (New England Biolabs (NEB)), NEB Blunt/TA Ligase Master Mix (NEB), and NEBNext® Quick Ligation Module (NEB).

value: synthetic construct


title: Group B colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 14 passages


title: MAH,rep1

description: Library name: SAMPLE 4


title: Group A colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 14 passages


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq3_S6

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq3_S6
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt


title: TPK-Veh_ATAC

description: Library name: Sample 3

value: Veh.


title: TP-ENZ_ATAC

description: Library name: Sample 2

value: prostate organoid


title: Group B colorectal cancer cells HT-29 treated with MG132 (0.2 µM) for 21 passages


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq2_S9

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq2_S9
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt


title: HSV-1 lacking expression of ICP4, replicate 2

source_name: human fetal foreskin fibroblasts

growth_protocol: Human fetal foreskin fibroblasts were cultured in DMEM supplemented with 10% FBS, non-essential amino acids and P/S. Cells were infected at 60-80% confluency 24h after seeding (100000 cells/condition).

extract_protocol:
Infected cells were harvested by scraping at the indicated time points, washed, lysed with mild lysis buffer according to the published ATAC-seq protocol, incubated with Tn5 transposase (tagmentase) for 30 minutes, lysed in Qiagen's PB buffer, DNA purified according to the MinElute protocol.
12 PCR cycles according to the Illumina Nextera protocol using barcoded Nextera Primers.

treatment_protocol: HFFF cells were inoculated for 15 minutes with an MOI of 10 and the time of the experiment started after the inoculum was removed.

value: human fetal foreskin fibroblasts

value: 8 hpi

tag: hsv-1 strain

value: strain KOS, n12 (delta-ICP4)


title: MAC,rep2

description: Library name: SAMPLE 2


title: Group B colorectal cancer cells HT-29 treated with DMSO

description: CtrlB

value: DMSO


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq2_S6

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq2_S6
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt


title: HSV-1 lacking expression of UL41, replicate 1 [reanalysis]

description:
dVHS_1
GSM5608534

value: strain 17, delta-vhs


title: TP-Veh_ATAC

description: Library name: Sample 1

value: prostate

tag: genotype

value: Tmprss2CreERT2; Ptenflox/flox


title: Group A colorectal cancer cells HT-29 treated with DMSO

description: CtrlA

value: colorectal cancer cells


title: HSV-1 lacking expression of UL41, replicate 2 [reanalysis]

description:
dVHS_2
GSM5608535


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq1_S9

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq1_S9
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt


title: HSV-1 lacking expression of ICP27, KOS, replicate 2 [reanalysis]

description:
dICP27_2
GSM5608533

value: strain KOS, 27LacZ


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles20,iSeq1_S6

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.iSeq1_S6
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles20.proportion.txt


title: TPK-ENZ-SREBF1C_CUT&Tag


title: 300mM_14d_3

city: Guangzhou

first: Yuchen

last: Yang

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
All the high-quality reads were merged together, and de novo assembled using Trinity to build a reference transcriptome for Hernandia nymphaeifolia. Reads of each sample were aligned to the constructed reference genome via hisat2 program
Gene counts were obtained using salmon.
Assembly: A reference transcriptome for Hernandia nymphaeifolia assembled using Trinity. FASTA file included on series record.
Supplementary files format and content: One csv file containing raw count values for each sample and one fasta file containing assembled reference transcriptome for Hernandia nymphaeifolia

organism: Hernandia nymphaeifolia

source_name: leaf

growth_protocol: H. nymphaeifolia seedlings used in this study were raised in the Agricultural Science Garden of Hainan University, Haikou, Hainan, China (20°3′33.35″N, 110°19′24.88″E). The average temperature during the experimental period was 26℃, with a maximum temperature of 31℃ and a minimum temperature of 17 ℃. The 2-year-old seedlings with good and similar growth status (~30 cm in height and with 6-9 leaves) were selected for the experiments.

extract_protocol:
Total RNAs was extracted from the leaves of each plant using OMEGA Plant RNA Kit
DNA nanoballs (DNBs) were prepared following manufacturer’s instruction

treatment_protocol: These seedlings were then assigned into five groups, where one group was treated with fresh water as control (CK), while the other four groups were treated with saline water at different NaCl gradients (150, 300, 500 and 700 mM). Each treatment consisted of three individuals as three biological replicates. To mimic the semi-diurnal tide under natural condition, the seedlings were submerged to the height of the branches for 3h every 12 h. During the experiment, water and fertilizer management, as well as pest and disease control, were carried out to guarantee the health growth, and the pot position was adjusted randomly each week to ensure same light condition for each individual.

