title: Tubular epithelial cells_stimulated_24 hour_rep1


title: siPARP1_Knockdown_H4K20me3_ChIP_rep2

status: Public on Nov 17 2022

type: SRA

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

country: USA

institute: New England Biolabs

library_source: genomic

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
ChIP-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. H4K20me1 enriched regions were identified by calling broad peaks (target over input) using MACS2. Signal tracks were generated using deeptools bamCoverage with the parameters, -normalizeUsing RPKM -of bigwig. H4K20me1 peaks were annotated using HOMER annotatePeaks.pl.  Transcription factor binding motifs enrichment near H4K20me1peaks was searched using the HOMER tool findMotifsGenome.pl with default parameters
NicE-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. Open chromatin regions were identified by callingnarrow peaks using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were grown according to ATCC ‘s recommendations.

extract_protocol: ChiP-seq, One-pot UniNicE-seq

treatment_protocol: For PARP1 overexpression and knockdown study, HeLa cells were cultured in a 6 well plate format. After FLAG-PARP1 plasmid (control used as FLAG-plasmid) or esiRNA PARP1 (control used as esiRNA GFP) transfections for 48hrs, chromatin and DNA was extracted according to New England Biolabs's recommendations and submitted to ChIP-seq and NicE-seq respectively.

tag: cell type

value: Cervical cancer cells

tag: condition

tag: antibody


title: siGFP_control_H4K20me1_ChIP_BR2_1

value: Control


title: siGFP_control_H4K20me1_ChIP_BR2_2


title: serum-ALMS-77678

type: RNA

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Data processing
Matrix non-normalized: Assays with multiple melting curve peaks or inconsistent with the specifications (more details in label protocol) or differing by less than 5 Cq from negative control were removed. Data from two batches of assays were included in a single table. Otherwise data are unprocessed.
Matrix normalized: For further analysis, miRNAs were filtered so that the final set contains miRNAs with Cq<37 in at least half of the samples in each of the four groups (ALMS, BBS, control, obesity). Batch effect was removed using ComBat run in R with batch marked as A or B as indicated in samples’ characteristics. Finally, Cq values were normalized by subtracting each Cq value from mean Cq for 80 miRNAs detected in all samples. As a result, higher normalized values indicate higher expression (contrary to raw Cq). All above-described steps, except ComBat, were implemented in Python.
Fold Change: Data in this sheet were generated using limma algorithm in R.
Data description
Matrix non-normalized: Data as provided by laboratory after background filtration. Values within 5 Cq from negative control were considered as noise and removed. No further processing was applied.
Matrix normalized: Data filtered and normalized as described in “data processing” section.
Fold Change: Presented fold-changes (FC) were calculated on preprocessed data (matrix normalized) using limma in R. The limma model included only one explanatory variable: group, taking one of the following values for each patient: ALMS, BBS, obesity, control as indicated in samples’ characteristics. Single model was developed including all four groups. FC values were calculated for pairwise comparisons of the groups.

label: SYBR green

molecule: total RNA

source_name: Serum

label_protocol: 19 µl RNA was reverse transcribed in 95 µl reactions using the miRCURY LNA RT Kit (QIAGEN). cDNA was diluted 50 x and assayed in 10 µl PCR reactions according to the protocol for miRCURY LNA miRNA PCR; each miRNA was assayed once by qPCR on the miRNA Ready-to-Use PCR, Human panel I+II using miRCURY LNA SYBR Green master mix. Negative controls excluding template from the reverse transcription reaction were performed and profiled like the samples. The amplification was performed in a LightCycler 480 Real-Time PCR System (Roche) in 384 well plates. The amplification curves were analyzed using the Roche LC software, both for determination of Cq (by the 2nd derivative method) and for melting curve analysis.

extract_protocol: The serum was thawed on ice and centrifuged at 3000 x g for 5 min in a 4°C. An aliquot of 200 μL per sample was transferred to a FluidX tube and 60 μl of Lysis solution BF containing 1μg carrier-RNA per 60μl Lysis Solution BF and RNA spike-in template mixture was added to the sample and mixed for 1 min and incubated for 7 min at room temperature, followed by addition of 20 μL Protein Precipitation solution BF. Total RNA was extracted from the samples using miRCURY RNA isolation Kit – Biofuids; high-throughput bead-based protocol (Hilden, Germany) in an automated 96 well format. The purified total RNA was eluted in a final volume of 50 μl.

tag: group

value: Alström syndrome (ALMS)

tag: gender

value: male

tag: batch

value: B

tag: age

tag: tissue

value: serum from blood


title: Tubular epithelial cells_stimulated_1 hour_rep3

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

library_source: transcriptomic

data_processing:
RNA-sequencing data was processed as previously described in Chothani et al, 20191. Raw sequencing data (.bcl files) were demultiplexed into fastq files with Illumina’s bcl2fastq v2.16.0.10 based on unique index pairs. Adaptors and low quality reads were trimmed using Trimmomatic V0.362, retaining reads >20 nucleotides. Read mapping was carried out using STAR v2.5.2b3 to the Ensembl Human GRCh38 v86 reference genome using standard parameters for full-length RNA-seq in the ENCODE project. Read counting was carried out using featureCounts4 to get gene-level quantification of genomic features: featureCounts -t exon -g gene_id -O -s 2 -J -p -R -G. Quality check for sequencing data and mapping data was carried out using FastQC v0.11.55 and MultiQC6. Differential expression (DE) was performed with DESeq2 v1.14.17 by using raw reads count from featureCounts. Baseline samples were used as the reference level for each paired two-group comparison with 1h, 6h and 24h samples.
Assembly: hg38

molecule: polyA RNA

source_name: Renal tubular epithelial cells

extract_protocol: Primary human renal proximal tubular epithelial cells (TECs, 4100, lot 19754, ScienCell) isolated from healthy human kidney (20 year old female) were grown and maintained in complete renal epithelial cell growth medium (4101, ScienCell) containing fetal bovine serum (FBS, 0010, ScienCell), epithelial cell growth supplement (EpiCGS, 4152, ScienCell) and antibiotic solution (P/S, 0503, ScienCell).

value: Renal tubular epithelial cells

tag: treatment

value: stimulated 1 hour


title: siPARP1_Knockdown_H4K20me3_ChIP_rep1


title: siGFP_control_H4K20me3_ChIP_rep2


title: Tubular epithelial cells_stimulated_1 hour_rep1


title: Tubular epithelial cells_stimulated_1 hour_rep2


title: serum-ALMS-77675

value: female


title: Tubular epithelial cells_stimulated_24 hour_rep4

value: stimulated 24 hour


title: siGFP_control_H4K20me3_ChIP_rep1


title: serum-ALMS-77674


title: serum-ALMS-77676


title: serum-ALMS-77673


title: chl1-5 N-3

city: Boston

first: Jen

last: Sheen

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5).
The RNA-seq reads were mapped to the Arabidopsis (TAIR10) genome with Tophat program (version 2.1.1). The featureCount program of HTseq package (version 0.6.1) was used to quantify the RNA-seq expression levels of the TAIR10 annotated gene models.
Assembly: TAIR10
Supplementary files format and content: Htseq count

organism: Arabidopsis thaliana

source_name: Seven-day-old seedlings

growth_protocol: For RNA-seq analysis of nitrate response in chl1-5, seedlings were germinated in one well of the 6-well tissue culture plate(Falcon) with 1 ml of the basal medium (10 mM KH2PO4/K2HPO4, 1 mM MgSO4, 1 mM CaCl2, 0.1 mM FeSO4-EDTA, 50 μM H3BO4, 12 μM MnSO4·H2O, 1 μM ZnCl2, 1 μM CuSO4·5H2O, 0.2 μM Na2MoO4·2H2O, 0.1% MES and 0.5% sucrose, pH 5.8) supplemented with 2.5 mM ammonium succinate as the sole nitrogen source. Plates were sealed with parafilm under constant light (100 μmol m-2 s-1) at 23℃ for 7 days. The medium was refreshed at day 6.

extract_protocol:
For-RNA-seq, whole seedlings from liquid medium or protoplasts were harvested and frozen in liquid nitrogen.  Total RNA was isolated from liquid nitrogen ground samples with the Trizol reagent (Invitrogen), The resulting RNA (0.5 μg) was used for preparing the library
For-RNA-seq, NEBNext® Ultra II™ RNA Library Prep Kit for Illumina® using 500 ng of total RNA per library.

treatment_protocol: Before nitrate induction, seedlings were treated washed three times with 1 ml basal medium. Seedlings were induced in 1 ml of basal medium with 10 mM KCl or KNO3 for 20 min.

tag: genotype

tag: developmental stage

value: Seven-day-old seedlings


title: VC_Input

city: nanjing

first: tengxiao

last: guo

address: nanjing road

country: China

institute: State Key Laboratory of Experimental Hematology

data_processing:
illimina casava1.7 software used for basecalling.
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: RPMI 1640 (w/o Hepes)10%FBS

extract_protocol:
After harvesting cells, add trizol and freeze them in - 80 ° refrigerator
RNA libranries were prepared for sequencing using stanard illumina protocols

treatment_protocol: RIP

tag: cell line

value: leukemia cells

value: empty vector


title: serum-BBS-77672

value: Bardet-Biedl syndrome (BBS)


title: HeLa cells, siGFP_Input_BR1

data_processing:
Adaptor and low-quality sequences were trimmed from paired-end sequencing reads using Trim Galore v 0.5.0
ChIP-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. H4K20me1 enriched regions were identified by calling broad peaks (target over input) using MACS2. Signal tracks were generated using deeptools bamCoverage with the parameters, -normalizeUsing RPKM -of bigwig. H4K20me1 peaks were annotated using HOMER annotatePeaks.pl.  Transcription factor binding motifs enrichment near H4K20me1peaks was searched using the HOMER tool findMotifsGenome.pl with default parameters
RNA-seq: The raw fastq files were trimmed and quality check was performed using Trim Galore and FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) respectively. Trimmed reads were mapped to the human reference assembly hg38 using STAR. Transcript abundance was estimated from these high-quality mapped reads using htseq count module. DESeq2  was used to normalize the count matrix and identification of differentially expressed genes.
NicE-seq:Trimmed read pairs were mapped to the reference genome (human: hg38) using Bowtie2 v. 2.3.4.3. PCR duplicates and mitochondrial reads were removed using Picard tools and samtools. The aligned bam files of technical replicates were merged using Sambamba. Open chromatin regions were identified by callingnarrow peaks using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwigs were generated using 100bp bins using deeptools bamCoverage with the following parameters: --normalizeUsing RPKM

source_name: HeLa cells, siGFP_Input

extract_protocol:
For PARP1 overexpression and knockdown study, HeLa cells were cultured in a 6 well plate format. After FLAG-PARP1 plasmid (control used as FLAG-plasmid) or esiRNA PARP1 (control used as esiRNA GFP) transfections for 48hrs, chromatin, DNA or RNA were extracted according to New England Biolabs's recommendations and submitted to ChIP-seq, NicE-seq or RNA-seq respectively.
ChiP-seq, RNA-seq, One-tube NicE-seq

value: HeLa

tag: chip antibody

value: none (Input)


