title: MLC10874

value: Former smoker

value: Bronchial epithelial cell


title: Definitive Endoderm - Day 4_TNF_2.5_TP-8_REP-B [Bas155]

status: Public on Feb 18 2021

type: SRA

city: Leiden

first: Bob

last: van de Water

address: Einsteinweg 55

department: Division of Drug Discovery and Safety

country: Netherlands

institute: Leiden Academic Centre for Drug Research (LACDR), Leiden University

description:
Bas155
Cell lysate
count.txt
count_log2LibSizenorm.txt

library_source: transcriptomic

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

molecule: total RNA

organism: Homo sapiens

source_name: Definitive Endoderm - Day 4

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

tag: cell type

value: Definitive Endoderm

tag: compound

value: TNF-alpha

tag: concentration

value: 2.5 ng/mL

tag: time point

value: 8 hr

tag: replicate


title: SE4_unstim

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

data_processing:
Constructed libraries were sequenced using Novogene RNA-seq, Illumina Platform PE150 (NovoSeq 6000)
Basecalling was performed by Novogen company
Sequenced reads were mapped to the reference genome (GRCm38.p6.genome.fa) using STAR software (version 2.7.). Annotation file used: gencode.vM23.annotation.gtf
Raw counts were obtained using –quantMode GeneCounts option in STAR. The raw count matrix was imported into R and used as input for DESeq2 for normalization and differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv – collected read counts from STAR-generated output files
Supplementary_files_format_and_content: DESeq2_normalized_counts.csv – read counts following DESeq2 normalization. Rows (corresponding transcripts, marked with ENSEMBL ID) with zero values in all columns (corresponding EL-4 clones with or without stimulation) are filtered.

organism: Mus musculus

source_name: EL-4 cell line

growth_protocol: Wild type (“empty”, e) and super-enhancer deleted (SE) EL-4 clones were maintained in growth medium: RPMI-1640, 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 U/ml streptomycin, 1 mM sodium pyruvate, 4.5 g/l glucose, 0.05 mM 2-mercaptoethanol.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen) according to the manufacturer’s protocol.
rRNA removed using the Ribo-Zero kit. Libraries were prepared according to Illumina's instructions. Briefly, the RNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using RNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
RNA-Seq (lncRNA library)

treatment_protocol: Prior activation, cells were first starved in 1% FBS containing culture medium for 1 h then left unstimulated or stimulated with 10 ng/ml PMA  and 100 ng/ml ionomycin for 6 h.

value: Lymphoblast

tag: genotype

value: SE-deleted

tag: treatment

value: unstimulated


title: MLC10774

city: Hangzhou

first: Yang

last: Xia

state: Zhejiang

address: 88 Jiefang Road

department: Department of Respiratory and Critical Care Medicine

country: China

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

organism: Bronchus

source_name: Bronchial epithelial cell

extract_protocol:
Bronchial epithelial cells were obtained via bronchial brushings. RNA was extracted using a protocol of the RNeasy Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared according to the manufacturer’s instructions for the NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

tag: diagnosis

value: Cancer

tag: smoking status

tag: Sex

value: Male

tag: tissue


title: Definitive Endoderm - Day 4_TNF_2.5_TP-8_REP-A [Bas154]

description:
Bas154
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: e105_PMAiono

value: wild type

value: PMA (10 ng/ml) + ionomycin (100 ng/ml)


title: YoungTreg_naive_1_RRBS

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

country: USA

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with BCL2FASTQ v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

source_name: Lung Treg cells (CD3e+CD4+CD25hiFR4+)

extract_protocol:
Genomic DNA was extracted from sorted cells using the Qiagen AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. Genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.5% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

tag: age

value: 2-months old

tag: exposure

value: naïve

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: YoungTreg_naive_2_RRBS


title: AgedTreg_flu_1_RNAseq

data_processing:
Basecalls performed using Illumina RTA2 software.
BCL2FASTQ v2.17.1.14 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the mm10 reference genome using Tophat v.2.1.0, and SeqMonk v1.45.4 was used to generate gene and transcript expression levels for protein-coding genes.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.45.4.

extract_protocol:
RNA was extracted from sorted cells using the Qiagen AllPrep DNA/RNA Micro Kit.
NEB Next RNA Ultra, with polyA enrichment (Total, ribodRNA) and dual indexes

value: 18-months old

value: flu


title: e104_unstim


title: MLC10474

institute: Second Affiliated Hospital of Zhejiang University School

value: Non-smoker

value: Bronchial epithelial cell


title: MLC10374

value: Female


title: e104_PMAiono


title: YoungTreg_naive_3_RRBS


title: MLC10574

value: Former smoker


title: e1_PMAiono


title: MLC10546


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-C [Bas137]

description:
Bas137
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: MEDIUM

value: 8 hr


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-B [Bas176]

description:
Bas176
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: AgedTreg_naive_2_RRBS


title: AgedTreg_naive_3_RRBS


title: AgedTreg_naive_1_RRBS


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-B [Bas129]

description:
Bas129
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s4647.HSC_wt_PBS.4

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description:
wild type HSCs, PBS treated
s4647.HSC_wt_PBS.4

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: 8 week old

value: HPCs

value: vehicle (PBS) x3 days


title: e1_unstim

value: Lymphoblast

value: wild type

value: unstimulated


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-A [Bas169]

description:
Bas169
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s4647.HSC_wt_PBS.3

description:
wild type HSCs, PBS treated
s4647.HSC_wt_PBS.3


title: MLC10346

value: Cancer


title: s4647.HSC_wt_PBS.2

description:
wild type HSCs, PBS treated
s4647.HSC_wt_PBS.2


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-A [Bas121]

description:
Bas121
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Definitive Endoderm - Day 4_MEDIUM_0_TP-8_REP-C [Bas183]

description:
Bas183
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: YoungTreg_flu_2_RRBS

value: 2-months old

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: MLC10274

value: Current smoker


title: e105_unstim


title: YoungTreg_flu_3_RRBS

value: flu


title: MLC10174

value: Non-cancer

value: Non-smoker

value: Male

value: Bronchial epithelial cell


title: MLC10246

value: Female


title: YoungTreg_flu_1_RRBS


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-C [Bas161]

description:
Bas161
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: DMSO

value: 8 hr


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-C [Bas113]

description:
Bas113
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC10146

value: Former smoker


title: AgedTreg_flu_2_RRBS

value: 18-months old


title: MLC10074


title: s4647.HSC_wt_IL1.3

description:
wild type HSCs, IL-1 treated
s4647.HSC_wt_IL1.3

value: 8 week old

value: wild type

value: HPCs

value: IL-1 0.5 ug/mouse x3 days


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-B [Bas105]

description:
Bas105
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: AgedTreg_flu_1_RRBS

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: MLC10046


title: s4647.HSC_wt_IL1.2

description:
wild type HSCs, IL-1 treated
s4647.HSC_wt_IL1.2


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-B [Bas153]

description:
Bas153
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC09630

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Current smoker


title: s4647.HSC_ko_PBS.3

description:
Kmt2c -/- HSCs, PBS treated
s4647.HSC_ko_PBS.3

value: Kmt2c f/f; Vav-Cre

value: vehicle (PBS) x3 days


title: MLC09530

value: Cancer


title: WT pooled

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

country: Canada

institute: The Hospital for Sick Children

data_processing:
Base-calling performed with Illumina's bcl2fastq follwed by Picard FastqToSam. Read1 contains cellular and molecular barcodes (20 bp), Read2 contains cDNA sequence (50 bp).
Read2 was aligned with STAR v2.6.0b and tagged with its respective cellular and molecular barcode.
Aligned exonic reads were tagged with the name of the respective gene.
Digital gene expression (DGE) matrix was extracted from the aligned library, with a row for each gene and a column for each cell. The "knee" of the cummulative distribution plot of reads was used to estimate the number of cells being sequenced.
Cells from sample 1-2 were merged into a single DGE matrix for analysis using Seurat v3, where cells expressing less than 200 genes and genes expressed in less than 3 cells were filtered out.
Dead/dying cells (determined by mitochonrial gene percentage >10%) and cell doublets (gene expressed > 4500) were removed.
Gene measurements in each cell were normalized by the total expression, multiplied by 10,000 and log-transformed.
Following identification of highly-variable genes and data scaling, the dimensionality of the dataset was heuristically dertermined by ElbowPlot (a ranking principle components based on the percentage of variance explained by each one).
Cell were clustered using the graph-based clustering approach applied in Seurat, followed by vizualization through t-SNE plots.
Merged_DGE.txt in supplementary file contains cells and genes extracted from final Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include DGE matrices for each sample, with a row for each gene and a column for each cell. Cell number was determined by plotting the cummulative distribution plot of reads.

source_name: Arcuate nucleus-median eminence

extract_protocol:
Micro-dissected arcuate nucleus and median eminence were dissociated to single-cell suspensions. Live cells were sorted and processed through Drop-seq with flow rates of 3000 μL/hr (cells and beads) and 13,000 μL/hr (oil) were used, and beads were resuspended at 167,000 per mL. Droplets were broken with perfluorooctanol in SSC to release beads.
The beads were washed and resuspended in a reverse transcriptase mix, followed by a treatment with exonuclease I to remove unextended primers. The beads were then counted and PCR amplified. The amplified cDNA was fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers that enabled the specific amplification of only the 3' ends (described in Macosko et al. Cell 2015).