value: leaf

value: 300mM NaCl for 14d


title: TPK-ENZ-ΔNp63_CUT&Tag


title: TPK-Veh-ΔNp63_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq3_S8

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq3_S8
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt


title: TP-ENZ-ΔNp63_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq3_S5

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq3_S5
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt


title: 300mM_14d_2


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 4 [reanalysis]

description:
dICP22_4
GSM5608529

value: 12 hpi

value: strain F, R325


title: 300mM_14d_1


title: Group C colorectal cancer cells HT-29 treated with DMSO

description: CtrlC


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq2_S8

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq2_S8
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt


title: TP-Veh-ΔNp63_CUT&Tag


title: HSV-1 lacking expression of ICP27, KOS, replicate 1 [reanalysis]

description:
dICP27_1
GSM5608532


title: 300mM_7d_3

value: 300mM NaCl for 7d


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 3 [reanalysis]

description:
dICP22_3
GSM5608528


title: TPK-ENZ-AR_CUT&Tag


title: HSV-1 lacking expression of ICP4, replicate 1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq2_S5

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq2_S5
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt

value: synthetic construct


title: 300mM_7d_2


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 2 [reanalysis]

description:
dICP22_2
GSM5608527


title: TPK-Veh-AR_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq1_S8

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq1_S8
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt


title: HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 1 [reanalysis]

description:
dICP22_1
GSM5608526


title: HSV-1 lacking expression of ICP0, replicate 2 [reanalysis]

description:
dICP0_2
GSM5608525

value: strain 17, dl1403


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles16,iSeq1_S5

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.iSeq1_S5
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles16.proportion.txt


title: CK_3

value: CK


title: HSV-1 lacking expression of ICP0, replicate 1 [reanalysis]

description:
dICP0_1
GSM5608524

value: human fetal foreskin fibroblasts


title: TP-Veh-AR_CUT&Tag

value: prostate organoid


title: 300mM_7d_1


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles10,iSeq3_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.iSeq3_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.proportion.txt


title: CK_2


title: HSV-1 wt, strain 17, +PAA, replicate 2 [reanalysis]

description:
WT_plus_PAA_2
GSM5608523

value: 10 hpi

value: PAA 300ug/ml

value: strain 17


title: HSV-1 wt, strain 17, +PAA, replicate 1 [reanalysis]

description:
WT_plus_PAA_1
GSM5608522

value: 9 hpi


title: CK_1


title: TPK-ENZ-H3K4me3_CUT&Tag

value: prostate


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles10,iSeq1_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.iSeq1_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.proportion.txt


title: TPK-ENZ-Kmt2c_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles10,iSeq2_S7

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.iSeq2_S7
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles10.proportion.txt


title: TP-ENZ-Kmt2c_CUT&Tag

value: Tmprss2CreERT2; Ptenflox/flox


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles5,iSeq2_S4

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.iSeq2_S4
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles5,iSeq3_S4

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.iSeq3_S4
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.proportion.txt


title: HSV-1 wt, strain 17, replicate 2 [reanalysis]

description:
WT_2
GSM5608521

value: 8 hpi


title: HSV-1 wt, strain 17, replicate 1 [reanalysis]

description:
WT_1
GSM5608520


title: TPK-Veh-Kmt2c_CUT&Tag


title: Mediastinal lymph node biol rep 3, BCR

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
Library name: Sample 7 BCR
5' VDJ library: read1 contains 10X cell barcode and UMI; read2 file contains BCR transcript

data_processing:
*library strategy: BCR-seq
Data was processed with 10X Genomics Cell Ranger multi (v9.0.0). Transcriptome data was mapped using 10X mm10-2020-A reference, contigs were assembled using 10X reference vdj_GRCm38_alts_ensembl-7.0.0
Assembly: Mus musculus : GRCm38
Supplementary files format and content: Cell Ranger output files for individual samples: HDF5 filtered feature matrix
Supplementary files format and content: Cell Ranger output files for individual samples: filtered contig annotations in csv format

source_name: Mediastinal lymph node

extract_protocol:
The lung and mediastinal lymph node were dissected from the same mouse (i.e. lymph node 1 is paired with lung 1, lymph node 3 is paired with lung 3). Lymph node samples were pressed through a wet 70 µm cell strainer, before being washed through with 3 mL of flow buffer (PBS + 2% FBS + 1 mM EDTA). Lungs were chopped using scissors before being digested for 30 minutes at 37°C in a 500RPM shaker, in RPMI containing 100 µg/mL Liberase TL (Roche, Basel, Switzerland) and 100 µg/mL DNase I (Roche). Lung pieces were then pressed through a wet 70 µm cell strainer. Lung samples were resuspended in ACK red cell lysis buffer, incubated for 5 minutes and then washed and resuspended in flow buffer. Cells were washed and resuspended in a fluorescently-conjugated antibody cocktail made up in flow buffer and stained for 1 hour. Live isotype-switched endogenous germinal centre B cells (CD45.2+B220+CD19+IgD-CD95+CD38-) and memory B cells (CD45.2+B220+CD19+IgD-CD95-CD38+) were sorted using a FACSAria Fusion (Becton Dickinson). Cells were sorted into flow buffer and prepared for 10x sequencing.
Library was performed according to the manufacturer's instructions (single cell 5' v2 protocol, 10x Genomics). Briefly, FACS sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identified (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: B1-8i adoptive cell transfer, followed by NP-KLH/HDM administration on days 0, 2, 4, 7. Mice were culled at 21 days post-transfer.