title: HeLa cells, siPARP1_Input_BR1

source_name: HeLa cells, siPARP1_Input


title: chl1-5 N-2


title: OE_Input


title: serum-ALMS-77671


title: celf2_IP2


title: chl1-5 N-1


title: chl1-5 K-3


title: HeLa cells, siPARP1_Knockdown_H4K20me1_ChIP_BR1_2

description:
siPARP1_H4K20me1_ChIP.bw
siPARP1_H4K20me1_ChIP.broadPeak

source_name: HeLa cells, siPARP1_Knockdown_H4K20me1


title: chl1-5 K-2


title: HeLa cells, siGFP_control_H4K20me1_ChIP_BR1_2

description:
siGFP_H4K20me1_ChIP.bw
siGFP_H4K20me1_ChIP.broadPeak

source_name: HeLa cells, siGFP_control_H4K20me1


title: HeLa cells, siGFP_control_H4K20me1_ChIP_BR1_1


title: serum-ALMS-77670


title: serum-BBS-77669


title: serum-control-50901

value: A


title: serum-control-50898


title: HeLa cells, FLAG-PARP1_Input_rep2

source_name: HeLa cells, FLAG-PARP1_Input_rep2

value: Cervical cancer cells


title: T24-shRNA2-3,bladder cancer cell lines T24 cell, MTHFD2-shRNA2, rep3

city: Nanchang

first: Bin

last: Fu

state: Jiangxi

address: No.17, Yong Wai Zheng Street, Donghu Districtstrict,

department: department of urology

institute: The First Affiliated Hospital of Nanchang Universi

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2(v2.0.4)mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: bladder cancer cell line

growth_protocol: T24 cells were cultured in high-glucose DMEM (Gibco; Thermo Fisher Scientific, Inc.) containing 10% fetal bovine serum (FBS; HyClone; Cytiva), 100 U/ml penicillin and 100 µg/ml streptomycin. The cells were cultured at 37˚C with 5% CO2.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral construction. Packaging lentivirus was purchased from Hanheng Biological Co., Ltd. T24 Bladder cell lines were infected with lentiviral knockdown MTHFD2 (HBLV-h-MTHFD2shRNA1/2/3-ZsGreen-PURO) or NC (HBLV-ZsGreen-PURO) constructs. The stably transfected cell lines were screened with puromycin.

value: bladder cancer cell line


title: T24-shRNA2-1,bladder cancer cell lines T24 cell, MTHFD2-shRNA2, rep1


title: nlp2,4,5,6,7,8,9 N-3

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5).
The RNA-seq reads were mapped to the Arabidopsis (TAIR10) genome with Tophat program (version 2.1.1). The featureCount program of HTseq package (version 0.6.1) was used to quantify the RNA-seq expression levels of the TAIR10 annotated gene models.

growth_protocol: For RNA-seq analysis using transient expression of NLPs in protoplasts system, wild type seedlings were grown at 23/20 °C, 12 h/12 h light/dark, 60% RH, and 75 μmol m-2 s-1mol of light for 3-4 weeks in soil (Giffy pellet).  For RNA-seq analysis of nitrate response in wild type and nlp2,4,5,6,7,8,9, 10 seedlings were germinated in one well of the 6-well tissue culture plate(Falcon) with 1 ml of the basal medium (10 mM KH2PO4/K2HPO4, 1 mM MgSO4, 1 mM CaCl2, 0.1 mM FeSO4-EDTA, 50 μM H3BO4, 12 μM MnSO4·H2O, 1 μM ZnCl2, 1 μM CuSO4·5H2O, 0.2 μM Na2MoO4·2H2O, 0.1% MES and 0.5% sucrose, pH 5.8) supplemented with 2.5 mM ammonium succinate as the sole nitrogen source. Plates were sealed with parafilm under constant light (100 μmol m-2 s-1) at 23℃ for 7 days. The medium was refreshed at day 6.

tag: ecotype


title: nlp2,4,5,6,7,8,9 N-2


title: T24-shRNA2-2,bladder cancer cell lines T24 cell, MTHFD2-shRNA2, rep2


title: serum-obesity-50896

value: Obesity


title: HeLa cells, FLAG-PARP1_Input_rep1

source_name: HeLa cells, FLAG-PARP1_Input_rep1


title: serum-control-50890

value: Control


title: T24-NC-3,bladder cancer cell lines T24 cell, control group, rep3

value: negative control


title: HeLa cells, siPARP1_Knockdown_H4K20me1_ChIP_BR1_1


title: nlp2,4,5,6,7,8,9 N-1


title: celf2_IP1


title: T24-NC-2,bladder cancer cell lines T24 cell, control group, rep2


title: chl1-5 K-1


title: nlp2,4,5,6,7,8,9 K-3


title: serum-control-50884

value: male

value: serum from blood


title: serum-obesity-50883


title: HeLa cells, FLAG-PARP1_H4K20me1_ChIP_rep2

description:
FLAG-PARP1_H4K20me1_ChIP.bw
FLAG-PARP1_H4K20me1_ChIP.broadPeak

source_name: HeLa cells, FLAG-PARP1_H4K20me1


title: nlp2,4,5,6,7,8,9 K-2


title: serum-control-50880


title: HeLa cells, FLAG-PARP1_H4K20me1_ChIP_rep1


title: Wild type N-3


title: MDA-MB-231 tumorspheres with M2 treatment

city: Kolkata

first: Ananya

last: Roy

state: West Bengal

address: EN 80

department: Bio physics

country: India

institute: Bose Institute

data_processing:
NGS analyses of LINC00273 overexpressed and M2 (10 μM)-treated samples were performed at Medgenome India Pvt. Ltd. using Illumina platform to obtain 150-bp paired-end reads.
The sequencing depth for each sample was 100 million reads. The raw reads were filtered using Trimmomatic (v-0.36) for retaining high-quality sequence and adapter trimming.
Unwanted sequences, such as mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences using Bowtie2 (2.2.4).
Filtered reads were aligned to Human genome (hg19) using splice aware aligner like STAR to quantify reads mapped to each transcript. Total number of uniquely mapped read counts were estimated using FeatureCount (1.5.2). The raw read counts for control and treated samples were normalized using DESeq2.
GO annotation and Reactome pathway information for differentially expressed genes were done using Panther database.
Assembly: hg19
Supplementary files format and content: normalized read count

source_name: MDA-MB-231 tumorspheres, Wild type with M2 treatment

growth_protocol: MDA-MB-231 cells were cultured in DMEM media supplemented with 20ng/ml recombinant epidermal growth factor, B27 supplement (BD biosciences), 5mg/ml insulin, 0.4% BSA and 500ml DMEM media in humidified atmosphere with 5% CO2 at 37C. Tumorspheres were cultured in ultra low adhesion plates.

extract_protocol: RNA was harvested using TRIzol following standard protocol, Protein and carbohydrate contamination and RNA intigrity was examined using capillary electrophoresis (BioAnalyzer 2100, Agilent Technologies, Santa Clara, CA) to ensure the achievement of RNA integrity number (RIN) (28S to 18S ribosomal RNA) >9, required for the preparation of the libraries for next generation sequencing (NGS). The total RNA was processed with RiboCop rRNA depletion kit (Lexogen) following manufacturer’s recommendation to remove ribosomal RNA from total RNA content.

treatment_protocol: MDA-MB-231 tumorspheres with LINC00273 over-exprerssion and M2 treatment for 24 hours

value: Epithelial human breast cancer cell

tag: time

value: 24 hours

value: WT control

tag: phenotype

value: tumor regression


title: HeLa cells, FLAG_control_H4K20me1_ChIP_rep2

description:
FLAG_H4K20me1_ChIP.bw
FLAG_H4K20me1_ChIP.broadPeak

source_name: HeLa cells, FLAG_control_H4K20me1


title: MDA-MB-231 tumorspheres without treatment

source_name: MDA-MB-231 tumorspheres, Wild Type (No treatment)

tag: treatment  No treatment

value: control


title: Wild type N-2

value: Seven-day-old seedlings


title: HeLa cells, FLAG_control_H4K20me1_ChIP_rep1

tag: cell type


title: HEK293_ Xrn2_D235A_NETseq Rep3

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3’ end
GRCh37/hg19 assembly
BigWig
Library strategy: eNET-seq

molecule: nuclear RNA

source_name: HEK293 Flp-in Trex pcDNA5 Xrn2 D235A Avitag

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3650
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep  DMSO, doxycycline (2.0 ug/ml) 24hr


title: HeLa cells, FLAG_Input_rep2

source_name: HeLa cells, FLAG_Input_rep2

value: HeLa

value: none (Input)


title: serum-control-50870

value: A


title: serum-control-50873


title: MIG_ON_3

city: Cambridge

first: William

last: Plumbly

address: Island Research Building, Cambridge Biomedical Campus

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were mapped to genome using STAR v2.7.3 aligner
Mapped reads were counted using featureCounts from Subread package and GRCh38 v99 annotations
Genome_build: NCBI GRCh Build 38
Supplementary_files_format_and_content: csv file containing count matrix providing raw gene counts for all experiment samples and all genes

source_name: iPSC derived sensory neurons

extract_protocol:
Total RNA was extracted from samples with the Qiagen Rneasy Plus Mini Kit (#74134) following the manufactures instructions.
Illumina TruSeq Stranded mRNA Library Kits (#20020595). Libraries produced following the manufactuters instructions. Samples indexed with TruSeq RNA single Indexes.

tag: exposure

value: Overnight

value: Migrane Model - IMs

tag: div


title: Wild type N-1


title: HEK293_ Xrn2_D235A_NETseq Rep2

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3649
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

value: HEK293 Flp-in Trex pcDNA5 Xrn2 D235A Avitag

tag: antibody


title: serum-obesity-50869

source_name: Serum

tag: group

value: Obesity

tag: gender


title: Wild type K-3


title: HEK293_ Xrn2_D235A_NETseq Rep1

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3648
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)


title: MIG_ON_2


title: Wild type K-2


title: T24-NC-1,bladder cancer cell lines T24 cell, control group, rep1

value: bladder cancer cell line

value: negative control


title: HeLa cells, FLAG_Input_rep1

source_name: HeLa cells, FLAG_Input_rep1

value: Cervical cancer cells

value: Control


title: HEK293_ Xrn2 WT_NETseq Rep3

source_name: HEK293 Flp-in Trex pcDNA5 Xrn2 WT Avitag

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3647
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)


title: serum-obesity-50867

value: male

tag: batch

tag: age

value: serum from blood


title: Wild type K-1

source_name: Seven-day-old seedlings

tag: tissue


title: nlp2,4,5,6,7,8,9 K-1


title: MDA-MB-231 tumorspheres with LINC00273 overexpressed

source_name: MDA-MB-231 tumorspheres, Wild type transfected with LINC00273-pcDNA-CMV clone

value: Epithelial human breast cancer cell

tag: treatment

value: 24 hours

tag: genotype

value: LINC00273 overexpression

value: enhanced metastatic tumor


title: MIG_ON_1


title: serum-control-50865


title: serum-obesity-50878

value: female


title: MIG_L_3

value: Long (90 mins)