tag: strain

value: Microdissected Arcuate nucleus and median eminence of the hypothalamus

value: 7-8 weeks

value: Wildtype

tag: number of mice pooled


title: s4647.HSC_ko_PBS.4

description:
Kmt2c -/- HSCs, PBS treated
s4647.HSC_ko_PBS.4


title: s4647.HSC_wt_PBS.1

description:
wild type HSCs, PBS treated
s4647.HSC_wt_PBS.1


title: Definitive Endoderm - Day 4_DEM_1000_TP-8_REP-C [Bas128]

description:
Bas128
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: Diethyl-maleate (DEM)


title: HD14.TC

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Tconvs were sorted from thawed PBMCs as DAPI– CD4+CD25–CD127hi

data_processing:
Reads were mapped to the mouse reference genome (GRCh38) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (v34)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read counts

source_name: CD4 Tconv Cell

extract_protocol:
Male IPEX and healthy donor whole-blood samples were obtained under protocols reviewed and approved by the local Institutional Review Boards. After PBMC isolation, the samples were frozen and keep in liquid nitrogen. Human Tregs and Tconvs were sorted from thawed PBMCs as DAPI– CD4+CD25hiCD127lo and CD4+CD25–CD127hi, respectively on a Moflo Astrios Cell Sorter. A total of 1,000 cells were double-sorted directly into 5ul of lysis buffer (TCL Buffer (QIAGEN) supplemented with 1% 2-Mercaptoethanol). RNA-seq was performed with the standard ImmGen low-input protocol (www.immgen.org) using the SmartSeq2 libraries.
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

value: HD

value: Blood

value: WT

tag: cohort

value: male

tag: donor


title: Irx3/5dHet pooled


title: MLC09430

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: MLC09330

value: Male


title: HD14.TR

description: Tregs were sorted from thawed PBMCs as DAPI– CD4+CD25hiCD127lo

source_name: CD4 TReg Cell


title: Definitive Endoderm - Day 4_DEM_1000_TP-8_REP-B [Bas127]

description:
Bas127
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type

value: 8 hr


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-A [Bas145]

description:
Bas145
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: compound

value: DMSO


title: AgedTreg_flu_3_RRBS

value: 18-months old

value: flu

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: Definitive Endoderm - Day 4_DEM_1000_TP-8_REP-A [Bas126]

description:
Bas126
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: concentration


title: s4647.HSC_wt_IL1.1

description:
wild type HSCs, IL-1 treated
s4647.HSC_wt_IL1.1

value: 8 week old

value: wild type

value: HPCs

value: IL-1 0.5 ug/mouse x3 days


title: s4647.HSC_ko_IL1.4

description:
Kmt2c -/- HSCs, IL-1 treated
s4647.HSC_ko_IL1.4

value: Kmt2c f/f; Vav-Cre


title: MLC09230

value: Cancer

value: Former smoker


title: Definitive Endoderm - Day 4_DMSO_0_TP-8_REP-A [Bas097]

description:
Bas097
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

tag: time point


title: HD13.TC

value: HD

value: Blood

value: WT

value: male


title: Definitive Endoderm - Day 4_DEM_333_TP-8_REP-C [Bas120]

description:
Bas120
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)

value: 8 hr

tag: replicate


title: s4647.HSC_ko_IL1.3

description:
Kmt2c -/- HSCs, IL-1 treated
s4647.HSC_ko_IL1.3

tag: genotype


title: HD13.TR


title: MLC09130

value: Non-cancer

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: s4647.HSC_ko_PBS.2

description:
Kmt2c -/- HSCs, PBS treated
s4647.HSC_ko_PBS.2

value: 8 week old

tag: treatment

value: vehicle (PBS) x3 days


title: s4647.HSC_ko_IL1.2

description:
Kmt2c -/- HSCs, IL-1 treated
s4647.HSC_ko_IL1.2

value: HPCs

value: IL-1 0.5 ug/mouse x3 days


title: s4647.HSC_ko_PBS.1

description:
Kmt2c -/- HSCs, PBS treated
s4647.HSC_ko_PBS.1

value: Kmt2c f/f; Vav-Cre


title: Definitive Endoderm - Day 4_DEM_333_TP-8_REP-A [Bas118]

description:
Bas118
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HD12.TC


title: Definitive Endoderm - Day 4_DEM_333_TP-8_REP-B [Bas119]

description:
Bas119
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC08577

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

tag: diagnosis

value: Cancer

value: Male


title: s4647.HSC_ko_IL1.1

description:
Kmt2c -/- HSCs, IL-1 treated
s4647.HSC_ko_IL1.1


title: MLC08575

tag: smoking status


title: s4647.HPC_wt_PBS.3

description:
wild type HPCs, PBS treated
s4647.HPC_wt_PBS.3

value: wild type


title: Definitive Endoderm - Day 4_DEM_100_TP-8_REP-C [Bas112]

description:
Bas112
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm


title: B6.TC

description: Tconvs were sorted from thawed PBMCs as DAPI– CD4+CD25–CD127hi

value: IPEX

value: Blood

tag: Sex


title: Definitive Endoderm - Day 4_DEM_100_TP-8_REP-B [Bas111]

description:
Bas111
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: MLC08477

tag: tissue


title: Definitive Endoderm - Day 4_DEM_100_TP-8_REP-A [Bas110]

description:
Bas110
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: s4647.HPC_wt_PBS.2

description:
wild type HPCs, PBS treated
s4647.HPC_wt_PBS.2

tag: age


title: B6.TR

description: Tregs were sorted from thawed PBMCs as DAPI– CD4+CD25hiCD127lo

value: male


title: s4647.HPC_wt_PBS.1

description:
wild type HPCs, PBS treated
s4647.HPC_wt_PBS.1


title: MLC08475

value: Non-smoker


title: Definitive Endoderm - Day 4_DEM_10_TP-8_REP-C [Bas104]

description:
Bas104
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: B5.b.TC


title: B5.b.TR


title: s4647.HPC_wt_IL1.3

description:
wild type HPCs, IL-1 treated
s4647.HPC_wt_IL1.3


title: MLC08677

value: Current smoker

value: Bronchial epithelial cell


title: s4647.HPC_wt_IL1.2

description:
wild type HPCs, IL-1 treated
s4647.HPC_wt_IL1.2

value: 8 week old


title: HD12.TR

value: HD

value: WT


title: s4647.HPC_wt_IL1.1

description:
wild type HPCs, IL-1 treated
s4647.HPC_wt_IL1.1

value: HPCs

value: IL-1 0.5 ug/mouse x3 days


title: B4.2017b.TC


title: Definitive Endoderm - Day 4_DEM_10_TP-8_REP-A [Bas102]

description:
Bas102
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC08377

value: Cancer

value: Male


title: MLC08309


title: s4647.HPC_ko_PBS.3

description:
Kmt2c -/- HPCs, PBS treated
s4647.HPC_ko_PBS.3

value: Kmt2c f/f; Vav-Cre

value: vehicle (PBS) x3 days


title: MLC08409

value: Former smoker


title: Definitive Endoderm - Day 4_DEM_1_TP-8_REP-C [Bas096]

description:
Bas096
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: Diethyl-maleate (DEM)

value: 1 uM


title: B1.2017b.TC

value: IPEX

value: Blood

value: male


title: B4.2017b.TR


title: Definitive Endoderm - Day 4_DEM_1_TP-8_REP-B [Bas095]

description:
Bas095
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: B1.2017b.TR


title: MLC08277

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Current smoker

value: Bronchial epithelial cell


title: MLC08209


title: s4647.HPC_ko_IL1.3

description:
Kmt2c -/- HPCs, IL-1 treated
s4647.HPC_ko_IL1.3

value: 8 week old


title: s4647.HPC_ko_PBS.1

description:
Kmt2c -/- HPCs, PBS treated
s4647.HPC_ko_PBS.1

value: HPCs


title: s4647.HPC_ko_PBS.2

description:
Kmt2c -/- HPCs, PBS treated
s4647.HPC_ko_PBS.2


title: MLC08177


title: Definitive Endoderm - Day 4_DEM_10_TP-8_REP-B [Bas103]

description:
Bas103
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Definitive Endoderm - Day 4_CPT_100_TP-8_REP-C [Bas182]

description:
Bas182
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: HD16.TC

description: Tconvs were sorted from thawed PBMCs as DAPI– CD4+CD25–CD127hi

value: HD

value: WT


title: Definitive Endoderm - Day 4_CPT_100_TP-8_REP-A [Bas180]

description:
Bas180
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s4647.HPC_ko_IL1.2