value: Mediastinal lymph node

value: B1-8i, NP-KLH/HDM x4


title: Lung biol rep 1, BCR

description:
Library name: Sample 6 BCR
5' VDJ library: read1 contains 10X cell barcode and UMI; read2 file contains BCR transcript

source_name: Lung

value: Lung


title: mock infection, replicate 2 [reanalysis]

description:
Mock_2
GSM5608519

value: no infection


title: Lung biol rep 3, BCR

description:
Library name: Sample 8 BCR
5' VDJ library: read1 contains 10X cell barcode and UMI; read2 file contains BCR transcript


title: TP-ENZ-AR_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles5,iSeq1_S4

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.iSeq1_S4
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles5.proportion.txt


title: mock infection, replicate 1 [reanalysis]

description:
Mock_1
GSM5608518


title: Mediastinal lymph node biol rep 1, BCR

description:
Library name: Sample 5 BCR
5' VDJ library: read1 contains 10X cell barcode and UMI; read2 file contains BCR transcript


title: TP-Veh-Kmt2c_CUT&Tag


title: TPK-ENZ-H3K27ac_CUT&Tag


title: Lung biol rep 3, GEX

description:
Library name: Sample 8 GEX
5' GEX library: read1 contains 10X cell barcode and UMI; read2 file contains transcript

data_processing:
Data was processed with 10X Genomics Cell Ranger multi (v9.0.0). Transcriptome data was mapped using 10X mm10-2020-A reference, contigs were assembled using 10X reference vdj_GRCm38_alts_ensembl-7.0.0
Assembly: Mus musculus : GRCm38
Supplementary files format and content: Cell Ranger output files for individual samples: HDF5 filtered feature matrix
Supplementary files format and content: Cell Ranger output files for individual samples: filtered contig annotations in csv format


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles2,iSeq2_S3

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.iSeq2_S3
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.proportion.txt


title: TPK-Veh-H3K27ac_CUT&Tag


title: TP-ENZ-H3K27ac_CUT&Tag


title: Mediastinal lymph node biol rep 3, GEX

description:
Library name: Sample 7 GEX
5' GEX library: read1 contains 10X cell barcode and UMI; read2 file contains transcript


title: Lung biol rep 1, GEX

description:
Library name: Sample 6 GEX
5' GEX library: read1 contains 10X cell barcode and UMI; read2 file contains transcript


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles2,iSeq1_S3

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.iSeq1_S3
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.proportion.txt


title: TP-Veh-H3K27ac_CUT&Tag


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles1,iSeq3_S2

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.iSeq3_S2
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles1,iSeq2_S2

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.iSeq2_S2
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.proportion.txt


title: Mediastinal lymph node biol rep 1, GEX

description:
Library name: Sample 5 GEX
5' GEX library: read1 contains 10X cell barcode and UMI; read2 file contains transcript


title: Mouse melanoma Cd45 cells, 20M

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
PIP-seq samples were processed using Pipseeker pipeline version 2.1.3, STAR aligner version 2.7.10a, mouse genome version GRCm38, and Gencode annotations version M25.
Assembly: GRCm38
Supplementary files format and content: Counts matrix, barcodes, and features output from Pipseeker pipeline

source_name: Melanoma

growth_protocol: YUMM1.7 cells were cultured in DMEM media with 10% FBS. Mice were injected subcutaneously (s.c.) with 500,000 YUMM1.7 cells.

extract_protocol:
4-, 12-, and 20-months old mice (7 mice for each age) were sacrificed 18 days after tumor cell inoculation. Tissues were excised, minced, and digested with 1 mg/ml collagenase D (Roche) and 100 µg/ml DNase I (Sigma) at 37°C for 45 minutes. Digests were then passed through a 70-μm cell strainer to generate a single-cell suspension. Single cell suspensions were washed with 1XPBS-4%FBS before incubation for 20 min on ice at 5•107 cells/ml with 500 ng/ml Fc block (2.4G2, BD Pharmingen). Cells were then incubated for 1 hour on ice with AF700 conjugated CD45.2 monoclonal antibody (104, Biolegend). For scRNA-seq libraries, DAPI negative (live) CD45+ cells were sorted using a flow cytometer, and sorted cells were resuspended in RPMI for counting.
Libraries were prepared using the Fluent Biosciences PIP-seq v4.0 Plus T20 3’ Single Cell RNA kit according to the User Guide. Libraries were sequenced on an Element Biosciences AVITI sequencer with 60x100bp sequencing to a read depth of 20k – 27k reads per cell.