title: serum-obesity-50864

value: A


title: HEK293_ Xrn2 WT_NETseq Rep2

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3646
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

tag: cell line

value: HEK293 Flp-in Trex pcDNA5 Xrn2 WT Avitag

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep  DMSO, doxycycline (2.0 ug/ml) 24hr


title: NLP9-2

source_name: Mesophyll protoplasts

value: Mesophyll protoplasts


title: MIG_L_2

value: Migrane Model - IMs


title: HEK293_ Xrn2 WT_NETseq Rep1

extract_protocol:
Pol II-associated nascent RNA was isolated by IP and processed by the eNETseq protocol Fong etal Mol Cell 82: 3632-3645
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)


title: NLP9-1


title: MIG_L_1


title: serum-control-50863


title: serum-ALMS-50859

value: Alström syndrome (ALMS)


title: HEK293_ Xrn2_D235A_5'Bruseq Rep3

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 5’ end
GRCh37/hg19 assembly
BigWig
Library strategy: 5'PO4 Bru-seq

extract_protocol:
BrU-labeled RNA 2mM 30 min, was fragmented with micrococcal nuclease, immunopurified with anti BrdU, 3' ends repaired with T4 PNK, and converted into sequencing libraries
10-20ng of RNA was used with the QIAseq miRNA  kit (#331565)

value: HEK293 Flp-in Trex pcDNA5 Xrn2 D235A Avitag

value: monoclonal anti-BrdU 3D4 (Pharmingen Cat 555627)


title: NLP8-1


title: HEK293_ Xrn2_D235A_5'Bruseq Rep2


title: NLP8-2


title: MIG_M_3

value: Mid (50 mins)


title: MIG_M_1


title: HEK293_ Xrn2_D235A_5'Bruseq Rep1


title: serum-control-50858

value: Control

value: male

value: serum from blood


title: serum-ALMS-50852


title: NLP7-1


title: HEK293_ Xrn2 WT_5'Bruseq Rep2


title: NLP6-2


title: MIG_S_3

value: Short (20 mins)


title: MIG_S_1


title: serum-control-50849


title: HEK293_ Xrn2 WT_5'Bruseq Rep1


title: serum-obesity-50848

value: Obesity


title: HEAT_L_3

value: Heat


title: HEK293_Xrn2_WT_triptolide_PolII

data_processing:
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7.
Read coordinates were centered assuming a fragment size of 90-180 bp
GRCh37/hg19 assembly / or GRCh38/hg38 assembly
BigWig

extract_protocol:
Cross-linked chromatin was sonicated with a Covaris ME220 ultrasonicator
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.


title: serum-control-50847

value: female


title: NLP5-2


title: HEAT_L_2

value: Long (90 mins)


title: MIG_M_2


title: HEK293_Xrn2_WT_DMSO_PolII

value: HEK293 Flp-in Trex pcDNA5 Xrn2 WT Avitag


title: serum-control-50841

value: A


title: NLP7-2


title: serum-obesity-50853


title: HEAT_L_1


title: NLP5-1


title: HEK293_Xrn2_WT_DMSO_AviXrn2

value: rabbit anti-Avitag

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep  DMSO, doxycycline (2.0 ug/ml) 24hr


title: HEAT_M_3


title: HEK293_Xrn2_WT_triptolide_AviXrn2


title: NLP4-1

value: Mesophyll protoplasts


title: HEAT_M_2


title: NLP6-1


title: hiHeps_W2C_2

city: Beijing

first: Bingqing

last: Xie

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
The generated sequencing reads were mapped against the human genome build hg19 using STAR aligner
The read counts for each gene were calculated using featureCounts
The low expression genes with total counts across all samples less than 10 were excluded
Gene expression was normalized by DESeq2 (v1.22.2) with variance-stabilizing transformation (VST) (Love et al., 2014)
Assembly: hg19
Supplementary files format and content: CSV files include the non-normalized expression values for each sample

source_name: human induced hepatocytes

extract_protocol:
Total RNA from each sample was isolated using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Hepatic progenitors  were induced from human embryonic fibroblasts by the well-establised two-step lineage reprogramming protocol. hiHeps derived from hepatic progenitors were cultured in W2C/W6C medium for 7 days.Primary huaman hepatocytes and human liver tissues were freshly isolated. All samples were colleted from RNA extraction.

value: human induced hepatocytes

value: cultured in W2C medium


title: NLP3-2


title: HEAT_M_1


title: NLP3-1


title: HEAT_S_3


title: HEAT_S_2


title: hiHeps_W6C_2

value: cultured in W6C medium


title: NLP2-2


title: hiHeps_W6C_1

value: cultured in W6Cmedium


title: hiHeps_W2C_1


title: NLP4-2


title: HEAT_S_1


title: NLP2-1


title: MXP5_IK1_2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

hyb_protocol: Biotin-laboeled samples were hybridized using GeneChip® Hybridization Oven to the Affymetrix miRNA microarray.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Dx v.2.

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
miRNA-4_0-st-v1.pgf
miRNA-4_0-st-v1.annotations.20160922.csv

label: biotin

source_name: MXP5 cells

label_protocol: From each sample, 1 μg total RNA was used for FlashTag™ Biotin HSR RNA Labeling Kit (thermoscientific) according to manufacter's recommendations.

growth_protocol: Cells were maintained at 37°C in humidified incubator with 5% CO2 in minimum essential medium alpha (MEMα) GlutaMAX (Gibco), supplemented with 20% FBS (Gibco). Cells were tested negative for mycoplasma contamination and authenticated with STR profiling.

extract_protocol: Total RNA was extracted using directzol (Zymo) according to manufacterer's recommendations.

treatment_protocol: Expression of wild-type IK1 and control samples was induced with the addition of 1ug/mL doxycycline.

tag: vector


title: PDX2_IK1_2

source_name: PDX2 cells


title: NLP1-2

tag: ecotype


title: COLD_L_3

value: Cold


title: PBMCs, COVID-19, WTA, Ab-Seq, SMK [B7]

city: Delhi

first: Rajesh

last: Pandey

address: Mall road

institute: CSIR-IGIB

description:
WTA + Ab-Seq + SMK Library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA (WTA) + Oligo-attached Antibody (Ab-Seq) + Oligo-attached Antibody for Sample Multiplexing (SMK)

data_processing:
The fastq files were generated follwed by demultiplexing using bcl2fastq, by using the index sequence used during index PCR steps. The read 1 and read 2 fastq files were then processed using BD Rhapsody WTA analysis pipeline, and aligned to GRCh38 and GencodeV29 for transcript annotation and quantitation.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: BD Rhapsody WTA analysis output

source_name: Blood

extract_protocol:
PBMCs were isolated from the healthy (n=4), COVID-19 positive (n=16) and recovered (n=13) individuals using BD vaccutainers Cell Preparation Tube (CPT). Samples were stained with BD Sample Multiplexing kit for Human, wherein unique oligo sequences were attached with a universal antibody. Further, the samples were pooled and stained using a pool of BD Ab-Seq oligo attached antibodies. After counting the tagged cells, an average of 30000 cells for each batch were loaded on to the BD Rhapsody cartridge to capture the single cells using BD Rhapsody Express Single-Cell Analysis System. Each Sample Tag has common 5' and 3' ends and the Sample Tag sequence: GTTGTCAAGATGCTACCGTTCAGAG[Sample Tag sequence]AAAAAAAAAAAAAAAAAAAAAAAAA. The Sample Tag oligo sequences and the Ab-Seq oligo sequences are available as supplementary files. The sample id, the experimental group, batch, corresponding sample tags and barcodes are available as supplementary data.
Library was prepared using BD Rhapsody WTA amplification kit. Briefly, cDNAs were prepared on the cell capture beads obtained from the BD Rhapsody cartridge. The Ab-Seq and sample tag oligos were separated from the Exonuclease I treated beads by denaturation, while the cDNA of the poly-A transcripts remained on the beads. A random priming and extension was performed on the beads, followed by Ampure XP based cleanup, amplification, secondary Ampure XP cleanup, indexing and a final dual-sided Ampure XP cleanup to make the WTA library. On the other side, the Ab-Seq/sample tag oligos were amplified using universal oligos followed by a Ampure XP cleanup. The Ab-Seq library prepared after an index-PCR, followed by a Ampure XP cleanup, while the sample tag oligos were enriched by an aditional PCR, followed by a Ampure XP cleanup. Finally, the SMK library was constructed using Index PCR of the enriched sample tag oligos, followed by final Ampure XP cleanup. The barcodes sequences and barcodes used for wach batch are available in supplementary file.
Following the final bead purification, all three libraries (per batch) were pooled in order to obtain a 30000 reads/cell for WTA library, 20000 reads/cell for Ab-Seq library and 120 reads/cell/sample tag/batch for the SMK library. Libraries of multiple batches were pooled based on the index sequences used during Index PCR steps.

value: Blood

tag: subject status

value: Peripheral Blood Mononuclear Cells (PBMCs)

tag: library type

value: mRNA + Ab-Seq + SMK

tag: antibodies/tags

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR11


title: PBMCs, COVID-19, WTA, Ab-Seq, SMK [B6]

tag: cell type

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR10


title: NLP1-1

extract_protocol:
For-RNA-seq, whole seedlings from liquid medium or protoplasts were harvested and frozen in liquid nitrogen.  Total RNA was isolated from liquid nitrogen ground samples with the Trizol reagent (Invitrogen), The resulting RNA (0.5 μg) was used for preparing the library
For-RNA-seq, NEBNext® Ultra II™ RNA Library Prep Kit for Illumina® using 500 ng of total RNA per library.


title: COLD_L_2

tag: exposure


title: Control-2 for NLP1,2,3,5,8,9


title: PBMCs, Healthy, Recovered, WTA, Ab-Seq, SMK [B5]

value: Healthy; recovered

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR9


title: COLD_L_1

value: Long (90 mins)

tag: div


title: PDX2_IK1_1


title: M20 [Bisulfite-Seq]

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4).
Reads were mapped to the lastest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version 0.20.1).
Duplicate alignments were removed using the tool deduplicate_bismark (version 0.20.1).
Methylation calling and extraction were performed using Bismark methylation extractor (version 0.20.1).
Assembly: Cow genome assembly: ARS-UCD1.2
Supplementary files format and content: Tab-delimited text files including chromosome, genomic start position, genomic end position, percentage of methylation at that position, number of Cs methylated, and number of Cs non-methylated

organism: Bos taurus

source_name: Loin muscle

extract_protocol:
Total DNA was extracted from muscle samples and DNA quality and quantity were tested using Nanodrop (OD260/OD280) and Qubit® 2.0.
Bisulfite treatment, library preparation and subsequent whole-genome sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).

value: Loin muscle

tag: breed

value: Brangus

value: maternal diet methionine


title: M19 [Bisulfite-Seq]

value: maternal diet control


title: MXP5_IK1_1


title: MXP5_CON_1

value: control


title: COLD_M_3

value: Mid (50 mins)


title: Control-2 for NLP7

value: Mesophyll protoplasts


title: M18 [Bisulfite-Seq]


title: PDX2_CON_2


title: PBMCs, COVID-19, WTA, Ab-Seq, SMK [B3]