description:
Kmt2c -/- HPCs, IL-1 treated
s4647.HPC_ko_IL1.2

value: Kmt2c f/f; Vav-Cre

value: IL-1 0.5 ug/mouse x3 days


title: MLC08109

value: Cancer

value: Non-smoker

value: Female


title: HD15.TC


title: s4647.HPC_ko_IL1.1

description:
Kmt2c -/- HPCs, IL-1 treated
s4647.HPC_ko_IL1.1


title: MLC08077

value: Male


title: HD15.TR

description: Tregs were sorted from thawed PBMCs as DAPI– CD4+CD25hiCD127lo

value: Blood


title: Definitive Endoderm - Day 4_CPT_33_TP-8_REP-C [Bas175]

description:
Bas175
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: 33 uM


title: MLC08075


title: P7.2016b.TC

value: IPEX

value: male


title: AdId4eGFPbright-Rapa_Release

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

description: single-cell

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq.
Primary data analysis (alignment, filtering, and UMI counting) to determine gene transcript counts per cell (producing a gene-barcode matrix), quality control, clustering and statistical analysis were performed using CellRanger v3.1 .0 count (10x Genomics) and a custom version of the mm10 (mouse) genome assembly/annotation reference containing the EGFP cds. Reads were hard trimmed as follows: R1=28, i7=8, R2=91.
Outputs from multiple independent samples of single-cells were combined using CellRanger aggr (10x Genomics) based on mapped read counts to normalize sequencing depth and produce aggregated gene-barcode matrices and clustering models.
Genome_build: Mouse reference genome NCBI build 38, GRCm38 (mm10) customized with EGFP
Supplementary_files_format_and_content: A single gene x. cell-barcode matrix file (MTX). Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

molecule: polyA RNA

source_name: Adult testis

growth_protocol: Normal mouse husbandry with ad libitum food and water.

extract_protocol:
Single-cell suspensions of seminiferous tubules were generated from adult mouse testes using a two-step enzymatic digestion approach. Briefly, testicular parenchyma from 2 or more adult mice were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37oC, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37oC, and quenched with 10% FBS. Testis cell suspensions were used for FACS to enrich spermatogonia essentially as described (Hermann et al., 2015). Briefly, cells were suspended (5-20 x 10^6 cells/ml) in ice-cold Dulbecco’s phosphate-buffered saline (DPBS) containing 10% FBS (DPBS+S). Cells were pre-enriched for spermatogonia by density centrifugation in DPBS+S over a 30% Percoll cushion (Sigma) for 8 minutes at 600xg without braking. Pelleted cells were subjected to FACS and spermatogonia isolated based on gating CD9-bright and ID4-EGFP double-positive cells using  a FACS Aria (BD). Cells from adult Adult Id4-eGfp+ mouse were also enriched for spermatocytes and spermatids based on sedimentation velocity at unit gravity (Romrell et al., 1976; Bellve et al., 1977). Briefly, testis cells (10^6-10^7) suspended in 2 ml of buffer plus 0.5% BSA were loaded onto a 50 ml gradient of 2-4% BSA (McCarrey et al., 1992) and allowed to sediment for 2.5 hr at 4°C. Approximately one hundred 0.5 ml fractions were then collected in microcentrifuge tubes and analyzed for content of spermatocytes or spermatids on the basis of morphology under phase contrast optics (which typically yields ≥85% purity). Fractions containing spermatocytes or spermatids were pooled separately, concentrated (to ~2 x106 cells/ml) and stored in buffer containing FBS on ice until use. Ultimately, CD9bright/ID4-EGFP-birght testis cells from adult mice were used for single-cell RNA-seq facilitated by the 10x Genomics Chromium approach. Briefly, cell suspensions were loaded into Chromium microfluidic chips with 3’ v3 chemistry and used to generate single-cell gelbead emulsions (GEMs) with using the Chromium controller (10x Genomics) per manufacturer recommendations (Zheng et al., 2017). In all cases, suspensions containing ~7000 cells were loaded on the instrument with the expectation of collecting up to 4,000 GEMs containing single cells. GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
Single-cell 3' libraries were prepared according to manufacturer recommendations (v3 chemistry).

tag: number of cells

value: Spermatogonia


title: Definitive Endoderm - Day 4_CPT_33_TP-8_REP-B [Bas174]

description:
Bas174
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: Definitive Endoderm - Day 4_CPT_100_TP-8_REP-B [Bas181]

description:
Bas181
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC07651

value: Former smoker

value: Bronchial epithelial cell


title: MLC08275


title: AdId4eGFPbright-Rapa

description: single-cell

value: Rapa


title: AdId4eGFPbright-Control

description: single-cell

value: Control


title: P7.2016b.TR


title: P4.2017.TC


title: Definitive Endoderm - Day 4_CPT_10_TP-8_REP-A [Bas166]

description:
Bas166
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)

value: 10 uM


title: MLC07451

value: Cancer

value: Current smoker


title: Definitive Endoderm - Day 4_CPT_3.3_TP-8_REP-C [Bas160]

description:
Bas160
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC07351

value: Non-cancer


title: HYPO5_bulkRNA

city: Cincinnati

first: Yin Yeng

last: Lee

state: Ohio

address: 3333 Burnet Avenue

department: Department of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw fastq files were mapped to mouse genome using STAR v2.5. HTSeq v0.6.0 was used to quantified read count for each gene.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: HTSeq quantified count for all libraries

source_name: whole lung

extract_protocol:
mRNA enrichment was performed using Polyadenylated (PolyA+) mRNA Magnetic Isolation Module (New England Biolabs)
Library preparation was perform using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). All 12 samples were pooled together and sequenced in one lane.

tag: strain

value: 8-10 weeks

value: whole lung


title: P4.2017.TR

value: Blood


title: P4.2015.TC


title: HYPO4_bulkRNA


title: P4.2015.TR


title: Definitive Endoderm - Day 4_CPT_3.3_TP-8_REP-A [Bas158]

description:
Bas158
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm


title: MLC07251

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Non-smoker

value: Female


title: Definitive Endoderm - Day 4_CPT_1_TP-8_REP-C [Bas152]

description:
Bas152
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: Definitive Endoderm - Day 4_CPT_10_TP-8_REP-C [Bas168]

description:
Bas168
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: HYPO3_bulkRNA


title: HD07.TC

value: HD

value: WT

value: male


title: Definitive Endoderm - Day 4_CPT_1_TP-8_REP-B [Bas151]

description:
Bas151
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HYPO2_bulkRNA


title: MLC07151

value: Male

value: Bronchial epithelial cell


title: HD07.TR


title: Definitive Endoderm - Day 4_CPT_10_TP-8_REP-B [Bas167]

description:
Bas167
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)

value: 10 uM


title: MLC07551

value: Cancer

value: Current smoker


title: Definitive Endoderm - Day 4_CPT_1_TP-8_REP-A [Bas150]

description:
Bas150
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HYPO1_bulkRNA

value: 8-10 weeks


title: MLC05522

value: Former smoker


title: HD06.TC

description: Tconvs were sorted from thawed PBMCs as DAPI– CD4+CD25–CD127hi

value: Blood


title: MLC05322

value: Non-cancer


title: HYPO6_bulkRNA

value: whole lung


title: CTRL6_bulkRNA


title: HD06.TR


title: MLC05122


title: B4.2017a.TC

value: IPEX


title: Definitive Endoderm - Day 4_CPT_0.01_TP-8_REP-A [Bas142]

description:
Bas142
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm


title: CTRL4_bulkRNA


title: Definitive Endoderm - Day 4_CPT_0.01_TP-8_REP-B [Bas143]

description:
Bas143
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: B4.2017a.TR


title: MLC05022


title: CTRL3_bulkRNA


title: CTRL5_bulkRNA


title: HD04.TC

value: HD


title: 10x ApoeKO White Matter Batch 3

city: Munich

first: Ozgun

last: Gokce

address: Feodor-Lynen-Strasse 17

country: Germany

institute: Institute for Stroke and Dementia Research

description: processed data file: 10xapoeko.tsv

data_processing:
BCL files were demultiplexed with the bcl2fastq software from Illumina.
Quality was assessed with FastQC
Trimming and QC filtering was performed with trim-galore and following command trim_galore -j 2 --paired -q 20 --nextera --stringency 1
Reads were aligned using rnaSTAR (Dobin et al., 2013). Read counts were collected using the parameter “quantMode GeneCounts” of rnaSTAR and using the unstranded values.
For 10x datasets, fastq files were processed with Cell Ranger v4
Genome_build: mm10
Supplementary_files_format_and_content: 5x expression matrices of raw counts as tab-separated files, for each dataset. First (unnamed) column are the gene names, each column depicts a single-cell.