value: Melanoma


title: TPK-ENZ-H3K4me1_CUT&Tag


title: TPK-Veh-H3K4me1_CUT&Tag


title: TP-ENZ-H3K4me1_CUT&Tag


title: Mouse melanoma Cd45 cells, 12M


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles2,iSeq3_S3

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.iSeq3_S3
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles2.proportion.txt

value: synthetic construct


title: PBS(Cy5) x PACAP(Cy3) Treatment in HCEC2 Wound assay at 18hr

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of PBS vs PACAP Treatment in HCEC2 Wound assay at 18hr

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Agilent Technologies Scanner G2505C US82800151

data_processing: Software: Feature Extraction ver 12.0.3.1

source_name: 18hr scratch+PACAP treated HCEC2 cells Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Normal human corneal epithelial cells (HCEC2, KC-4009) were obtained from Kurabo Industries Ltd., (Osaka, Japan). Cells were cultivated in OcuLife BM (basal medium; LCB-LM0012, Kurabo) using a CO2 incubator (37ºC, 5%) in conjunction with OcuLife LifeFactorsLCK-LS1057, Kurabo) and antibiotics (Gentamicin/Amphotericin, Kurabo, Japan).

extract_protocol: QIAGEN, Rneasy Micro kit

treatment_protocol: A HCEC2 cell solution (7×103 to 9×103 cells in 100 μL/well) was seeded in a 96 well microplate. After 24 hours, the medium was replaced with basal medium (OcuLife BM) and scratches were created with a yellow tip. PACAP was added to the cell culture medium at concentrations of 10-7 M, 10-9 M, and 10-11 M after scratches.

source_name: 18hr scratch+PBS treated HCEC2 cells Cy5


title: PBS(Cy3) x PACAP(Cy5) Treatment in HCEC2 at 18hr

description: Dye-swap (Cy3/Cy5) of PBS vs PACAP treated HCEC2 cells at 18hr

source_name: 18hr PBS treated HCEC2 cells Cy3

value: Normal human corneal epithelial cells (HCEC2, KC-4009)

source_name: 18hr PACAP treated HCEC2 cells Cy5


title: PBS(Cy5) x PACAP(Cy3) Treatment in HCEC2 at 18hr

description: Dye-swap (Cy5/Cy3) of PBS vs PACAP treated HCEC2 cells at 18hr

source_name: 18hr PACAP treated HCEC2 cells Cy3

source_name: 18hr PBS treated HCEC2 cells Cy5


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles0,iSeq3_S1

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.iSeq3_S1
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.proportion.txt


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles0,iSeq2_S1

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.iSeq2_S1
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.proportion.txt


title: TP-Veh-H3K4me1_CUT&Tag

source_name: prostate


title: PBS(Cy5) x PACAP(Cy3) Treatment in HCEC2 Wound assay at 3hr

description: Dye-swap (Cy5/Cy3) of PBS vs PACAP Treatment in HCEC2 Wound assay at 3hr

source_name: 3hr scratch+PACAP treated HCEC2 cells Cy3

source_name: 3hr scratch+PBS treated HCEC2 cells Cy5


title: TPK-ENZ-ATAC


title: PDO-WGH_KMT2C-T316S_H3K4me1

description: Library name: Sample 26

value: A patient-derived organoid with mutations in APC c.4666dupA, p.Thr1556AsnfsTer3; TP53 c.419_425delinsT, p.Thr140_Pro142delinsIle; NPM1 c.353C>T, p.Ala118Val; ADGRG6 c.1415A>C, p.Asp472Ala; STAT3 c.1295T>C, p.Val432Ala.


title: PBS(Cy3) x PACAP(Cy5) Treatment in HCEC2 Wound assay at 18hr

description: Dye-swap (Cy3/Cy5) of PBS vs PACAP Treatment in HCEC2 Wound assay at 18hr

source_name: 18hr scratch+PBS treated HCEC2 cells Cy3

source_name: 18hr scratch+PACAP treated HCEC2 cells Cy5


title: PBS(Cy3) x PACAP(Cy5) Treatment in HCEC2 at 3hr

description: Dye-swap (Cy3/Cy5) of PBS vs PACAP treated HCEC2 cells at 3hr

source_name: 3hr PBS treated HCEC2 cells Cy3

source_name: 3hr PACAP treated HCEC2 cells Cy5


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles0,iSeq1_S1

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.iSeq1_S1
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles0.proportion.txt

source_name: synthetic construct


title: PBS(Cy5) x PACAP(Cy3) Treatment in HCEC2 at 3hr

description: Dye-swap (Cy5/Cy3) of PBS vs PACAP treated HCEC2 cells at 3hr

source_name: 3hr PACAP treated HCEC2 cells Cy3

source_name: 3hr PBS treated HCEC2 cells Cy5


title: ML1

status: Public on Feb 26 2025

city: Lexington

first: Kinga

middle: B.