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR7


title: COLD_M_2

value: Cold


title: MXP5_CON_2


title: PBMCs, Recovered, WTA, Ab-Seq, SMK [B2]

value: Blood

value: Recovered

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR6


title: COLD_M_1


title: M16 [Bisulfite-Seq]


title: PDX2_CON_1


title: COLD_S_3

value: Short (20 mins)


title: M14 [Bisulfite-Seq]


title: M15 [Bisulfite-Seq]


title: PBMCs, Recovered, WTA, Ab-Seq, SMK [B4]

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: mRNA + Ab-Seq + SMK

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR8


title: hAxioloid 96h_MG_RAL_H3K27me3_2

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

country: Japan

institute: Kyoto University

data_processing:
Nextera adapter sequences were removed with cutadapt (version 3.4) .
Paired-end reads were aligned to hg38 using Bowtie2 (version 2.2.4) with options --very-sensitive -X 2000 .
From mapped reads, properly paired (samtools flag 0 × 2), MAPQ >=20, and non-mitochondrial chromosomal reads were extracted using samtools version 1.12.
Reads mapped to blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) were removed with bedtools (version 2.30).
Bam files were converted to bigwig format with deeptools (version 3.5).
Assembly: hg38
Supplementary files format and content: bam files and bigwig contain mapping information
Library strategy: CUT&Tag

source_name: hAxioloid

growth_protocol: Human iPS cells were seeded on iMatrix-511 silk (Nippi) coated dishes at a density of 1.3×104 cells/well into 6 well plates 5 days prior to Axioloid induction and used at ~ 60% confluency. All subsequent induction steps were performed in AK02N (Reprocell) medium without component C (AK02N-C). Initially, hiPSCs were pulsed with a strong mesoderm and primitive streak fate inducing combination of bFGF (20 ng ml−1) and WNT agonist CHIR99021 (5 μM) for 24 h. CHIR99021 concentration may need to be adjusted depending on the used iPSC line, but remains usually in the range of 3-5 μM. 24 h after the initial pulse, cells were dissociated with Accutase (Thermo Fisher Scientific) and cultured for 24 h in 96 well U-bottom low attachment plates (Sumilon) at 500 cells/well in 50 μl of AK02N-C based aggregation medium supplemented with CHIR99021 (5 μM), basic FGF (20 ng ml−1), TGF inhibitor SB431542 (10 μM) and ROCK inhibitor Y27632 (10 μM). 24 h after aggregation, 150 μl of AK02N-C medium was added into each well and exchanged again after 24 h with 150 μl of fresh AK02N-C medium. 48 h after aggregation Axioloids were transferred one-by-one into BSA-treated 96 well flat-bottom low attachment plates (Watson) and embedded into 80 μl of AK02N-C medium containing 10% growth factor-reduced Matrigel (Corning) and cultured further at 37°C and 5% CO2 for 24 to 48 h. All trans-retinal (RAL) (1 µM) was added to the MG containing medium throughout the embedding phase.

extract_protocol:
Axioloids were collected into wells of a 96-well plate and washed three times by transferring to another well filled with 0.1% BSA (SIGMA) in HBSS(-). Axioloids of the desired stage and number were then transferred to another well filled with 100 μl of enzyme P solution of the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) and incubated at 37 ℃ for 10 minutes. After adding 100 μl of 0.1% BSA in HBSS(-) Axioloids were dissociated  by pipetting with an uncut P200 tip 20 times.
The collected cells were pelleted and snap-frozen in liquid nitrogen. Later on, 50,000 cells per experiment were first washed with Wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1X Protease Inhibitor (Roche, Cat#11873580001)), and then resuspended in the Wash buffer again. Then we mix the cell suspension with Concanavalin A-coated beads (Bangs Laboratories, Cat#BP531) resuspended in Binding buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Next, we resuspended cells in 100 µL of ice-cold Wash buffer, supplemented with 0.05% digitonin, 0.1 mM EDTA, and 0.1% BSA together with each 0.5 µL primary antibody. The antibodies used were mouse monoclonal IgG1 antibodies against H3K4me3 (MAB Institute, Cat#MA304B) and H3K27me3 (MAB Institute, Cat#MA323B). After incubation at room temperature for 2 hours, the buffer containing the primary antibody was replaced with 100 µL of ice-cold Wash buffer, supplemented with 0.05% digitonin, together with 1 µL secondary rabbit anti-mouse IgG antibody (abcam, ab46540), and was incubated at 4 °C for overnight. After washing the beads with Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 1X Protease Inhibitor (Roche, Cat#11873580001)) twice,we applied 100 µL of the Dig-300 buffer containing 0.5 femtomol pA-Tn5 transposome assembled above and incubated for 1 hour at room temperature. After washing the beads with Dig-300 buffer twice, we resuspended the beads in 50 µL of Dig-300 buffer supplemented with 10 mM MgCl2 and incubated them at 37 °C for 1 hour. We then removed the supernatant and resuspended the beads in 20 µL of 10 mM TAPS buffer (pH 8.5). We then added thermolabile proteinase K (NEB, Cat#P8111S), and incubated the mixture at 37 °C for 30 minutes, followed by incubation at 55 °C for 20 minutes to inactivate the proteinase. We directly performed PCR-amplification of the library from the tube after adding the reaction mixture (KAPA BIOSYSTEMS, Cat#KK2502). The amplified libraries were purified with 1.3 volumes of AMPure XP beads.

value: iPSC-derived mesodermal cell aggregates

tag: time point

tag: embedding

value: Matrigel

value: retinal

tag: antibody


title: Control-1 for NLP4,6


title: COLD_S_2


title: Vanillate Replicate 3

city: Evanston

first: Ludmilla

last: Aristilde

state: IL

address: 2145 Sheridan Rd

department: Civil and Environmental Engineering

institute: Northwestern University

data_processing:
Reads were mapped to the C. testosteroni KF-1 genome (ASM16885v1) obtained from NCBI using Kallisto.
Transcript abundance and differential gene expression were calculated with Voom and Limma using Degust. Raw counts per gene is reported in a single file, Wilkes_ALL_counts.tsv
Annotation information was obtained using RAST
Genome_build: ASM16885v1
Supplementary_files_format_and_content: raw count measurement

organism: Comamonas testosteroni

source_name: C. testosteroni in Minimal media with Vanillate

growth_protocol: Cells were grown in triplicate on minimal-nutrient media with 100 mM C of succinate, 4HB, VAN, or TER as sole carbon sources.

extract_protocol:
Samples were pelleted by centrifugation at 5000 g for 10 min and stored overnight at -80 °C before total RNA extraction. Enzymatic lysis of the bacteria cells was conducted using lysozyme prepared in molecular grade TE buffer and extractions were conducted using RNeasy Mini Kit (Qiagen).
Samples were sent to NUSeq Core Facility (Northwestern University, Chicago, IL) for TruSeq Total RNA-seq Library Prep and Illumina HiSeq Sequencing, 50 bp, single-end reads.

treatment_protocol: At an OD600 of about 1.0 (mid-exponential growth), an aliquot of cell culture (500 μL) was added to a double volume (1 mL) of RNAprotect Bacteria Reagent (Qiagen).

tag: strain

value: Comamonas testosteroni KF-1

value: Minimal media with Vanillate


title: M13 [Bisulfite-Seq]

tag: tissue

value: Loin muscle

value: Brangus

value: maternal diet methionine


title: Vanillate Replicate 2

tag: treatment


title: M17 [Bisulfite-Seq]


title: hAxioloid 96h_MG_RAL_H3K27me3_1


title: Control-1 for NLP1,2,3,5,8,9

value: Mesophyll protoplasts


title: hAxioloid 96h_MG_RAL_H3K4me3_2


title: M12 [Bisulfite-Seq]

value: maternal diet control


title: hAxioloid 96h_MG_RAL_H3K4me3_1


title: Control-1 for NLP7


title: Vanillate Replicate 1


title: CON_2

value: Control (Before Treatment)

value: Control


title: CON_3


title: PBMCs, Healthy, WTA, Ab-Seq, SMK [B1]

value: Blood

value: Healthy

value: SMK Antibody + Anti-CD195; Anti-CD74; Anti-CD40; Anti-CD184; Anti-CD49d; Anti-TCR-alpha_beta; Anti-CD152; Anti-CD95; Anti-CD127; Anti-CD25; Anti-CD62L; Anti-CD3; Anti-GITR; Anti-CD19; Anti-CD194; Anti-CD161; Anti-LAG-3; Anti-CD183; Anti-CD39; Anti-CD45RA; Anti-CD7; Anti-CD16; Anti-CD27; Anti-CD197; Anti-CD154; Anti-CD294; Anti-Tim3; Anti-CD5; Anti-CD14; Anti-CD8; Anti-CD56; Anti-CD21; Anti-CD279; Anti-CD45; Anti-CD69; Anti-CD28; Anti-CD38; Anti-TCR-gamma_delta; Anti-CD4; Anti-CXCR5


title: Terepthalate Replicate 3

source_name: C. testosteroni in Minimal media with Terepthalate

value: Minimal media with Terepthalate


title: CON_1


title: M11 [Bisulfite-Seq]


title: M10 [Bisulfite-Seq]


title: EndoMT4

city: Baltimore

first: Patrick

last: Cahan

address: 733 N. Broadway

institute: Johns Hopkins University

data_processing:
The FASTQ files for each in vitro sample were generated from the raw bcl data by bcl2fastq. The FASTQ files were subsequently processed using Cell Ranger 3.0 with default parameters. In brief, the alignment was performed by STAR with the human reference genome GRCh38 to generate the bam file. The BAM files were then subjected to the Velocyto pipeline to estimate the unspliced and the spliced read counts. We removed the low-quality cells that expressed less than 200 genes, or the expression of mitochondria genes exceeded 25% of total counts. Any genes that expressed less than 3 cells were excluded.
Genome_build: GRh38
Supplementary_files_format_and_content: TSV, MTX

source_name: endothelial cells

growth_protocol: Human coronary artery endothelial cells (ECs, passage 3-8, Lonza) were expanded in endothelial growth media (EGM-2MV, Lonza).

extract_protocol:
At day 14, cells cultures on 4 kPa hydrogel and TC with and without TGF-β stimulation were dissociated and resuspended in DMEM supplemented with 10% FBS. Single cell libraries were prepared using a 10X Chromium v3 microfluidic chip, targeting for 8000 cells per sample.
The barcoded libraries from individual samples were then pooled and multiplexed, followed by sequencing on an Illumina NovaSeq 6000 platform using a NovaSeq-S1 (2x100bp) flow cell.

treatment_protocol: The cells were seeded at a density of 120,000 cells/well onto the 4kPa hydrogels or tissue culture plates (TC). The day after cell seeding, the media was switched to a control medium comprising of endothelial basal medium (EBM, Lonza) supplemented with 5% fetal bovine serum (FBS, Lonza) with or without supplemented TGF-β (20 ng/ml, Peprotech).