source_name: Pool of 2 mice

extract_protocol:
Briefly, the mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected and dissociated same as described above. After dissociation, myelin debris is removed using Myelin Removal Beads II (Miltenyi Biotec). The cells were resuspended in 0.04% BSA+PBS and cell are counted using automated cell counter (TC20 Bio-Rad) before loading to Chromium Controller.
Single-cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure beads (Beckman Coulter). Libraries were sequenced on the DNBSEQ Sequencing System (BGI group).
10x Genomics Single Cell 3’ Library v3.1

value: 18 months

value: ApoeKO

value: White Matter

value: Brain cells

tag: technology

value: scRNA-seq 10x


title: MLC03773

value: Male

value: Bronchial epithelial cell


title: CTRL2_bulkRNA


title: MLC03673

value: Cancer

value: Current smoker


title: CTRL1_bulkRNA

value: 8-10 weeks


title: P2.TC

value: Blood

tag: cohort

value: male


title: 10x ApoeKO White Matter Batch 4

description: processed data file: 10xapoeko.tsv


title: 10x ApoeKO White Matter Batch 2

description: processed data file: 10xapoeko.tsv


title: 10x ApoeKO White Matter Batch 1

description: processed data file: 10xapoeko.tsv


title: MLC03598


title: P2.TR

tag: donor


title: Definitive Endoderm - Day 4_CPT_0.01_TP-8_REP-C [Bas144]

description:
Bas144
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type

value: Cisplatin (CPT)


title: ATAC-seq_Yap-3

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description:
tranposed DNA
Pcm1(+) nuclei extracted from skeletal muscle

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the mouse genome (GRCm38.96) using Burrows-Wheeler Aligner (BWA, version 0.7.17).
Duplicated reads were removed using Samtools (Samtools, version1.8). Peak calling was performed using MACS (version 1.4.2-1). Peaks that were detected in at least 2 samples were used to curate a peak set.
Mapped reads were counted to 1kb ± transcription start site with featureCounts (v1.5.0). Individual sample’s peaks counted to the curated peak sets using FeatureCounts (v1.5.0).
Genes or peaks were filtered if the sums of reads across all samples was less than 10.
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw counts of sequencing reads.

source_name: mouse skeletal muscle

extract_protocol:
DNA transposition was performed from sorted Pcm1(+) nuclei as previously described (Buenrostro JD, Wu B, Chang HY, and Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9.).
Library was prepared as previously described (Buenrostro JD, Wu B, Chang HY, and Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9.).

treatment_protocol: AAV6:Yap-shRNA and AAV6:LacZ-shRNA (control) vectors were administered to the contralateral gastrocnemius (Gastroc) and tibialis anterior (TA) muscles of 8 week-old male C57BL/6J mice and tissues were collected at 28 days post-treatment.

value: skeletal muscle

tag: muscle type

value: 4 x Gastrocnemius and 4 x tibialis anterior muscles

tag: knockdown

tag: cell sorting criteria

value: Pcm1(+) nuclei


title: 10x Aged Wild type White Matter Batch 3

description: processed data file: 10xaged.tsv

source_name: Pool of 3 mice

value: 24 months


title: ATAC-seq_Yap-2


title: MLC05222

value: Former smoker


title: MLC03573


title: P6.TC

value: IPEX


title: MLC03498

value: Non-smoker

value: Female


title: 10x Aged Wild type Grey Matter Batch 3

description: processed data file: 10xaged.tsv

value: Wild type

value: Grey Matter

value: Brain cells

value: scRNA-seq 10x


title: P6.TR

description: Tregs were sorted from thawed PBMCs as DAPI– CD4+CD25hiCD127lo


title: ATAC-seq_Yap-1


title: MLC03473

value: Cancer

value: Male

value: Bronchial epithelial cell


title: ATAC-seq_LacZ-3

value: male


title: HD04.TR

value: HD

value: Blood

value: WT


title: P8.TC


title: MLC03398

value: Non-cancer


title: 10x Aged Wild type White Matter Batch 1

description: processed data file: 10xaged.tsv

source_name: Pool of 4 mice

value: 24 months

value: White Matter


title: ATAC-seq_LacZ-2

value: skeletal muscle

value: 4 x Gastrocnemius and 4 x tibialis anterior muscles

value: Pcm1(+) nuclei


title: MLC03373

value: Former smoker


title: 10x Aged Wild type Grey Matter Batch 1

description: processed data file: 10xaged.tsv

value: Wild type

value: Grey Matter


title: ATAC-seq_LacZ-1


title: RNA-seq_Yap-3

description:
rRNA depleted RNA
Pcm1(+) nuclei extracted from skeletal muscle

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the mouse genome (GRCm38.96) using STAR (version 2.5.3a).
Mapped reads were counted with featureCounts (v1.5.0).
Genes were filtered if the sums of reads across all samples was less than 10.
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw counts of sequencing reads.

extract_protocol:
RNA extraction was performed from sorted Pcm1(+) nuclei. Nuclei were lysed in TRIzol® Reagent (15596018, Invitrogen) and then processed with Direct-zol™ RNA Microprep kit (Zymo/ Integrated Science, R2061).
Ribosomal RNA was depleted from total RNA using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (E6310, New England Biolabs) followed by library generation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, New England Biolabs) to select library fragment sizes of 200-400bp.

tag: muscle name


title: P7.2016a.TC

tag: genotype

value: IPEX


title: P8.TR


title: MLC03298


title: P7.2016a.TR


title: HD02.TC


title: RNA-seq_Yap-2


title: wildtype_M82_Single_Meristem_Transcriptomes_1stSeason_lowCoverageDepth

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description: bulk MARS-seq of WT tomato shoot apical meristems (covered in low Sampling depth during an independent collection season - as described in Meir, Aviezer et al., 2021)

data_processing:
.Read-1 files were mapped to the SL3.0 genome assembly using Bowtie2 (default parameters). Gene annotations were based on ITAG3.2 version, but ‘3 UTR ends of genes were elongated by 1kbp or by half the distance to ‘5 of next gene (for each gene, the smaller between the two). Genes that had overlapping annotations on the same genomic orientation were fused and annotated with “;” sign between them.
.Demultiplexing and counts of UMIs per well (technical replicate) were based on 8bp of UMI and 7bp of cell-barcodes in Read-2 (see attached Readme table for further details), and performed with the pipeline described in Jaitin et al. 2014. UMIs obtained from wells that were assigned to the same meristem in each plate were aggregated based on 1) conversion key of well-barcode to well-position. 2) plate design template, assigning each unique meristem-ID to a well-position in that plate.
Genome_build: Solanum lycopersicum (SL3.0)

organism: Solanum lycopersicum

source_name: Tomato plants (cv M82-SP)

extract_protocol:
RNA capture from shoot apical meristems for SMT:  The next steps for purification of RNA were conducted consecutively on batches of 24-96 meristems at each time, and typically within 1-2 hours: First, the samples were homogenized by putting the tubes (containing the glass bead) to bead beater instrument (Retsch, Mixer Mill MM 400) for 2 minutes. We then spin-downed the tubes and added 50ul of Lysis/Binding buffer (Dyanbeads, mRNA DIRECT Purification Kit) before applying another round of 2 minutes in bead beater. The homogenized samples were then kept on ice and transferred to 96-well plates before further RNA purification. In the 96-well plates, we captured RNA by adding 15uL of poly-dT beads (Dyanbeads, mRNA DIRECT Purification Kit) to each sample, which followed by washes and elution in 16-30uL of TRIS-HCl pH 7.5
Preparaion of bulk cDNA library by MARS-seq: 1ul purified RNA was transferred either manually, by an E1 Clip tip equalizer pipette (Thermo Fisher), or by a custom robotized dispensing protocol (Agilent, Automated liquid-handling platform, Bravo model with 96ST head)  into barcoded lysis solution (4nM of RT-barcodes) in 384-well MARS-seq plates, and by assigning 12-24 wells to each meriste to serve as technical replicates. During cDNA preparation, only deviation from the original MARS-seq scRNA protocol describied by Jaitin et al 2014 was extending the first evaportaion step at 95 degree from 3 to 4 minutes, in order to compensate for the additional volume. UMIs obtained from the 12-24 libraries originated from same meristem (technical replicates) were summed prior to downstream analysis of SMT data (see Meir, Aviezer et al. for graphical overview of the protocol).

treatment_protocol: Dissection of tomato shoot apical Meristems for SMT analysis: Individual SAMs were dissected under examination by binocular (Leica Stereozoom S9i), and by using an opthalamic knife (MANI INC., MST15 straight). Each meristem assigned with one of five developmental scores based on morphology (VM - vegetative non-domed meristem, TM0/1/2 - transition meristems at progressed doming stages, LTM - late transition and early signs for bifurcation, and EFM - early flowering with apparent intiaiting floral organs). Single dissected meristems were then transferred immediately to a safe-lock 2ml tube (Eppendorf, #0030120230), which already contained a single 5mm glass bead (Sigma-Aldrich). Tubes with dissected samples were immediately transferred to liquid nitrogen, and then stored in -80 degrees until RNA extraction.