last: Graniczkowska

state: KY

address: 675 Rose St

department: Biology

institute: University of Kentucky

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads.
Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting.
STAR Aligner version 2.7.1a was used to align the reads.
Picard tools (version 2.20.4) was applied to mark duplicates of mapping.
The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts and calculate FPKM values.
Assembly: NC_008095.1 and  CP002830.1
Supplementary files format and content: Comma Separated Values file containing normalize counts for M.macrosporus
Supplementary files format and content: Comma Separated Values file containing normalize counts for M. xanthus

organism: Corallococcus macrosporus

source_name: bacterial cells

growth_protocol: Bacteria were grown in CTTYE 1% casitone (Difco, Franklin Lakes, NJ), 10 mM Tris-HCl (pH 7.6), 1 mM KH2PO4, 8mM MgSO4) broth for 36 hours at 33°C in constant darkness or in 12:12 light-dark cycle, we implemented white light (380 lux).

extract_protocol:
Total RNA was isolated using the hot phenol method followed by ribosomal RNA (rRNA) depletion implementing previously validated protocol (Sharma 2021). Briefly, approximately 4 μg total RNA was mixed with 10× hybridization buffer (1 M Tris-HCl (pH 7.0), 2 M NaCl, RNase-free H2O), 2 μL 16S and 23S synthetic DNA oligonucleotide probes (developed by our lab previously (Sharma 2021)), and RNase-free H2O. Hybridization was performed at 45°C for 5 min. Hybridization reaction was treated with thermostable RNaseH (NEB, M0523S) and corresponding buffer, followed by incubation at 45 °C for 40 min. The reaction was transferred to ice and then treated with RNase-free DNaseI (NEB, M0303S) according to manufacturers protocol. The DNaseI treated samples were shifted to ice then followed with an Agencourt RNAClean™ XP bead cleanup (Beckman Coulter, Brea, CA) with a 1.8× volume of beads to sample as per manufacturers protocol. RNA samples depleted of rRNAs were eluted off the beads in RNase-free H2O.
Libraries were generated using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB #E7765), according to manufacturer’s protocol without without PolyA selection and rRNA depletion steps.

treatment_protocol: Transcription was stopped immediately upon collection using stop solution (5% acidic phenol in ethanol (Rhodius, 2009)), centrifuged at 3000 rpm and 4 °C, bacterial pellets were frozen in liquid nitrogen, and stored at −80 °C until the extraction.

value: bacterial cells

value: light


title: PBS(Cy3) x PACAP(Cy5) Treatment in HCEC2 Wound assay at 3hr

description: Dye-swap (Cy3/Cy5) of PBS vs PACAP Treatment in HCEC2 Wound assay at 3hr

source_name: 3hr scratch+PBS treated HCEC2 cells Cy3

source_name: 3hr scratch+PACAP treated HCEC2 cells Cy5


title: MD4

value: dark


title: TypeI,QIAseq1-StepAmpliconLibraryKit,Illumina,iSeq100,PCRcycles1,iSeq1_S2

description:
Library name: TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.iSeq1_S2
Type I
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.count.txt
TypeI_QIAseq1-StepAmpliconLibraryKit_Illumina_iSeq100_PCRcycles1.proportion.txt


title: MD3


title: MD2


title: Mouse melanoma Cd45 cells, 4M

source_name: Melanoma


title: MD1


title: MxD22

organism: Myxococcus xanthus


title: MxD12


title: MxD1


title: MxL22


title: MxL2


title: MxL1


title: PDO-WGH_KMT2C-WT_H3K4me1

description: Library name: Sample 25

value: prostate organoid


title: MxL12


title: ML4


title: ML3


title: ML2


title: Subject UAMS45 F

type: protein

city: Stanford

first: Allan

last: Feng

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description:
raw data file: Protein Fragment Array Platform Raw MFI.xlsx
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: Barebeed MFI values were subtracted from the MFI values for all analytes in each sample and replicate MFI values were averaged.

label: R-PE conjugated goat anti-human IgG secondary antibody

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from iMCD patients, Hodgkin lymphoma patients, and healthy controls. Blood was then processed into serum or plasma.