value: TC+TGFB


title: EndoMT3

value: TC


title: M9 [Bisulfite-Seq]


title: COLD_S_1

value: Short (20 mins)

value: Cold


title: Terepthalate Replicate 2

value: Comamonas testosteroni KF-1


title: E15.5_F_Snf5_CKO2

city: Sagamihara

first: Toshiaki

last: Ito

state: Kanagawa

address: 1-15-1, Kitasato, Minami-ku

department: Biosciences

institute: Kitasato university

description: 50-bp reads

data_processing:
Trimmed by Trim-galore v0.6.5
Mapped by Bowtie2 v2.4.2
sorted by samtools v1.10
Remove PRC dupilcate by Picard v2.25.2
Peak call by MACS2 v2.2.7.1
Assembly: mm10
Supplementary files format and content: bam files which done mapping and removing PCR duplicate

organism: Mus musculus

source_name: embryo

extract_protocol:
Transposase reaction was done by Tagment DNA Enzyme and Buffer Small Kit or Large Kit (Illumina) and purified using MinElute PCR Purification Kit (QIAGEN, 28004).
Amplified using a NEBNext High Fidelity 23 PCR Master Mix (New England Biolabs) with indexed primers and purified using SPRIselect beads (Beckman Coulter).

treatment_protocol: Germ cells were sorted by Oct4-EGFP

tag: Sex

value: female

tag: developmental stage

tag: genotype

value: Snf5 CKO

value: embryo

value: Sorted by using Oct4-EGFP


title: Terepthalate Replicate 1


title: EndoMT2


title: M8 [Bisulfite-Seq]

value: Loin muscle

value: Brangus

value: maternal diet methionine


title: M7 [Bisulfite-Seq]


title: EndoMT1


title: E15.5_F_Snf5_CKO1

description: 50-bp reads


title: 4-hydroxybenzoate Replicate 2

source_name: C. testosteroni in Minimal media with 4-hydroxybenzoate

value: Minimal media with 4-hydroxybenzoate


title: E15.5_F_Snf5_Ctrl2

description: 50-bp reads

value: Control


title: HEK293_ Xrn2 WT_5'Bruseq Rep3

tag: cell line

value: HEK293 Flp-in Trex pcDNA5 Xrn2 WT Avitag

value: monoclonal anti-BrdU 3D4 (Pharmingen Cat 555627)

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep  DMSO, doxycycline (2.0 ug/ml) 24hr


title: E15.5_F_Snf5_Ctrl1

description: 50-bp reads


title: SN_Diff41_G3_D40

description: Single Cell Pool

data_processing:
Sequencing reads were intially processed using the 10X Cell Ranger pipeline v6.1.
Raw base call data data was converted to FASTQ with cellranger mkfastq and subsequently aligned filtered and counted using cellranger count. Sample data across multiple runs were agrregated and nomalised as required using cellranger aggr.
Futher data processing and analysis was performed as required with R and Seurat v3.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: Three processed files are included for each sample and represent the output files from the 10X Cell ranger pipeline.  These incldue the single cell barcodes, genes (features) and counts for each cell in the sample pool. The format is compressed tsv or mtx files.

source_name: iPSC derived sensory neurons

extract_protocol: Single Cell suspensions were processed following the 10X Genomics Chromium Single Cell Expression v2 pipeline and protocols

tag: differentiation

value: Sensory Neuron


title: iNeuron_Diff5_G3_D21

description: Single Cell Pool

source_name: iPSC derived cortical neurons

value: Cortical Neuron (iNeuron)


title: M6 [Bisulfite-Seq]


title: 4-hydroxybenzoate Replicate 1


title: M3 [Bisulfite-Seq]

value: maternal diet control


title: scRNA-seq_Rumen_newborn_2

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

source_name: Rumen

extract_protocol:
The rumen tissues isolated from adult and newborn cows were stripped of the outer muscle layers, and then minced into 10×0.5mm2 pieces on ice with scissors. The tissues were incubated in a 37℃ water bath with 20 mM EDTA for 30 min, and then were rinsed with DPBS and chopped into 1 mm pieces. Tissue pieces were transferred to a 15 mL centrifuge tube, and re-suspended with 0.25% Trypsin-EDTA (Gibco). After incubated in a 37℃ water bath for 5 min, the centrifuge tube containing tissues was inserted into ice for 2min, and pre-chilled HBSS was added to stop the digestion. After centrifuged at 300 × g for 2 min at 4℃, the supernatant was discarded, and samples were washed twice with cold HBSS and then re-suspended with dissociation enzymes (1.5mg/ml collagenase I, 1.5ml/ml collagenase IV,1.5mg/ml dispase, 100U/ml hyaluronidase, and 50U/ml DNase I) for 30 min at 37℃.
The single-cell RNA-seq library preparation was performed using the Chromium Single Cell 3' Reagent Kits v3.

value: Holstein dairy cows

value: rumen

value: newborn


title: scRNA-seq_Rumen_newborn_3


title: Succinate Replicate 3

source_name: C. testosteroni in Minimal media with Succinate

value: Comamonas testosteroni KF-1

value: Minimal media with Succinate


title: SN_Diff24_G3_D11

description: Single Cell Pool


title: M2 [Bisulfite-Seq]


title: hepatic_progenitor

description: total RNA

data_processing:
The generated sequencing reads were mapped against the human genome build hg19 using STAR aligner
The read counts for each gene were calculated using featureCounts
The low expression genes with total counts across all samples less than 10 were excluded
Gene expression was normalized by DESeq2 (v1.22.2) with variance-stabilizing transformation (VST) (Love et al., 2014)
Genome_build: hg19 for human
Supplementary_files_format_and_content: CSV file includes the non-normalized expression values for each sample

source_name: human hepatic progenitor-like cells

treatment_protocol: Hepatic progenitors were induced from human embryonic fibroblasts by the well-establised two-step lineage reprogramming protocol. hiHeps derived from hepatic progenitors were cultured in W2C/H2C/W3C/W6C medium for 7-14 days.Primary huaman hepatocytes and human liver tissues were freshly isolated. All samples were colleted from RNA extraction.

value: human hepatic progenitor-like cells

value: reprogrammed from human fibroblasts


title: scRNA-seq_Rumen_newborn_1


title: Succinate Replicate 2


title: Succinate Replicate 1


title: primary_hepatocyte

description: total RNA

source_name: primary human hepatocyte

value: primary human hepatocyte

value: freshly isolated


title: 4-hydroxybenzoate Replicate 3

value: Minimal media with 4-hydroxybenzoate


title: hepatic progenitor

data_processing:
Data were processed according to the 10x Cell Ranger pipeline with version v3.1.0
Reads were aligned with GRCh38 genomes.
Quality control was performed with R package Seurat (v3.2.0) by removing genes expressed in fewer than three cells and low-quality cells with less than 500 genes expressed. In addition, cells expressed more than 6000 genes and with more than 10% mitochondrial counts were also excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of detected genes; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: hepatic progenitor

extract_protocol:
Cell suspensions (600-1300 living cells per microliter determined by trypan blue staining) were loaded on a 10x Genomics Chromium™ Controller Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs) by using Chromium™ Single Cell 3' Library & Gel Bead Kit V2 (10x Genomics, 120237) and Single Cell A Chip Kit (10x Genomics, 120236). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEM. Barcoded cDNAs were pooled and cleanup by using DynaBeads MyOne Silane Beads (Thermo Fisher, 37002D), and then amplified and cleanup for further next generation library construction.
Single-cell RNA-seq libraries were prepared using Chromium™ Single Cell 3' Library & Gel Bead Kit V2 (10x Genomics, 120237) and i7 Multiplex Kit (10x Genomics, 120262), following the manufacture’s instructions. Sequencing was performed on an Illumina HiSeq X Ten (Illumina, San Diego, CA, USA) with pair end 150bp (PE150).

treatment_protocol: Hepatic progenitors  were induced from human embryonic fibroblasts by the well-establised two-step lineage reprogramming protocol. Cells were harvested and resuspended at 1e6 cells per milliliter in 1xPBS with 0.04% BSA.

value: hepatic progenitor


title: primary_liver_tissue

description: total RNA

source_name: human liver tissue

value: human liver tissue


title: M1 [Bisulfite-Seq]

value: Loin muscle

value: Brangus


title: M4 [Bisulfite-Seq]

value: maternal diet methionine


title: 16_D0

status: Public on Nov 16 2022

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

hyb_protocol: NuGEN Ovation WB

scan_protocol: GeneChip(r) Scanner

data_processing: R/Bioconductor; GCRMA

source_name: PBMC

label_protocol: NuGEN Ovation WB

extract_protocol: Standard Qiagen Kit

value: PBMC

tag: gender

value: F

tag: timepoint

tag: subjectid

tag: group

value: TB-TRT

tag: centre

value: Estonia


title: 29_D37

tag: cell type

value: M


title: 29_D0


title: 22_D30


title: 16_D30


title: 46_D30


title: 29_D7


title: 22_D37


title: 16_D7


title: 16_D37


title: 46_D37


title: 52_D37


title: 22_D0


title: 62_D0


title: 29_D30


title: 46_D7


title: 22_D7


title: 62_D30


title: 61_D7


title: 41_D0


title: 52_D30


title: 54_D7


title: 20_D0


title: 54_D0


title: 46_D0


title: 41_D37


title: 20_D37


title: 52_D0


title: Control-2 for NLP4,6

data_processing:
The quality of each sequencing library was assessed by examining fastq files with FastQC (version 0.11.5).
The RNA-seq reads were mapped to the Arabidopsis (TAIR10) genome with Tophat program (version 2.1.1). The featureCount program of HTseq package (version 0.6.1) was used to quantify the RNA-seq expression levels of the TAIR10 annotated gene models.

source_name: Mesophyll protoplasts

tag: ecotype

value: Mesophyll protoplasts


title: 54_D37


title: 37_D0


title: 37_D37


title: 2_D37


title: 38_D37


title: 38_D30


title: 38_D0


title: 23_D30


title: 25_D7


title: 25_D0


title: 2_D7


title: 38_D7


title: 23_D7


title: 37_D7


title: 2_D0


title: 70_D0


title: 25_D30


title: 70_D37


title: 70_D30


title: 53_D30


title: 70_D7


title: 25_D37


title: 53_D37


title: 53_D0


title: 53_D7


title: 15_D37

value: Taiwan


title: 15_D30


title: 15_D0


title: 23_D37


title: 9_D7


title: 15_D7


title: 9_D37


title: 9_D30


title: 67_D30


title: 19_D37


title: 67_D0


title: 67_D37


title: 19_D30


title: 44_D37


title: 44_D30


title: 44_D7


title: 56_D7

value: TBDN-NEG


title: 69_D0

value: TBDN-POS


title: 44_D0


title: 69_D7


title: 19_D7


title: 69_D30


title: 56_D37


title: 56_D0


title: 4_D0


title: 51_D7


title: 51_D37


title: 4_D30


title: 4_D7


title: 69_D37


title: 51_D0


title: 37_D30


title: 51_D30


title: 10_D30


title: 10_D37


title: 42_D0


title: 12_D7


title: 42_D7


title: 12_D0


title: 42_D30


title: 10_D7


title: 12_D37


title: 4_D37


title: 42_D37


title: 5_D0


title: 66_D7


title: 10_D0


title: 5_D7


title: 12_D30


title: 5_D37


title: 66_D37


title: 66_D30


title: Casp8-/-Ripk3-/-Ripk1-/-_rep1

city: Memphis

first: Raghvendra

last: Mall

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Clariom S Mouse GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: Bone marrow derived macrophages (BMDMs) from Casp8-/-Ripk3-/-Ripk1-/- mouse