value: shoot apical meristem


title: uf_Single_Meristem_Transcriptomes

description: bulk MARS-seq of shoot apical meristems (as described in Meir, Aviezer et al., 2021) for mutated uf tomato plants (UF: UNIFLORA)

value: uf mutant


title: MLC03273

value: Cancer

value: Male

value: Bronchial epithelial cell


title: MLC03198

value: Current smoker


title: sft_dst_Single_Meristem_Transcriptomes

description: bulk MARS-seq of shoot apical meristems (as described in Meir, Aviezer et al., 2021) for double-mutants sft, dst tomato plants

value: sft, dst double mutant


title: RNA-seq_Yap-1

value: male


title: HD02.TR

value: HD

value: Blood

value: WT


title: 10x Aged Wild type Grey Matter Batch 2

description: processed data file: 10xaged.tsv

value: 24 months

value: Brain cells

value: scRNA-seq 10x


title: MLC03098

value: Non-cancer

value: Non-smoker

value: Female


title: RNA-seq_LacZ-3

value: skeletal muscle

value: 4 x Gastrocnemius and 4 x tibialis anterior muscles

value: Pcm1(+) nuclei


title: P1.TC

value: IPEX

value: NM_014009.3:promoter and exon 1 deletion


title: MLC00674

value: Bronchial epithelial cell


title: RNA-seq_LacZ-2


title: sft_Single_Meristem_Transcriptomes

description: bulk MARS-seq of shoot apical meristems (as described in Meir, Aviezer et al., 2021) for mutated sft tomato plants (SFT: Singe Flowering Truss, florigen)

value: sft mutant (n7187 allele)

value: shoot apical meristem


title: RNA-seq_LacZ-1

value: male


title: dst_Single_Meristem_Transcriptomes

description: bulk MARS-seq of shoot apical meristems (as described in Meir, Aviezer et al., 2021) for mutated dst tomato plants (DST: Delayed Sympodial Termination)

value: dst mutant (dst-1 / e137 allele)


title: MLC00574

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Cancer

value: Current smoker

value: Male


title: P4.2016.TC

value: Blood


title: MLC00474


title: MLC00346


title: MLC00374


title: P4.2016.TR


title: HD03.TR

value: HD

value: WT


title: S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 90 minutes  Replicate 3

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: UA159 Zinc 90 minutes 3

data_processing:
Read mapping was performed on a Galalxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the S. mutans UA159 genome (NC_004350.2)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Genome_build: NC_004350.2
Supplementary_files_format_and_content: The processed .csv data files contain comparisons of the pooled data (three replicates for each sample type if available) between two samples, represented as the log2 fold change of expression of each coding region (SMU).

organism: Streptococcus mutans UA159

source_name: Laboratory stock

growth_protocol: Cells were grown to OD600 = 0.4

extract_protocol:
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized S. mutans cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcodes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.

treatment_protocol: Cells were grown to OD600 of 0.4, exposed to zinc for 90 minutes, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use

tag: genotype/variation

value: wild type

tag: treatment

value: ZnSO4 for 90min


title: S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 90 minutes  Replicate 1

description: UA159 Zinc 90 minutes 1


title: MLC00246

tag: diagnosis

tag: smoking status

value: Former smoker


title: S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 90 minutes  Replicate 2

description: UA159 Zinc 90 minutes 2


title: wildtype_M82_Single_Meristem_Transcriptomes

description: bulk MARS-seq of WT tomato shoot apical meristems (as described in Meir, Aviezer et al., 2021)

value: Wild type

tag: tissue


title: HD03.TC

tag: Sex


title: HD01.TC


title: E1E21

city: Geneva

first: Martina

last: Valentini

address: 1, rue Michel Servet

department: Department of Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

description:
replicate 1
Swarming cells

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed using fastp 0.20.0, mapped using bowtie2 2.3.4.3.
Reads were counted using HTSeq 0.11.1.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: tab-delimited text files include

organism: Pseudomonas aeruginosa PAO1

source_name: bacteria

growth_protocol: Swarming plates consisted of 0.5% (wt/vol) Difco bacto-agar with MMP medium supplemented with 20 mM glucose and 0.1% (w/v) casamino acids. Cells were inoculated onto swarm plates using 5µl of standardized overnight cultures and incubated overnight at 37°C.

extract_protocol:
Total RNAs was extracted and purified using Monarch RNA isolation kit (NEB), treated with DNase I (Promega) three times to remove contaminating genomic DNA and re-purified again using phenol-chloroform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using the RNA bacteria protect solution (QIAGEN).


title: E21

description:
replicate 1
Swarming cells


title: E22

description:
replicate 2
Swarming cells


title: MLC00174

value: Non-cancer


title: S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 15 minutes  Replicate 2

description: UA159 Zinc 15 minutes 2

treatment_protocol: Cells were grown to OD600 of 0.4, exposed to zinc for 15 minutes, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use

value: ZnSO4 for 15 min


title: P1.TR

value: IPEX

value: NM_014009.3:promoter and exon 1 deletion


title: E1E22

description:
replicate 2
Swarming cells


title: E12

description:
replicate 2
Swarming cells


title: MLC00146

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 3

description: UA159 Complete 3

treatment_protocol: Cells were grown to OD600 of 0.4, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use


title: E11

description:
replicate 1
Swarming cells


title: HD05.TC

value: male


title: S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 2

description: UA159 Complete 2


title: MLC00074

value: Cancer


title: MLC00046

value: Male


title: WT1

description:
replicate 1
Swarming cells

value: wild-type


title: CB_2

status: Public on Feb 17 2021

city: Yangling, Shanxi

first: Guangdong

last: Zhang

address: No.22 Xinong Road, Yangling, Shanxi, China

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic).
Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05.
To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Genome_build: ASM60005v1
Supplementary_files_format_and_content: genes.count.txt: Tab-delimited text file includes gene count for each Sample.

organism: Brucella suis

growth_protocol: The bacterial strains were cultured in TSB with shaking or on TSA at 37 °C. Single bacterial colonies from freshly streaked TSA plates were inoculated into 50 ml TSB and grown at 37 °C for 2 days with gentle shaking. Subsequently, the cultures were diluted 100-fold with TSB and incubated at 37°C to exponential growth phase (OD600nm~0.6).

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200-300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end libraries were sequenced by Illumina NovaSeq 6000 sequencing (150bp*2).

value: vaccine strain S2

value: BI-1 complementary strain (cBI-1)


title: CB_1


title: BS_3

value: WT


title: BS_2


title: DB_1

value: BI-1 deletion mutant (<delta>BI-1)


title: DB_2


title: CB_3


title: BS_1


title: IVAR9

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

state: MD

address: 1661 Orleans St

institute: Johns Hopkins SOM

data_processing:
The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform.
Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the mm10 mouse transcriptome and create a gene by cell count matrix.
Seurat was used for downstream analysis
Genome_build: Hg37
Supplementary_files_format_and_content: For each library preparation includes the following files: matrix.mtx, barcodes.tsv, genes.tsv

source_name: PBMC

extract_protocol: 10x Genomics

tag: disease status


title: IVAR8


title: IVAR7


title: S. mutans UA159 grown in FMC to OD600 = 0.4, then exposed to 4mM ZnSO4 for 15 minutes  Replicate 1

description: UA159 Zinc 15 minutes 1

value: wild type


title: IVAR6


title: HD01.TR

value: HD

value: Blood


title: IVAR10

value: Healthy


title: IVAR5


title: HD16.TR


title: IVAR4


title: IVAR3


title: HD05.TR


title: WT2

description:
replicate 2
Swarming cells


title: IVAR2


title: M/30y donor, hypoxia, dynamic Compression

city: Edmonton

first: Adetola

middle: B

last: Adesida

state: Alberta

address: 3.002E Li Ka Shing Centre for Health Research Innovation

department: Surgery

institute: University of Alberta

description: HD3 (Hypoxia Dynamic 3 -> M/30y, HYP, Dynamic Compression)

data_processing:
Partek Flow: Trim bases: Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a): Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M): Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features: Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts: Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs: Factors: Oxygen Tension + Mechanical Loading + Donor (Random) + Oxygen Tension*Mechanical Loading. Shrinkage of error term variance: Limma-trend

source_name: human engineered meniscus

growth_protocol: Meniscus cells (meniscus fibrochondrocytes) were isolated from partial meniscectomy tissue samples. They were expanded in normoxia (standard 5% CO2, 95% air incubator) to passage 2 (~7 population doublings) with supplementation of TGF-beta1 and FGF-2. They were then seeded onto cylindrical type I collagen scaffolds (10 mm diameter, 3.5 mm height) at a density of 5x10^6 million/cm^3 and cultured for 6 weeks in normoxia in a standard chondrogenic medium containing TGF-beta3 to form engineered meniscus tissues before treatment.

extract_protocol:
RNA was extracted through chloroform phase-separation and isopropanol precipitation. RNA was purified using QIAGEN RNeasy mini kits with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from 3-4 replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability (18 pools in total). These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

treatment_protocol: Tissues were randomly allocated into treatments in hypoxia (3% O2, 5% CO2) or normoxia (20% O2, 5% CO2) for 24h. The loading treatments were then applied: 1. Baseline: tissues placed in bioreactor but with no compression; 2. Static Compression: tissues ramped to 30% strain over 30s and then held for 5 minutes; or 3. Dynamic Compression: tissues ramped to 30% strain as before and then cycled between 30-40% total compressive strain for 5 minutes at 1 Hz. Tissues were then allowed 30 minutes to rest and then were put into TRIzol reagent and snap frozen in liquid nitrogen to preserve RNA level changes.