tag: condition

value: iMCD patient


title: Subject UAMS43 F


title: Subject UAMS42 F


title: Subject UAMS40 F


title: Subject UAMS39 R


title: Subject UAMS44 F


title: Subject UAMS41 R


title: Subject UAMS36 F


title: Subject UAMS38 F


title: MxD2


title: Subject UAMS35 R


title: Subject UAMS34 F


title: Subject UAMS30 R


title: Subject UAMS32 F


title: Subject UAMS33 R


title: Subject UAMS26 R


title: Subject UAMS25 R


title: Subject UAMS28 R


title: Subject UAMS29 R


title: Subject UAMS27 R


title: Subject UAMS24 R


title: Subject UAMS21 R


title: Subject UAMS19 R


title: Subject UAMS20 F


title: Subject UAMS22 R


title: Subject UAMS17 F


title: Subject UAMS18 R


title: Subject UAMS37 R


title: Subject UAMS31 F


title: Subject UAMS16 R


title: Subject UAMS11 R


title: Subject UAMS14 R


title: Subject UAMS10 R


title: Subject UAMS12 R


title: Subject UAMS23 R


title: Subject UAMS07 R


title: Subject UAMS08 R


title: Subject UAMS06 F


title: Subject UAMS09 R


title: Subject UAMS15 R


title: Subject UAMS03


title: Subject UAMS04


title: Subject UAMS02


title: Subject UAMS05


title: Subject HC49 (only used in UAMS cohort screen)

value: Healthy control


title: Subject HC50 (only used in UAMS cohort screen)


title: Subject HC47 (only used in UAMS cohort screen)


title: Subject UAMS01


title: Subject HC46 (only used in UAMS cohort screen)


title: Subject HC43 (only used in UAMS cohort screen)


title: Subject HC48 (only used in UAMS cohort screen)


title: Subject HC45 (only used in UAMS cohort screen)


title: Subject HC44 (only used in UAMS cohort screen)


title: Subject HC42 (only used in UAMS cohort screen)


title: Subject HC41 (only used in UAMS cohort screen)


title: Subject UAMS13 F


title: Subject HC39 (only used in UAMS cohort screen)


title: Subject HC40 (only used in UAMS cohort screen)


title: Subject HC38 (only used in UAMS cohort screen)


title: Subject HC35 (only used in UAMS cohort screen)


title: Subject UP38 F


title: Subject HC32 (only used in UAMS cohort screen)


title: Subject HC37 (only used in UAMS cohort screen)


title: Subject HC33 (only used in UAMS cohort screen)


title: Subject HC36 (only used in UAMS cohort screen)


title: Subject HC34 (only used in UAMS cohort screen)


title: Subject UP37 F


title: Subject UP26 R


title: Subject UP27 F


title: Subject HC31 (only used in UAMS cohort screen)


title: Subject UP29 R


title: Subject UP28 R


title: Subject UP32 F


title: Subject UP34 F


title: Subject UP35 F


title: Subject UP31 R


title: Subject UP33 F


title: Subject UP36 F


title: Subject UP24 F


title: Subject UP22 R


title: Subject UP25 R


title: Subject UP23 F


title: Subject UP20 R


title: Subject UP19 R


title: Subject UP18 R


title: Subject UP17 R


title: Subject UP21 R


title: Subject UP30 R


title: Subject UP15 R


title: Subject UP16 R


title: Subject UP13 R


title: Subject UP08 R


title: Subject UP10 R


title: Subject UP12 R


title: Subject UP11 R


title: Subject UP14 R


title: Subject UP07 F


title: Subject UP03


title: Subject UP04


title: Subject UP05


title: Subject UP06


title: Subject HC21 (only used in UP cohort screen)


title: Subject HC19 (only used in UP cohort screen)


title: Subject HC17 (only used in UP cohort screen)


title: Subject HC15 (only used in UP cohort screen)


title: Subject UP02


title: Subject HC26 (only used in UP cohort screen)


title: Subject UP01


title: Subject HC22 (only used in UP cohort screen)


title: Subject HC25 (only used in UP cohort screen)


title: Subject HC18 (only used in UP cohort screen)


title: Subject HC24 (only used in UP cohort screen)


title: Subject HC14 (only used in UP cohort screen)


title: Subject UP09 R


title: Subject HC11 (only used in UP cohort screen)


title: Subject HC10 (only used in UP cohort screen)


title: Subject HC16 (only used in UP cohort screen)


title: Donor 15_HKSA stimulation_plate 1

city: Siena

first: Elisabetta

last: Soldaini

address: via Fiorentina, 1

institute: GSK

description: Library name: GSK-MM-s023

data_processing:
https://www.scdiscoveries.com/
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Staphylococcus aureus subsp. aureus USA300

source_name: Blood from healthy donor

extract_protocol:
PBMCs isolated from 6 healthy donors were separated via negative selection into CD4+ and CD4- fractions. After irradiation of CD4- cells, both fractions were re-mixed at a 1:1 ratio and stimulated with heat-killed S. aureus or  α-CD3/CD28 antibodies. After 24 h stimulation, for each stimulus CD4+ T cells co-expressing OX40 and CD137 (AIM+)  were sorted in single wells of 2 replicate 384-well plates from Single Cell Discoveries precast for SORT-seq. From each plate a library was generated by Single Cell Discoveries (https://www.scdiscoveries.com/).
https://www.scdiscoveries.com/