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: Primary mouse bone marrow-derived macrophages (BMDMs) were generated from the bone marrow of wild type and the indicated mutant mice. Cells were grown for 5–6 days in IMDM (Thermo Fisher Scientific, 12440053) supplemented with 1% non-essential amino acids (Thermo Fisher Scientific, 11140-050), 10% FBS (Biowest, S1620), 30% L929 conditioned media, and 1% penicillin and streptomycin (Thermo Fisher Scientific, 15070-063). BMDMs were then seeded into the growth media at a concentration of 1 x 10^6 cells into 12-well plates and incubated overnight.

extract_protocol: RNA was extracted from BMDMs using TRIzol™ Reagent (ThermoFisher P/N 15596026)

value: Bone marrow derived macrophages (BMDMs)


title: 11_D37


title: 11_D30


title: 11_D7


title: Casp8-/-Ripk3-/-Ripk1-/-_rep2


title: Ripk3-/-_rep2

source_name: Bone marrow derived macrophages (BMDMs) from Ripk3-/- mouse


title: 11_D0


title: 5_D30


title: 66_D0


title: day 8, exhausted CD8+ T cells, donor 10

city: Hong Kong

first: Weixin

last: Chen

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimed reads were mapped to UCSC human genome GRCh38/hg38 using Bowtie2.
Peaks were called using MACS2.
bigWig files were generated using samtools and deeptools.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: peripheral blood

growth_protocol: Purified CD8+ T cells were maintained in T cell medium (RPMI 1640 medium supplemented with 10% FBS, 50M -mercapteoethanol, 1M HEPES, 1X non-essential amino acids (NEAA), 100mM sodium pyruvate, and 1% penicillin-streptomycin)

extract_protocol: 50,000 alive CD8+ T cells were sorted for library established. ATAC-seq libraries were prepared for the paired-end sequencing using Omni-ATAC protocol (Corces et al. Nature Methods 2017)

treatment_protocol: CD8+T cells were then stimulated with anti-CD3/anti-CD28-coated microbeads (Dynabeads M-450 Epoxy, Invitrogen; bead to cell ratio of 1:1) in the presence of 10U/ml recombinant human IL-2 (PeproTech) in the medium. In these conditions, human universal Type I interferon (PBL Assay science) was added at 1000U/mL throughout the culture for the IFN-Is treatment group.

value: peripheral blood

value: CD8+ T cells


title: day 8, exhausted CD8+ T cells, donor 9


title: HCMV-infected Kasumi-3 latency, replicate 2

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: longread-featurecount.tsv

data_processing:
Raw FAST5 files were basecalled with guppy (v4.2).
Sample quality including sequencing quality and alignment quality is checked with pycoQC (v2.5.0.19).
Basecalled fastq files are mapped using minimap2 (v2.17) with parameters "-k 13 -w x splice -N 32 -un".
Poly(A) tail analysis was done with nanopolish (v0.32).
Modification analysis was done with eligos2 (v2.1.0) pair_diff_mod, using IVT sampel as control.
Assembly: Human (hg38), Human herpesvirus strain Toledo (GU937742.2), nanopore DRS callibration strand (YHR174W)
Supplementary files format and content: tab-delimited text files include read count values for each sample

growth_protocol: HFF were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin (100 U/ml)-streptomycin (100 µg/ml). Kasumi-3 were maintained in RPMI supplemented with 20% FBS, penicillin-streptoycin, 100 µg/mL gentamicin. Cells were incubated at 37ºC under 5% CO2 atmosphere.

extract_protocol:
Total RNAs were extracted using TRIzol reagent and treated with recombinant DNAse 1 for 1h at 37ºC, followed by purification using NucleoSpin RNA Clean-up kit.
Library preparation for nanopore sequencing was performed using the Oxford Nanopore Technologies’s direct RNA sequencing kit (SQK-RNA002) according to the manufacturer’s instruction. To improve the efficiency, we performed reverse transcription using SuperScript III (Thermo Scientific) after the adapter ligation.

treatment_protocol: HFFs were incubated with virus in serum-free DMEM for 1h, washed twice with PBS, and incubated in complex media. For HCMV latent and reactivation infection, Kasumi-3 cells were incubated in X-VIVO 15 for 48h before infection. Cells were infected with HCMV MOI of 1 by incubation in X-VIVO 15 for 4h with rocking every 30 min, followed by spinfection at 1000xg for 30 min. After overnight incubation with virus, cells were treated with trypsin-EDTA to detach remaining viruses and then cushioned onto Ficoll-Pacque to collect live cells from debris and viruses. Cells over cushion were washed with PBS, incubated in X-VIVO 15. For reactivation assay, cells were treated with 20 mM PMA or DMSO for additional 2 days.

value: Lymphoblast

value: WT


title: HCMV-infected Kasumi-3 reactivation, replicate 2

description: longread-featurecount.tsv

value: PMA for differentiation


title: HCMV-infected Kasumi-3 latency, replicate 1

description: longread-featurecount.tsv


title: 8_D7


title: 9_D0


title: Casp8-/-Ripk3-/-_rep1

source_name: Bone marrow derived macrophages (BMDMs) from Casp8-/-Ripk3-/- mouse


title: Ripk3-/-_rep1


title: 43_D0


title: 43_D7


title: 17_D0


title: 8_D30


title: HCMV-infected Kasumi-3 reactivation, replicate 1

description: longread-featurecount.tsv


title: 17_D30


title: 17_D37


title: 17_D7


title: WT_rep2

source_name: Bone marrow derived macrophages (BMDMs) from WT mouse


title: 43_D37


title: 8_D0


title: day 2, effector CD8+ T cells, donor 10


title: day 8, exhausted CD8+ T cells, donor 8


title: WT_rep1


title: Casp8-/-Ripk3-/-_rep2


title: 43_D30


title: 8_D37


title: HCMV-infected HFF lytic, replicate 1

description: longread-featurecount.tsv

source_name: Human foreskin fibroblast

value: Human foreskin fibroblast

value: Human Foreskin Fibroblast


title: day 2, effector CD8+ T cells, donor 8


title: day 0, naïve CD8+ T cells, donor 10


title: day 2, effector CD8+ T cells, donor 9


title: 1_D0

value: PBMC


title: 1_D30


title: day 0, naïve CD8+ T cells, donor 8


title: day 0, naïve CD8+ T cells, donor 9


title: Small Pre-B cells, Littermate control, biol rep 3 [sPreB_1353]

city: Lund

first: Joan

last: Yuan

address: Klinikgatan 17

country: Sweden

institute: Lund University

description:
sPreB_1348,sPreB_1349,sPreB_1351,sPreB_1352,sPreB_1353,sPreB_1356
sPreB_normalizedcounts
sPreB_deseq2_results

data_processing:
Reads were aligned using STAR aligner v2.7.1 and counted using RSEM v.1.28.
Assembly: mm10
Supplementary files format and content: DESeq2 normalized counts for all samples of indicated cell types
Supplementary files format and content: DESeq2 result file for indicated cell type, comparing Lin28b samples to littermate control samples

source_name: Bone marrow

growth_protocol: Co-housed littermate mice were fed with doxycycline chow (200 mg/kg) for 10 days before sacrificed and sorted for RNA-sequencing

extract_protocol:
Total RNA was isolated using RNAzol (Sigma-Aldrich)
Libraries were generated using the SMART-Seq v4 Ultra Low Input RNA Library Prep Kit (Clontech) and the Nextera XT DNA Indexing Kit (Illumina) according to the manufacturer’s instructions. Libraries were indexed using the Nextera XT v2 Indexing Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Bone marrow was isolated from back limbs and sternum, red blood cells were lysed (ACK lysis buffer), and resulting sample was lineage depleted for CD3+, TER119+, and GR1+ cells, before B cell progenitors were sorted.

value: Bone marrow

value: Small Pre-B cell

value: Littermate control

value: Doxycycline chow (200mg/kg) for 10 days


title: Small Pre-B cells, Littermate control, biol rep 2 [sPreB_1352]


title: Small Pre-B cells, Lin28b, biol rep 3 [sPreB_1356]


title: Small Pre-B cells, Littermate control, biol rep 1 [sPreB_1351]


title: Small Pre-B cells, Lin28b, biol rep 2 [sPreB_1349]


title: WT_all_combined

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Micro-C data for D. melanogaster were aligned to a custom genome edited from the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly (dos Santos et al. 2015) with BWA-MEM (Li and Durbin 2009) using parameters -S -P -5 -M. Briefly, the custom genome was designed to remove the visually obstructive ~5.6kb DIVER_I-int repeat element between Fub-1 and Fub. The specific region deleted was the entire repeat element, chr3R: 16756620-16762262 from the dm6 reference FASTA file. The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with pairtools (https://github.com/mirnylab/pairtools). We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three. The resultant files were indexed with pairix (https://github.com/4dn-dcic/pairix). The files from replicates were merged with pairtools before generating 100bp contact matrices with Cooler (Abdennur and Mirny 2019). Finally, balancing and mcool file generation was performed with Cooler’s zoomify tool. The mcool files were visualized using HiGlass (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1486-1).
Assembly: dm6
Supplementary files format and content: pairs
Supplementary files format and content: mcool
Library strategy: Micro-C

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Embryos were collected on yeasted apple juice plates in population cages. Plates were laid for 4 hours, incubated for 12 hours at 25℃, then subjected to fixation.

extract_protocol:
Embryos were collected in nylon mesh sieves, dechorionated for 2 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass vials containing 5 mL PBST (0.1% Triton-X in PBS), 7.5 mL N-heptane, and 1.5mL fresh 16% formaldehyde. Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 3.7 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction. Embryos were washed twice with 15 mL PBST and subjected to secondary crosslinking. Secondary crosslinking was done in 10mL of freshly prepared 3mM final DSG and ESG in PBST for 45 mins at room temperature with passive mixing. Reaction was quenched by addition of 3.7mL of 2M Tris-HCl pH7.5 for 5 mins, washed twice with PBST. Embryos were snap-frozen and stored at -80℃ until library construction.
Micro-C libraries were prepared as previously described (Batut et al. 2022) with the following modification: we used 50uL of 12-16hr embryos, non-sorted for each biological replicate. 60U of MNase was used for each reaction to digest chromatin to 80% mononucleosome vs 20% dinucleosome ratio. Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100 nt Flowcell (read length 50 bases per mate, 6-base index read).