tag: donor identifier

tag: gender

value: M

tag: age

value: human engineered meniscus

tag: oxygen tension

value: hypoxia

tag: loading group

value: Dynamic Compression


title: S. mutans UA159 grown to OD600 = 0.4 in FMC complete Replicate 1

description: UA159 Complete 1


title: M/30y donor, normoxia, dynamic Compression

description: ND3 (Normoxia Static 3 -> M/30y, NRX, Static Compression)

value: normoxia


title: M/30y donor, normoxia, static Compression

description: NS3 (Normoxia Static 3 -> M/30y, NRX, Static Compression)

value: Static Compression


title: M/30y donor, normoxia, baseline

description: NB3 (Normoxia Baseline 3 -> M/30y, NRX, Baseline)

value: Baseline


title: DB_3

tag: strain


title: M/24y donor, hypoxia, static Compression

description: HS2 (Hypoxia Static 2 -> M/24y, HYP, Static Compression)


title: M/24y donor, hypoxia, dynamic Compression

description: HD2 (Hypoxia Dynamic 2 -> M/24y, HYP, Dynamic Compression)


title: M/24y donor, hypoxia, baseline

description: HB2 (Hypoxia Baseline 2 -> M/24y, HYP, Baseline)


title: M/24y donor, normoxia, static Compression

description: NS2 (Normoxia Static 2 -> M/24y, NRX, Static Compression)


title: M/24y donor, normoxia, baseline

description: NB2 (Normoxia Baseline 2 -> M/24y, NRX, Baseline)


title: M/33y donor, hypoxia, static Compression

description: HS1 (Hypoxia Static 1 -> M/33y, HYP, Static Compression)


title: M/33y donor, normoxia, baseline

description: NB1 (Normoxia Baseline 1 -> M/33y, NRX, Baseline)


title: M/24y donor, normoxia, dynamic Compression

description: ND2 (Normoxia Static 2 -> M/24y, NRX, Static Compression)


title: M/33y donor, hypoxia, baseline

description: HB1 (Hypoxia Baseline 1 -> M/33y, HYP, Baseline)


title: M/33y donor, normoxia, static Compression

description: NS1 (Normoxia Static 1 -> M/33y, NRX, Static Compression)


title: M/33y donor, normoxia, dynamic Compression

description: ND1 (Normoxia Dynamic 1 -> M/33y, NRX, Dynamic Compression)


title: M/30y donor, hypoxia, static Compression

description: HS3 (Hypoxia Static 3 -> M/30y, HYP, Static Compression)


title: M/30y donor, hypoxia, baseline

description: HB3 (Hypoxia Baseline 3 -> M/30y, HYP, Baseline)


title: LNCaP EnzaR DMSO rep 2

city: Innsbruck

first: Tobias

last: Furlan

state: Tirol

address: Anichstraße 35

department: Urology

country: Austria

institute: Medical University Innsbruck

data_processing:
Demultiplexing and trimming of Illumina adaptor residuals
Sequences were aligned to HG38 using HiSat2 v2.1.0
HTSeq v0.61 was used to generate count tables
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files

source_name: LNCaP, enzalutamide resistant subline

growth_protocol: All cells were cultured in RPMI 1640 with 10 % FCS , 1 % penicillin/streptomycin and 1 % Glutamax. Enzalutamide-resistant cells were additionally supplied with 8 µM (DuCaP EnzaR ) and 5 µM (LNCaP EnzaR) Enzalutamide.

extract_protocol:
Total RNA was extracted using the EXTRACTME RNA Isolation kit (Blirt) according to the manufacturer’s instructions.
Illumina stranded TruSeq RNA library, poly(A) enrichment

treatment_protocol: Cells were seeded in 6-well plates in growth medium. The next day cells were treated with 10 µM C646, 10 µM I-CBP112, 8 µM enzalutamide or vehicle (DMSO) for 24 hours.

tag: cell line

value: LNCaP, enzalutamide resistant subline

value: DMSO


title: LNCaP DMSO rep 1

source_name: LNCaP

value: LNCaP


title: LNCaP DMSO rep 2


title: DuCaP EnzaR 10 µM I-CBP112 rep 1

source_name: DuCaP, enzalutamide resistant subline

value: DuCaP, enzalutamide resistant subline

value: 10 microM I-CBP112


title: LNCaP DMSO rep 3


title: LNCaP EnzaR DMSO rep 3


title: LNCaP EnzaR DMSO rep 1


title: DuCaP EnzaR DMSO rep 2


title: DuCaP EnzaR 10 µM I-CBP112 rep 2


title: DuCaP EnzaR DMSO rep 1


title: DuCaP 8 µM enzalutamide rep 2

source_name: DuCaP

value: DuCaP

value: 8 microM enzalutamide


title: DuCaP EnzaR 10 µM C646 rep 1

value: 10 microM C646


title: DuCaP 8 µM enzalutamide rep 1


title: M/33y donor, hypoxia, dynamic Compression

description: HD1 (Hypoxia Dynamic 1 -> M/33y, HYP, Dynamic Compression)


title: DuCaP 10 µM C646 rep 1


title: DuCaP DMSO rep 2


title: DuCaP 10 µM I-CBP112 rep 1


title: DuCaP 10 µM C646 rep 2


title: DuCaP 10 µM I-CBP112 rep 2


title: DuCaP DMSO rep 1


title: H2AX ChIP-Seq NELFA siRNA

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Paired-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calculation was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Genome_build: hg38
Supplementary_files_format_and_content: all_genes_gH2AX:H2AX_quant.txt

source_name: fibroblast cells

growth_protocol: Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (H2AX: Merck, 07-627) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
Illumina's Nextera XT DNA Library Preparation Kit following manufacturer’s protocol

treatment_protocol: Asynchronous cells were transfected with 37.5 nM of indicated siRNA (Dharmacon) for 72 h.

value: hTERT-immortalized fibroblasts

value: skin; foreskin

tag: chip antibody

value: Rabbit polyclonal anti-Histone H2AX, Merck, Cat#07-627


title: H2AX ChIP-Seq con siRNA

description: siGENOME Non-Targeting siRNA Pool #2, Dharmacon,Cat#D-001206-14-05


title: Fraction 5 - replicate 2

description:
DNA synthesized in G2/M
FXN 5-2

data_processing:
Library strategy: REPLI-Seq
Single-end BrdU-Seq data from G2/M DNA synthesis samples were aligned to the hg38 genome using Bowtie 2 v.2.3.4.2 on the online platform Galaxy (https://usegalaxy.org)
Coverage counts calculation was done using the function "quantify" in EaSeq, from the start to the end of the gene of all annotated genes
Genome_build: hg38
Supplementary_files_format_and_content: all transcribed gene REPLI-Seq quant.txt

growth_protocol: BJ-hTERT cells were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin while U2OS were cultured in McCoy's 5A (Modified) Medium (Gibco) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin, both in 5 % CO2 at 37°C.

extract_protocol:
PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific)
Illumina sequencing libraries were constructed with 250 pg (or as much as available) of the random-primed BrdU-DNA material according to standard procedures. QIAseq Ultralow Input Library Kit protocol (QIAGEN) was used.
QIAseq Ultralow Input Library Kit protocol (QIAGEN) single end in 4 lanes (L1-L4)

treatment_protocol: The cells were unsynchronized and pulsed with both 25 μM EdU (Sigma-Aldrich) and 50 µM BrdU (Sigma-Aldrich) in fresh pre-warmed medium for 30 min in 5 % CO2 at 37°C. After one-time quick wash with ice-cold PBS, cells were collected by trypsinization followed by mixing with ice-cold regular DMEM to inactivate trypsin. Cells were washed once with ice-cold PBS and fixed and permeabilized for 20 min in PTEMF buffer at room temperature.  Fixed cells were washed twice in PBS and stored in PBS at 4°C until use.