value: Blood from healthy donor

value: primary cell

value: CD4+ T cell

value: heat-killed S. aureus


title: Subject HC13 (only used in UP cohort screen)


title: Donor 04_HKSA stimulation_plate2

description: Library name: GSK-MM-s016


title: Subject HC12 (only used in UP cohort screen)


title: Donor 02_HKSA stimulation_plate2

description: Library name: GSK-MM-s002


title: Donor 02_HKSA stimulation_plate 1

description: Library name: GSK-MM-s001


title: Subject HC09 (only used in UP cohort screen)


title: Subject HC20 (only used in UP cohort screen)


title: Donor 04_HKSA stimulation_plate 1

description: Library name: GSK-MM-s015


title: Subject HC23 (only used in UP cohort screen)


title: Donor 05_HKSA stimulation_plate2

description: Library name: GSK-MM-s012


title: Donor 09_HKSA stimulation_plate 1

description: Library name: GSK-MM-s007


title: Donor 15_HKSA stimulation_plate2

description: Library name: GSK-MM-s024


title: Donor 05_HKSA stimulation_plate 1

description: Library name: GSK-MM-s011


title: Chimpanzee male naive iPSC line CPU6, replicate 2

city: Minato-ku

first: Hideki

last: Masaki

state: Tokyo

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

data_processing:
Raw sequence reads were processed using the nf-core/methylseq v2.6.0 pipeline (DOI: 10.5281/zenodo.1343417), which is part of the nf-core collection of reproducible bioinformatics workflows (Ewels et al., 2020). The analysis was conducted within containerized environments provided by Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017), ensuring computational reproducibility. The pipeline was executed using Nextflow v24.04.2 (Di Tommaso et al., 2017). Alignment and quantification were performed with Bismark (Krueger et al., 2011), employing the 'pbat' option for library type and 'local' alignment mode. Paired-end reads were aligned to the Pan_tro_3.0 reference genome, focusing exclusively on autosomal chromosomes.
CpG methylation calls were filtered and normalized using the methylKit R package (v1.30.0) (Akalin et al., 2012), with the top 0.1% of read counts removed to control for outliers. For clustering and methylation distribution analysis in the combined sample group, only CpGs with a minimum coverage of 3× were used. Replicates were pooled for the combined analysis, while CpGs with a minimum coverage of 5× were retained for the replicate-specific analysis.
Promoter regions were defined as spanning from -900 to +100 base pairs (bp) relative to the transcription start site (TSS) of protein-coding genes, based on Ensembl release 112 annotations. Methylation analysis of these promoters included all CpG sites with at least 1× sequencing coverage. After pooling replicate samples, we applied the regionCounts function from the methylKit package, setting a minimum coverage threshold of 2×. For downstream analysis, only promoters with more than 5 methylation counts were selected. Gene ontology (GO) analysis was conducted using the R package gprofiler2 (Kolberg et al., 2020), with the human gene ontology database. The significance threshold was set at a p-value < 0.01 and a q-value < 0.05, using Bonferroni correction. Results are reported for the Biological Process category only.
Human imprinted control regions (ICRs) were obtained from a previous study (Guo et al., 2017) and mapped to the chimpanzee genome using UCSC's Liftover tool (Raney et al., 2024) with the hg38ToPanTro5.over.chain file. Liftover regions that were separated by less than 250 bp were merged into a single ICR. To standardize these regions for methylation quantification, they were resized to 2000 bp, centered, and defined as 1000 bp on either side of the midpoint. Only CpGs with at least 3× coverage were included, and replicates were pooled before applying the regionCounts function from methylKit, with a minimum of 2× coverage. ICRs with more than 5 methylation counts were selected for further analysis.
Assembly: Chimpanzee: Pan_tro_3.0; Human: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Pan troglodytes

source_name: Chimpanzee naive iPSCs

growth_protocol: Chimpanzee primed or capacitated iPSCs were cultured with AFX medium (N2B27 basal medium supplemented with 20ng/ml Activin-A, 20ng/ml bFGF, and 2-5μM XAV939). Chimp naive iPSCs were cultured with AE6 medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL Activin-A, 20 ng/mL IL6, and 0.5-1 μM EPZ-6438). Capacitated iPSCs were originated from naïve iPSCs following culture with N2B27 supplemented with 2 μM XAV. For TE induction, naive iPSCs were cultured with N2B27 supplemented with 3μM PD032590 and 3μM A83-01.Human naive ESCs, HNES1, was cultured with PXGL medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL) on MEF feeder, or with AE6 on feeder-free.