value: Embryo

value: yw

value: Insertion at eve


title: Fub1_rep2

value: Insertion at Fub1 in BX-C


title: 30_D37

value: M

value: TBDN-NEG

value: Taiwan


title: 30_D0


title: 59_D0

value: TBDN-POS


title: 36_D37

value: F


title: Small Pre-B cells, Lin28b, biol rep 1 [sPreB_1348]


title: Large Pre-B cells, Littermate control, biol rep 2 [GT109_LPreB]

description:
GT103_LPreB,GT104_LPreB,GT105_LPreB,GT107_LPreB,GT108_LPreB,GT109_LPreB,GT112_LPreB
LPreB_normalizedcounts
LPreB_deseq2_results

value: Large Pre-B cell


title: Large Pre-B cells, Littermate control, biol rep 3 [GT112_LPreB]


title: 59_D7


title: 59_D30


title: 1_D7


title: 30_D7


title: 1_D37


title: 59_D37


title: Large Pre-B cells, Lin28b, biol rep 4 [GT108_LPreB]


title: 36_D0


title: Fub1_rep1


title: Large Pre-B cells, Lin28b, biol rep 2 [GT105_LPreB]


title: 36_D7


title: 19_D0


title: 39_D37


title: Large Pre-B cells, Lin28b, biol rep 3 [GT107_LPreB]


title: Large Pre-B cells, Littermate control, biol rep 1 [GT104_LPreB]


title: 30_D30


title: 39_D30


title: 39_D7


title: 36_D30


title: 39_D0


title: Large Pre-B cells, Lin28b, biol rep 1 [GT103_LPreB]


title: 7_D7


title: 7_D30


title: Large Pro-B cells, Lin28b, biol rep 5 [GT114_LProB]

description:
GT103_LProB,GT104_LProB,GT105_LProB,GT107_LProB,GT108_LProB,GT109_LProB,GT112_LProB,GT113_LProB,GT114_LProB
LProB_normalizedcounts
LProB_deseq2_results

value: Large Pro-B cell


title: Large Pro-B cells, Littermate control, biol rep 4 [GT113_LProB]


title: 7_D37


title: Large Pro-B cells, Littermate control, biol rep 3 [GT112_LProB]


title: Large Pro-B cells, Lin28b, biol rep 4 [GT108_LProB]


title: Large Pro-B cells, Lin28b, biol rep 3 [GT107_LProB]


title: Large Pro-B cells, Lin28b, biol rep 1 [GT103_LProB]


title: Large Pro-B cells, Littermate control, biol rep 1 [GT104_LProB]


title: Large Pro-B cells, Littermate control, biol rep 2 [GT109_LProB]


title: 26_D30


title: 13_D37


title: 24_D30


title: 26_D7


title: 13_D0


title: 13_D7


title: 26_D37


title: 24_D7


title: Regen, Lmx1bCreERT2TdT, 14 DPA, scRNA-seq

city: Vancouver

first: Freda

last: Miller

address: 2125 East Mall

department: Medical Genetics

country: Canada

institute: The University of British Columbia

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite.
The number of cell barcodes per sample was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
Assembly: mm10_TdTomato
Supplementary files format and content: The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.

source_name: Adult regenerating digit tip

extract_protocol:
Tissue was dissected from the regenerating digit tip at 14DPA. Freshly dissected tissue was digested in Liberase (280ug/mL) at 37°C for 1 - 4hr, with constant aggitation. Cells were mechanically dissociated with a small-bore-hole glass pipette, filtered through a 20um cell strainer and pelleted by centrifugation at 1000 rpm for 5 min. The cell pellet was then washed in 1X HBSS and cells were counted with a haemocytometer and pelleted again by centrifugation at 1000 rpm for 5 min. The cell pellet was re-suspended in a solution containing 0.04% BSA in 1X HBSS at a concentration of 500-700 cells/ul, prior to collection of single cell transcriptomes.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

treatment_protocol: Mice were injected intraperitoneally with tamoxifen (3mg/day) for four consecutive days. Digits were then amputated 10 days post tamoxifen and the regenerating digit tips distal to the original amputation site were collected at 14 days post amputation. When processing the sequencing data, the reads were aligned to the mm10_TdTomato genome.

value: Adult regenerating digit tip

tag: regeneration timepoint

value: 14 Days

tag: age

value: 10-12 weeks


title: Regen, PdgfraCreERTTdT, 14 DPA, scRNA-seq

description: 10X Genomics

tag: strain


title: 13_D30

value: PBMC


title: Large Pro-B cells, Lin28b, biol rep 2 [GT105_LProB]

tag: tissue

value: Bone marrow


title: 26_D0


title: 7_D0


title: GC_5

city: Tsukuba

first: Masafumi

last: Muratani

state: Ibaraki

address: 1-1-1 Tennodai

department: Faculty of Medicine

institute: University of Tsukuba

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10) and quantified for 49,585 genes.
Total counts were normalized by quantile method.
Differentially expressed genes were identified using Empirical Analysis of DGE tool in CLC Genomics Workbench.
Assembly: mm10
Supplementary files format and content: CSV files for  gene name, raw read counts, TPM and RPKM.
Supplementary files format and content: Microsoft Excel file format with normalized counts. Gene annotation is provided in Supplementary file in Excel format.

source_name: Plasma

extract_protocol:
50 micro-litter of plasma aliquot after removal of cell debris was resuspended with 750 micro-litter of TRIzol-LS and 200 micro-litter of water. RNA was purified following standard protocol.
2.5 micro-litter of total RNA was used for library prep with NEBNext Small RNA Library Kit (New England Biolabs, cat. no. E7330S).
Small-RNA library preparation was used due to RNA degradation.

value: Plasma

value: 13 weeks

value: wild type

tag: treatment

value: Ground control


title: GC_3


title: GC_2


title: GC_4


title: MG_6

value: Microgravity


title: GC_1


title: MG_5


title: 24_D37

value: M


title: 24_D0


title: 32_D0


title: 32_D30


title: MG_4


title: 32_D7


title: 48_D37


title: 32_D37


title: 48_D30


title: AG_6


title: MG_3


title: MG_2


title: MG_1


title: AG_5


title: AG_4


title: AG_3


title: AG_1


title: 48_D7


title: ATAC MCM2_2A NPC rep1

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
mapped to mouse (mm10) reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Peaks were called by MACS by parameters “macs2 callpeak -g mm -f BAMPE -p 1e-04 --broad --broad-cutoff 1e-04 --llocal 10000 –nolambda” and the cutoff of peak is p=0.0001.
Assembly: mm10
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
Supplementary files format and content: bed, peak position

source_name: NPC

growth_protocol: Mouse ES cells were disaggregated and suspended in ES cell medium without LIF. EBs were formed using hanging drop method (300 cells per drop) on dish lids for 3 days. EBs were then collected and cultured in 10 cm low attachment Petri dish in ES cell culture medium without LIF, and the medium was changed every other day.

extract_protocol:
CUT&RUN was performed by following published protocol
DNA was purified using the QIAquick PCR Purification Kit (28104, Qiagen) and used for library preparation with the AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).
CUT&RUN

treatment_protocol: To generate pluripotency EGFP reporter mouse E14 WT and Mcm2-2A ES cell line, the lentivirus-based EGFP reporter vector PL-SIN-EOS-C(3+)-EGFP plasmid (Addgene) was used for infection. After selection, single cells were seeded and individual clones were then isolated, expanded and confirmed under fluorescence microscope.

value: NPC

value: ATAC


title: ATAC MCM2_2A NPC rep2


title: ATAC WT NPC rep1

value: WT


title: ATAC MCM2_2A mES rep2

source_name: mES

value: mES


title: ATAC WT NPC rep2


title: 31_D37

value: TBDN-POS

value: Taiwan


title: 47_D7

value: TBDN-NEG


title: 47_D37


title: 31_D0


title: 64_D37


title: ATAC WT mES rep2


title: 47_D30


title: AG_2


title: 64_D30


title: 31_D30


title: ATAC WT mES rep1


title: 64_D0


title: 64_D7


title: EZH2_RUN MCM2_2A NPC


title: 47_D0


title: 45_D0

value: F


title: EZH2_RUN WT NPC


title: ATAC MCM2_2A mES rep1


title: H3K27me3_RUN MCM2_2A NPC rep2


title: EZH2_RUN MCM2_2A mES


title: 31_D7


title: EZH2_RUN WT mES


title: 45_D30


title: H3K27me3_RUN MCM2_2A NPC rep1


title: H3K27me3_RUN WT NPC rep2


title: 49_D7


title: 49_D37


title: 49_D30


title: 49_D0


title: H3K27me3_RUN WT NPC rep1


title: 45_D37


title: H3K27me3_RUN MCM2_2A mES rep2


title: 18_D7

value: TB-TRT


title: 18_D0

value: PBMC


title: 18_D37


title: H3K4me3_RUN MCM2_2A NPC rep2


title: H3K4me3_RUN MCM2_2A NPC rep1


title: H3K27me3_RUN WT mES rep1


title: H3K4me3_RUN WT NPC rep2


title: 65_D0


title: 65_D30


title: 45_D7


title: 14_D0


title: 65_D7


title: H3K4me3_RUN MCM2_2A mES rep2


title: 18_D30


title: H3K4me3_RUN WT NPC rep1


title: 14_D7


title: 14_D37


title: 50_D7


title: H3K4me3_RUN WT mES rep1


title: 14_D30


title: H3K4me3_RUN WT mES rep2


title: MCM2_RUN WT mES antibody(flag) rep2

tag: chip antibody

value: Flag


title: H3K27me3_RUN WT mES rep2


title: MCM2_RUN WT mES antibody(flag) rep1


title: 6_D37


title: MCM2_RUN MCM2_2A NPC rep2


title: 50_D37


title: 65_D37


title: MCM2_RUN MCM2_2A NPC rep1


title: H3K4me3_RUN MCM2_2A mES rep1


title: 50_D30


title: MCM2_RUN WT NPC rep2


title: 6_D30


title: MCM2_RUN WT NPC rep1


title: 33_D37


title: MCM2_RUN WT mES rep2


title: 33_D7


title: Plate4_H8_S380

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Raw fastq sequence files generated from Smartseq2 libraries were aligned to the mouse genome (v. mm10) associated with the mouse transcriptome annotations (v. gencode M23) using STAR. Subsequently, genome-mapped BAM files were processed through RSEM (v. 1.3.1) for gene quantification. The matrix of gene counts was then used as input for analysis by the R package Seurat (v. 4.1.0). Next, the dataset was normalized by the LogNormalize method implemented by Seurat. To control unwanted experimental noise sources, we “regressed out” the mitochondrial gene abundance and the library size with the ScaleData function.
Additionally, cells containing more than 10% of sequence reads aligned to mitochondrial genes were excluded before normalization. Single cells were clustered, and gene expression was evaluated with the Seurat workflow. Gene signature scoring was performed by using Seurat’s AddModuleScore. Heatmaps were produced with the ComplexHeatmaps package for R. Differentially expressed gene analyses between clusters or biological groups were performed by the Seurat function FindAllMarkers with the non-parametric Wilcoxon Rank sum test. Genes were considered to downstream analysis when having a log2 fold change greater or smaller than 0.5 and exhibiting an adjusted p-value of at least 0.05. We used the Wilcoxon rank-sum test to compare specific genes between b-hex cells (Fig. 3G), and p values were corrected by the Benjamini Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: Rsem gene counts

source_name: Intraepithelial Lymphocytes

extract_protocol:
IELs were stained as above, washed, filtered, and resuspended in complete RPMI before sorting. Single-cells were index-sorted directly into 96-well plates containing 5ul of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol using a BD FACS Aria II instrument. After sorting, plates were immediately frozen on dry ice and stored at -80ºC before processing. All sorting data were analyzed using FlowJo software v.10.
Each sorted plate contained all conditions assayed in each replicate and libraries were prepared as previously described (9). RNA was extracted from single cells using RNAClean XP Solid Phase Reversible Immobilization (SPRI) beads (Agentcourt, Beckman Coulter), and hybridized first using RT primer (/5BiosG/AAGCAGTGGTATCAA CGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN) and then reverse transcribed into cDNA using TSO primer (59-AAG- CAGTGGTATCAACGCAGAGTACATrGrGrG-39) and RT maxima reverse transcription (Thermo Fisher Scientific). cDNA was amplified using ISPCR primer (59-AAGCAGTGGTATCAACGCAGAGT- 39) and KAPA HiFi HotStart ReadyMix (Thermo Fisher Scientific), cleaned up using RNAClean XP SPRI beads three times, and tagmented using Nextera XT DNA Library Preparation Kit (Illumina) following manufacturer’s instructions. For each sequencing batch, up to four plates were barcoded at a time with Nextera XT Index Kit v2 Sets A–D (Illumina). Finally, barcoded libraries were pooled and sequenced using Illumina Nextseq 500 platform.