tag: brdu antibody

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8442


title: H2AX ChIP-Seq SUPT5H siRNA


title: Fraction 4 - replicate 2

description:
DNA synthesized in G2/M
FXN 4-2

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8441


title: BJ-hTERT G-MIDS

description: DNA synthesized in G2/M

data_processing:
Library strategy: BrdU-Seq
Single-end BrdU-Seq data from G2/M DNA synthesis samples were aligned to the hg38 genome using Bowtie 2 v.2.3.4.2 on the online platform Galaxy (https://usegalaxy.org)
no data analysis file linked to it because we have used it only for metagene profiles data analysis.
Genome_build: hg38
Supplementary_files_format_and_content: none

tag: cell type

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8434


title: U2OS G-MIDS

description: DNA synthesized in G2/M

source_name: osteosarcoma cells

value: bone


title: Fraction 2 - replicate 2

description:
DNA synthesized in G2/M
FXN 2-2

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8439


title: Fraction 3 - replicate 2

description:
DNA synthesized in G2/M
FXN 3-2

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8440


title: Fraction 1 - replicate 2

description:
DNA synthesized in G2/M
FXN 1-2

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8438


title: Fraction 4 - replicate 1

description:
DNA synthesized in G2/M
FXN 4-1

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8436


title: Fraction 1 - replicate 1

description:
DNA synthesized in G2/M
FXN 1-1


title: Fraction 3 - replicate 1

description:
DNA synthesized in G2/M
FXN 3-1

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8435


title: Fraction 5 - replicate 1

description:
DNA synthesized in G2/M
FXN 5-1

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8437


title: FL24

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

data_processing:
Raw sequencing reads were trimmed and filtered for low-quality bases using Trimmomatic, followed by alignment to the human genome reference (hg19) using Bowtie2 (v 2.2.6) with the end-to-end alignment mode.
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length.
Aligned read pairs were then sorted, indexed and deduplicated using Picard (v 2.6.0). Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project (release 19), using featureCounts from R package Rsubread (v 1.30.9) without strand information.
The 5hmC-Seal libraries were sequenced to produce a median number of ~20 million reads in each sample, and a median number of ~7 million unique reads were mapped to the ~20,000 gene body regions
Genome_build: hg19
Supplementary_files_format_and_content: Read counts files were generated by featureCount as described in the data processing step

source_name: Plasma

extract_protocol:
For each study subject, approximately 2-3 mL of frozen plasma was processed by centrifuging twice at 1,350 × g for 12 min, and then centrifuging at 13,500 × g for 12 min, followed by cfDNA extraction using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany).
Each cfDNA sample was first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (“click”) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for each cfDNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) on the Illumina NextSeq500 platform at Shanghai Epican Genetech Co. Ltd. (Shanghai, China), according to the manufacturer’s protocol. We randomized cfDNA samples when constructing the 5hmC-Seal libraries and sequencing. The 5hmC-Seal was shown to be technically robust and stable in our previous studies using duplicate samples and spike-in controls.
5hmC-Seal

value: FL

value: Female


title: FL23

value: Male


title: FL25


title: DuCaP EnzaR 10 µM C646 rep 2

value: DuCaP, enzalutamide resistant subline

value: 10 microM C646


title: FL22


title: FL20


title: FL13


title: FL17


title: FL14


title: FL19


title: FL18


title: FL12


title: FL16


title: FL15


title: FL5


title: FL10


title: FL7


title: FL3


title: DLBCL44

value: DLBCL


title: FL1


title: FL4


title: DLBCL46


title: FL2


title: FL6


title: FL21


title: DLBCL47


title: DLBCL41


title: DLBCL48


title: FL9


title: DLBCL42


title: DLBCL40


title: DLBCL35


title: FL11


title: DLBCL36


title: DLBCL34


title: DLBCL33


title: DLBCL39


title: FL8


title: DLBCL32


title: DLBCL43


title: DLBCL45


title: DLBCL31


title: DLBCL30


title: DLBCL29


title: DLBCL21


title: DLBCL28


title: DLBCL19


title: DLBCL27


title: DLBCL20


title: DLBCL23


title: DLBCL25


title: DLBCL26


title: DLBCL17


title: DLBCL18


title: DLBCL16


title: DLBCL37


title: DLBCL15


title: DLBCL14


title: DLBCL13


title: DLBCL12


title: DLBCL10


title: DLBCL9


title: DLBCL11


title: DLBCL38


title: DLBCL7


title: DLBCL6


title: DLBCL8


title: DLBCL5


title: DLBCL24


title: DLBCL22


title: DLBCL3


title: Fraction 2 - replicate 1

description:
DNA synthesized in G2/M
FXN 2-1

value: hTERT-immortalized fibroblasts

value: skin; foreskin


title: DLBCL2


title: DLBCL1


title: Input 2 G-MiDS

description: DNA synthesized in G2/M

data_processing:
Library strategy: BrdU-Seq
Single-end BrdU-Seq data from G2/M DNA synthesis samples were aligned to the hg38 genome using Bowtie 2 v.2.3.4.2 on the online platform Galaxy (https://usegalaxy.org)
G-MiDS peaks were called against the Input DNA using MACS2 v.2.1.1 with the same parameters listed above on the online platform Galaxy (https://usegalaxy.org, Afgan et al., 2018).
The betools intersect intervals function on the online platform Galaxy was used to identify the G-MiDS specific peaks against the BrdU peaks called in all the S-phase timepoints combined together. This resulted in approximately 16600 G-MiDS specific peaks.
Genome_build: hg38
Supplementary_files_format_and_content: G-MiDS specific peaks contains the peaks specifically called in the G2/M DNA synthesis sequences towards all the S-phase peaks

treatment_protocol: The cells were synchronized for 26 h and released in regular DMEM medium. 24 h after release, 9 µM Ro 3306 were added to the cells for 16 h to arrest cells in G2. Then cells in early prophase were pulsed with both 25 μM EdU (Sigma-Aldrich) and 50 µM BrdU (Sigma-Aldrich) in fresh pre-warmed medium for 30 min in 5 % CO2 at 37°C. After one-time quick wash with ice-cold PBS, cells were collected by trypsinization followed by mixing with ice-cold regular DMEM to inactivate trypsin. Cells were washed once with ice-cold PBS and fixed and permeabilized for 20 min in PTEMF buffer at room temperature.  Fixed cells were washed twice in PBS and stored in PBS at 4°C until use. Asynchronous cells that were pulsed with 25 μM EdU for 30 min in 5 % CO2 at 37°C were also trypsinized, fixed with PTEMF, washed with PBS and stored in PBS until use.


title: NELFA siRNA 2 G-MIDS

description: DNA synthesized in G2/M


title: QRICH1 KO cells-3

city: Cambridge

first: Kwontae

last: You

state: MASSACHUSETTS

address: 415 main street

institute: Broad Institute

data_processing:
Processing the raw RNA-seq reads by Trimmomatic to remove the adapter and obtain a high-quality base.
The sequencing data were aligned to the reference genome using STAR.
The raw read counts from STAR were subject to DESeq2 to identify differential expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: raw count

source_name: HT29 Cas9 expressing cells

growth_protocol: 10% FBS, DMEM glutamax media,

extract_protocol:
For RNA-seq, add 200ul TCL lysis buffer and Scrap the cells.
Bulk RNA Sequencing library construction using a modified smartseq2 protocol. Libraries were prepared with the Nextera XT DNA library prep kit (Illumina), pooled, and sequence on the Illumina Nextseq 500

treatment_protocol: Treat 0.3ug/ml of Tm for 14hrs.

tag: tm treatment

value: DMSO

tag: lentiviral transduction

value: QRICH1-targeting guide


title: Tm treated QRICH1 KO cells-3

value: treated


title: WT cells-1

value: non-targeting guide


title: Tm treated WT cells-3


title: QRICH1-ChIP-seq in WT

data_processing:
The sequencing raw data were aligned to the reference genome using BWA.
The SAMtools and Picard's MarkDuplicates were used to post-alignment filtering including remove unmapped, multi-mapped reads, and PCR duplicates reads.
The retained high-quality alignment results were used to call peaks by MACS2 against an IgG control.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig format

extract_protocol:
For ChIP-seq, scrap the cells and follow the ChIP-seq protocol to extract the enriched gDNA from the IP samples.
we fixed the cells with 1% formaldehyde and quenched with glycine. We prepared the cell lysate and sonicated the lysates using sonifier (Branson 450 Ultrasonic 102C). We incubated the lysate with anti-QRICH1 antibody (Thermo), anti-ATF4 antibody (Cell signaling), or anti-normal rabbit IgG (Cell signaling) overnight in the cold room. We added the Protein G dynabeads (Invitrogen) for 4 hrs and performed the subsequent ten washes with RIPA bufferbuffer (0.1% SDS, 0.1% DOC, 1% Triton X-100, 1 mM EDTA, 10 mM Tris-HCl pH 8.1, 150 mM NaCl), high-salt RIPA buffer (RIPA with 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 0.5% Triton X-100, 0.5% DOC) and PBS. We incubated the DNA overnight at 65 °C to reverse crosslinking and extracted the enriched gDNA fragments after RNase A and Proteinase K treatment.  We generated the DNA library using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol.


title: Tm treated QRICH1 KO cells-2


title: QRICH1 KO cells-1


title: Tm treated QRICH1 KO cells-1


title: Tm treated WT cells-2


title: Rabbit IgG control

value: anti-normal rabbit IgG


title: WT cells-3


title: WT cells-2


title: Tm treated WT cells-1


title: QRICH1-ChIP-seq in QRICH1 KO


title: CRISPR screen_ER stress-UPR pathway

data_processing:
Library strategy: CRISPR guide library
Alignment and demultiplexing with poolq (https://portals.broadinstitute.org/gpp/public/software/poolq)
Differential expression with mageck_nest without outlier removal
The file sample_index.csv  includes the sample barcodes.  The file count.tsv includes the gene barcode.
Genome_build: Brunello
Supplementary_files_format_and_content: Read counts; differential expression.