extract_protocol:
Genomic DNA of each cell line was extracted by using kit.
PBAT libraries for whole-genome DNA methylation sequencing were created from 100 ng of purified genomic DNA. Bisulfite conversion was done using the EZ DNA Methylation-Gold Kit. First strand synthesis used a biotinylated primer with a 90-minute incubation. Second strand synthesis employed a modified primer for TruSeq dual indexed sequencing, also with a 90-minute incubation. The final PCR amplification involved 8 cycles using standard Illumina TruSeq dual-indexed primers.

value: Chimpanzee naive iPSCs


title: Chimpanzee female capacitated iPSC line CP127, replicate 2

source_name: Chimpanzee naive iPSC-derived cells capacitated in AFX medium


title: Chimpanzee male primed iPSC line, replicate 2

source_name: Chimpanzee primed iPSCs

value: Chimpanzee primed iPSCs


title: Donor 01_HKSA stimulation_plate 1

description: Library name: GSK-MM-s019


title: Chimpanzee female capacitated iPSC line CPR1, replicate 3

value: Chimpanzee naive iPSC-derived cells capacitated in AFX medium


title: Chimpanzee male naive iPSC line CPU6, replicate 1


title: Chimpanzee male primed iPSC line, replicate 3


title: Chimpanzee male primed iPSC line, replicate 1


title: Chimpanzee female capacitated iPSC line CPR1, replicate 2


title: Donor 09_HKSA stimulation_plate2

description: Library name: GSK-MM-s008


title: Chimpanzee female capacitated iPSC line CPR1, replicate 1


title: Chimpanzee female naïve iPSC line CPR1, replicate 2


title: Chimpanzee female naïve iPSC line CP127, replicate 2


title: Chimpanzee female primed iPSC line, replicate 1


title: Chimpanzee female primed iPSC line, replicate 2


title: Chimpanzee female naïve iPSC line CP127, replicate 3


title: Chimpanzee female naïve iPSC line CP127, replicate 1


title: scRNA-seq of chimpanzee blastoids-derived cell_263

description: fastq

data_processing:
Adaptor sequences and low-quality base calls were trimmed using Trim Galore! v0.6.6 with default parameters. Trimmed reads were aligned to the Chimpanzee reference genome (Pan_tro3.0) using STAR v2.7.7a (Dobin et al., 2013) in paired-end mode with default parameters.
Assembly: Chimpanzee: Pan_tro_3.0-rel109; Human: GRCh38-2020-A
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: blastoids-derived cell

extract_protocol:
Blastoids were dissociated into single cells enzymatically. Single cells were transferred into individual wells of a 96-well plate containing Smart-seq2 single-cell lysis buffer by using capillary.
cDNA library was synthesized by using SMART-seq2.

value: blastoids-derived cell

value: in vitro-differentiated cells from nPSC


title: scRNA-seq of chimpanzee blastoids-derived cell_264

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_261

description: fastq


title: Donor 01_HKSA stimulation_plate2

description: Library name: GSK-MM-s020


title: Chimpanzee female capacitated iPSC line CP127, replicate 1


title: scRNA-seq of chimpanzee blastoids-derived cell_259

description: fastq


title: Chimpanzee male naive iPSC line CPU6, replicate 3


title: scRNA-seq of chimpanzee blastoids-derived cell_256

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_257

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_255

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_254

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_252

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_253

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_250

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_246

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_249

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_251

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_245

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_242

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_238

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_241

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_232

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_239

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_231

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_233

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_236

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_227

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_228

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_226

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_223

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_224

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_220

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_248

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_217

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_221

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_218

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_219

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_243

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_213

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_237

description: fastq


title: Chimpanzee female naïve iPSC line CPR1, replicate 1


title: scRNA-seq of chimpanzee blastoids-derived cell_215

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_214

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_211

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_216

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_209

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_212

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_208

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_207

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_205

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_229

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_210

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_201

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_230

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_200

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_202

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_199

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_198

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_196

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_197

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_193

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_191

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_192

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_194

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_189

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_187

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_188

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_185

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_204

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_184

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_180

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_179

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_176

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_178

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_175

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_173

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_169

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_170

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_167

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_163

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_168

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_161

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_160

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_195

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_159

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_190

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_157

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_152

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_153

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_156

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_155

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_151

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_182

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_181

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_177

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_150

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_146

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_148

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_145

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_143

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_144

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_142

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_141

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_139

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_140

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_137

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_134

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_133

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_136

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_130

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_129

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_127

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_128

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_125

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_123

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_121

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_120

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_117

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_118

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_119

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_116

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_122

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_115

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_114

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_111

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_108

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_106

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_113

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_107

description: fastq


title: scRNA-seq of chimpanzee blastoids-derived cell_103

description: fastq