tag: biological sample

value: Pre-IEL


title: Plate4_G2_S362

value: Conventional


title: Plate4_H3_S375


title: Plate4_F9_S357


title: 6_D0


title: 40_D30


title: 33_D0


title: 33_D30


title: MCM2_RUN MCM2_2A mES rep2

tag: genotype


title: 40_D37


title: 40_D0


title: 40_D7


title: 6_D7


title: 27_D0


title: Plate4_F4_S352


title: MCM2_RUN MCM2_2A mES rep1

tag: cell line


title: Plate4_E1_S337


title: Plate4_E3_S339


title: MCM2_RUN WT mES rep1


title: 58_D0


title: 27_D7


title: 27_D30


title: 58_D7


title: 58_D30


title: Plate4_G1_S361


title: Plate4_D8_S332


title: Plate4_D7_S331


title: 27_D37


title: 58_D37


title: Plate4_D6_S330


title: Plate4_D2_S326


title: Plate4_D1_S325


title: 68_D0


title: Plate4_D3_S327


title: Plate4_D4_S328


title: 68_D30


title: 68_D7


title: Plate4_D9_S333


title: Plate4_C7_S319


title: Plate4_C5_S317


title: Plate4_C9_S321


title: 35_D37


title: 68_D37


title: Plate4_C3_S315


title: Plate4_C2_S314


title: Plate4_C1_S313


title: Plate4_B9_S309


title: 35_D30


title: 57_D0


title: 57_D37


title: 57_D30


title: Plate4_B4_S304


title: Plate4_B3_S303


title: 35_D0


title: 57_D7


title: Plate4_B5_S305


title: Plate4_B6_S306


title: 34_D7


title: Plate4_B2_S302


title: Plate4_B1_S301


title: Plate4_A9_S297


title: Plate4_A8_S296


title: Plate4_A7_S295


title: Plate4_A6_S294


title: Plate4_A5_S293


title: 63_D7


title: 3_D0


title: 3_D30


title: 63_D37


title: Plate4_A4_S292


title: 34_D37


title: 34_D0


title: Plate4_A2_S290


title: Plate4_A1_S289


title: Plate4_A3_S291


title: 3_D37


title: 63_D0


title: 34_D30


title: Plate3_H9_S285


title: Plate3_H7_S283


title: 60_D7


title: Plate3_H3_S279


title: 60_D0


title: Plate3_H2_S278


title: 63_D30


title: 28_D37


title: 60_D37


title: 55_D0


title: 28_D0


title: 55_D7


title: 28_D30


title: Plate3_G7_S271


title: Plate3_F9_S261


title: Plate3_F8_S260


title: H3K27me3_RUN MCM2_2A mES rep1


title: Plate3_F3_S255


title: Plate3_E9_S249


title: Plate3_F1_S253


title: 28_D7


title: Plate3_E7_S247


title: Plate3_F7_S259


title: Plate3_E5_S245


title: Plate3_E3_S243


title: Plate3_D8_S236


title: Plate3_E2_S242


title: Plate3_F5_S257


title: 21_D7


title: Plate3_D7_S235


title: Plate3_D6_S234


title: 55_D37


title: 21_D37


title: Plate3_D5_S233


title: 217 IBSP at 4D, biological rep1

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Line 217, IBSP at 4D, biological rep1

hyb_protocol: Affymetrix high-density oligonucleotide HG-U133A Plus 2.0 Human Arrays.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings,  background corrected, and Robust Multi-array Average (RMA)  as normalization method.

source_name: IBSP at 4D, biological rep1

label_protocol: manufacture protocol

growth_protocol: Tumors were cultured as described previously 6 in DMEM/F12 medium supplemented with B27 (GIBCO), 20 ng/ml bFGF (Peprotech), 50 ng/mL EGF, penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen) and 5 ug/ml heparin (Sigma-Aldrich).

extract_protocol: Trizol

treatment_protocol: IBSP at 250nM

tag: line

value: IBSP

tag: culture method


title: Plate3_D4_S232


title: 217 IBSP at 4D, biological rep3

description: Line 217, IBSP at 4D, biological rep3

source_name: IBSP at 4D, biological rep3


title: 55_D30

source_name: PBMC

tag: gender

tag: timepoint


title: 21_D0

tag: subjectid

tag: group


title: 217 control at 4D, biological rep3

description: Line 217, control at 4D, biological rep3

source_name: control at 4D, biological rep3

value: Control


title: 217 control at 4D, biological rep1

description: Line 217, control at 4D, biological rep1

source_name: control at 4D, biological rep1


title: 157 IBSP at 4D, biological rep1

description: Line 157, IBSP at 4D, biological rep1


title: 157 IBSP at 4D, biological rep2

description: Line 157, IBSP at 4D, biological rep2

source_name: IBSP at 4D, biological rep2


title: 60_D30

tag: cell type

tag: centre


title: 157 IBSP at 4D, biological rep3

description: Line 157, IBSP at 4D, biological rep3


title: 217 control at 4D, biological rep2

description: Line 217, control at 4D, biological rep2

source_name: control at 4D, biological rep2


title: 157 control at 4D, biological rep2

description: Line 157, control at 4D, biological rep2


title: Plate3_D3_S231


title: Plate3_C8_S224


title: Plate3_D2_S230


title: scRNA with Mixture of HL60, K562, SUDHL4, THP1. WT

city: Lausanne

first: Coudray

last: Alexandre

address: 25, Avenue Riant-Mont

department: SV

country: Switzerland

institute: EPFL

description: 10x Genomics Chromium Single Cell Controller

data_processing:
Single-cell RNA-seq reads were mapped and counted on human genome (hg19) using Cellranger-arc-2.0.0 with default parameters
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each single cell

source_name: Mix of HL60, K562, SUDHL4, THP1

growth_protocol: Cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Sequencing library were performed with SMARTer Stranded Total RNA-seq, Pico input (ref 635006) or Illumina Truseq Stranded mRNA LT

treatment_protocol:
No treatment
No treatment

value: Mix of HL60, K562, SUDHL4, THP1

tag: time

value: Day 0


title: Plate3_C9_S225


title: Plate3_C5_S221


title: Plate3_C6_S222


title: bulkRNA-seq Pure Cell line, SUDHL4, WT

data_processing:
RNA-seq reads were mapped to the human genome (hg19) using Hisat2 and counted on ensembl genes using featureCounts
Single-cell RNA-seq reads were mapped and counted on human genome (hg19) using Cellranger-arc-2.0.0 with default parameters
Assembly: hg19
Supplementary files format and content: tab-delimited text files include CPM values for each Sample


title: bulkRNA-seq Pure Cell line, K562, WT


title: bulkRNA-seq Pure Cell line, THP1, WT


title: bulkRNA-seq Mixture 6 of HL60, K562, SUDHL4, THP1. WT


title: Plate3_C4_S220


title: Plate3_C3_S219


title: 157 control at 4D, biological rep3

description: Line 157, control at 4D, biological rep3


title: bulkRNA-seq Mixture 4 of HL60, K562, SUDHL4, THP1. WT


title: Plate3_C2_S218


title: bulkRNA-seq Mixture 3 of HL60, K562, SUDHL4, THP1. WT


title: 157 control at 4D, biological rep1

description: Line 157, control at 4D, biological rep1


title: bulkRNA-seq Mixture 2 of HL60, K562, SUDHL4, THP1. WT


title: Plate3_B9_S213


title: Plate3_C1_S217


title: Plate3_B8_S212


title: bulkRNA-seq Mixture 1 of HL60, K562, SUDHL4, THP1. WT


title: Plate3_B7_S211


title: FMSV234

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover. Quality control of the reads was performed with FastQC v0.11.7.
Reads were aligned to the human GRCh38 reference using Bowtie (v1.2.3) (Langmead et al. 2009)  (command line parameters: -m 1 --best --strata -v 3), sorted using SAMtools (v1.13)
The differential enrichment of H3K4me3 regions in control and treatment was performed using csaw (v1.26.0) package with FC>1.5 and FDR<0.05
For the visualization of ChIP-seq tracks, Bedgraph tracks were generated using GenomeCoverageBed function from SAMtools.
Assembly: hg38
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: blood, H3K4me3, high BPA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using  Qsonica 700 sonicator supplied with cup horn 431C2  with parameters:  60% amplitude for 8 minutes, 20 seconds on, 20 seconds off.
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645S; NEB). We used 3 ng DNA for library preparation, and 15 cycles were used for library amplification. Sequencing was performed on an Illumina HiSeq4000 sequencer using a single-end 50-base read in multiplexed mode

value: blood

tag: Sex

value: male

tag: condition

value: high BPA


title: FMSV233

tag: tissue


title: bulkRNA-seq Pure Cell line, HL60, WT

value: WT

tag: treatment


title: Plate3_B6_S210


title: Plate3_B4_S208


title: FMSV226

source_name: blood, H3K4me3, low BPA

value: low BPA

tag: chip antibody


title: Plate3_B2_S206

tag: biological sample


title: Plate3_B3_S207


title: Plate3_B1_S205


title: 35_D7

value: M

value: Taiwan


title: bulkRNA-seq Mixture 5 of HL60, K562, SUDHL4, THP1. WT

tag: genotype


title: FMSV225


title: FMSV224


title: Plate3_A9_S201


title: FMSV222


title: FMSV221


title: FMSV220


title: Plate3_A8_S200


title: FMSV219


title: Plate3_A4_S196


title: Plate3_A7_S199


title: FMSV218


title: Plate3_A3_S195


title: FMSV178

source_name: blood, input

value: Input


title: FMSV177


title: Plate2_H8_S188


title: Plate3_A1_S193


title: Plate2_H3_S183


title: Plate2_G8_S176


title: Plate2_G3_S171


title: Plate2_F8_S164


title: FMSV175


title: FMSV170


title: FMSV167


title: FMSV173


title: Plate2_F6_S162


title: FMSV223