source_name: HT29 Cas9 expressing cells either Tunicamycin ™- or DMSO-treated

extract_protocol:
trypsin treat and count the cells, extract the gDNA using DNAzol from Invitrogen, PCR amplify according to Broad GPP sgRNA PCR protocol
Amplification of gRNA sequence from isolated gDNA simultaneously labeled each sample with a pooled P5 primer and unique P7 primer. The P5 primer includes the illumina flow cell attachment sequence, illumina sequencing primer, vector binding sequence, and a stagger region. The P7 primer includes the illumina flow cell attachment sequence, illumina sequencing primer, vector binding sequence and an 8 base pair UMI unique to each individual primer. Libraries from individual samples, each labeled with a unique P7 primer, were pooled and mixed with 10% PhiX Sequencing Control (Illumina) and sequenced on the Illumina Nextseq 500.

treatment_protocol: transduce 9M viruses (Brunello genome-wide library; > 100x complex of library) into 45M of cells (MOI = 0.2). Treat Tm for 14hrs.

tag: treatment

value: mixed sample (non-demultiplexed):includes Tunicamycin-treated and DMSO-treated

tag: number of sorted cells

value: 15million (M)


title: DLBCL4

city: Chicago

tag: diagnosis


title: CTR siRNA 2 G-MIDS

description: DNA synthesized in G2/M

tag: tissue

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8434


title: NELFA siRNA G-MIDS

description: DNA synthesized in G2/M


title: QRICH1 KO cells-2


title: CTR siRNA G-MIDS

description: DNA synthesized in G2/M


title: Chr-RNA-Seq 24h R2

description: chromatin-bound RNA

data_processing:
Single-end RNA-seq data were aligned to the hg38 genome assembly using STAR v.020201 (Dobin et al., 2013) with options “--alignIntronMax 500000”, “--outFilterScoreMinOverLread 0.3” and “--outFilterMatchNminOverLread 0.3”.
Reads were trimmed to remove RNA contamination via BBDuk (Bushnell, JGI BBTools Team).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
Counts for each transcribed gene were computed by featureCounts (Liao et al., 2014) using the annotation of the GENCODE genes (GRCh38.p10).
Read per million (RPM) were calculated over each gene in each replicate, and genes that had an RPM>1 in each timepoint and each replicate were considered as those transcribed in our system.
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described

extract_protocol:
Chromatin bound RNA (Chr-RNA) was prepared as previously described (Mayer and Churchman, 2016), with slight modification
200-300 ng of input RNA in each repeat were depleted of ribosomal RNA with Ribo-Zero Gold rRNA Removal Kit (Illumina) according to manufacturer’s guidelines. The recovered RNA was concentrated in 12 µl nuclease-free water using RNA Clean & Concentrator-5 (Zymo Research). The RNA samples were used to construct RNA libraries using KAPA RNA HyperPrep Kit (Kapa Biosystems, Roche) according to manufacturer’s guidelines, but without rRNA depletion step.

treatment_protocol: Cells fully confluent were seeded at 20 % confluence in 150 mm dishes, and grown overnight. Cells were synchronized in the G0/G1 phase in serum starvation medium (DMEM supplemented with 0.2 % FBS, 2mM L-glutamine and penicillin/streptomycin) in 5 % CO2 at 37°C for 26 h, and released into S-phase with regular DMEM for the indicated timepoints. 15.5 h after release, 100 ng/ml nocodazole (Sigma-Aldrich) was added to the later timepoint cell cultures (19 h, 22 h, 24 h, 28 h) to prevent cells from re-entering the cell cycle

tag: timepoint


title: Chr-RNA-Seq 16h R2

description: chromatin-bound RNA


title: Chr-RNA-Seq 22h R2

description: chromatin-bound RNA


title: Chr-RNA-Seq 14h R2

description: chromatin-bound RNA


title: Chr-RNA-Seq 28h R2

description: chromatin-bound RNA


title: Chr-RNA-Seq 19h R2

description: chromatin-bound RNA


title: ATF4-ChIP-seq in WT cells-1


title: Input G-MiDS

description: DNA synthesized in G2/M


title: gH2AX con siRNA

data_processing:
Paired-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
Illumina's Nextera XT DNA Library Preparation Kit following manufacturer’s protocol

value: Rabbit polyclonal anti-Phospho-Histone H2A.X (Ser139), Abcam, Cat#ab2893

value: siGENOME Non-Targeting siRNA Pool #2


title: Chr-RNA-Seq 16h R1

description: chromatin-bound RNA


title: Chr-RNA-Seq 24h R1

description: chromatin-bound RNA


title: H3 2 NELFA siRNA

value: Rabbit polyclonal anti-Histone H3, Abcam, Cat#ab1791

value: siGENOME Human NELFA siRNA Pool


title: Chr-RNA-Seq 14h R1

description: chromatin-bound RNA


title: Chr-RNA-Seq 22h R1

description: chromatin-bound RNA


title: Chr-RNA-Seq 19h R1

description: chromatin-bound RNA


title: gH2AX 2 SUPT5H siRNA

value: siGENOME Human SUPT5H siRNA Pool


title: H3 2 SUPT5H siRNA


title: gH2AX 2 con siRNA


title: gH2AX NELFA siRNA


title: BrdU-Seq Early S Trip DMSO

data_processing:
Library strategy: BrdU-Seq
Paired-end BrdU-Seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described

extract_protocol:
PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific)
Illumina's Nextera XT DNA Library Preparation Kit following manufacturer’s protocol

treatment_protocol: Cells fully confluent were seeded at 20 % confluence in 150 mm dishes, and grown overnight. Cells were synchronized in the G0/G1 phase in serum starvation medium (DMEM supplemented with 0.2 % FBS, 2mM L-glutamine and penicillin/streptomycin) in 5 % CO2 at 37°C for 26 h, and released into S-phase with regular DMEM for the indicated timepoints. 15.5 h after release, 100 ng/ml nocodazole (Sigma-Aldrich) was added to the later timepoint cell cultures (19 h, 22 h, 24 h, 28 h) to prevent cells from re-entering the cell cycle. For the triptolide treatment, cells were treated for 1 hour with the indicated concentration before being harvested at the 16h timepoint.

value: 16h timepoint Triptolide treatment


title: H3 2 con siRNA


title: BrdU-Seq Early S 2 NELFA siRNA

value: 16h timepoint repeat 2 siGENOME Human NELFA siRNA Pool


title: BrdU-Seq Early S 2 con siRNA

value: hTERT-immortalized fibroblasts

value: 16h timepoint repeat siGENOME Non-Targeting siRNA Pool #2


title: BrdU-Seq Early S 2 SUPT5H siRNA

value: skin; foreskin

value: 16h timepoint repeat 2 siGENOME Human SUPT5H siRNA Pool,


title: gH2AX 2 NELFA siRNA

value: siGENOME Human NELFA siRNA Pool, Dharmacon


title: H3 ChIP-Seq SUPT5H siRNA


title: H3 ChIP-Seq con siRNA


title: gH2AX SUPT5H siRNA


title: BrdU-Seq Early S Trip 100nM


title: BrdU-Seq Early S Trip 200nM


title: BrdU-Seq Early S Trip 50nM


title: BrdU-Seq Early S 2 Input


title: BrdU-Seq Early S Input

value: Input genomic DNA


title: BrdU-Seq Early S con siRNA

value: 16h timepoint siGENOME Non-Targeting siRNA Pool #2


title: BrdU-Seq Early S NELFA siRNA

value: 16h timepoint siGENOME Human NELFA siRNA Pool


title: RNA_seq_SingleCell_NP_dermis

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description:
Cont-f
scRNAseq

data_processing:
The 10X Genomics Cell Ranger pipeline (version 2.2.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the GFP sequence, barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample.

source_name: abdominal skin dermis

extract_protocol:
Subcutaneous fat was removed from the skin with a scalpel, and the whole skin was incubated for 30 min in 0.25% trypsin to separate into epidermis and dermis. Dermal cells were dissociated into single cells by pipetting and filtrated on a 40μm (Falcon) and 20μm (PLS). Single cell suspensions were resuspended in 1% BSA/PBS at 1000 cells/µL and barcoded with a 10× Chromium Controller (10× Genomics).
RNA from the barcoded cells of each sample was subsequently reverse transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell v2 reagent kit (10× Genomics), according to the manufacturer’s instructions. Sequencing was performed with a NextSeq 500 (Illumina), according to the manufacturer’s instructions.

tag: genotype

value: Col1a2creERT2; R26H2B EGFP

tag: perinatal date

value: 8-12week (non pregnant)

value: abdominal skin dermal cells


title: RNA_seq_SingleCell_dpp6

data_processing:
For bulk RNA-seq analysis, the sequenced reads were mapped to the mm10 mouse reference genome using Tophat2 (version 2.2.1) with the GENCODE M15 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-1.14. The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were calculated using Cuffdiff within Cufflinks version 2.2.1 package and the GENCODE M15 annotation file (protein coding).
For scRNA analysis, the 10X Genomics Cell Ranger pipeline (version 2.2.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the GFP sequence, barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10
Supplementary_files_format_and_content: For bulk RNAseq, a tsv file include FPKM values. For scRNAseq, tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: abdominal skin epidermis

extract_protocol:
Subcutaneous fat was removed from the skin with a scalpel, and the whole skin was trypsinized at 37 °C for an hour to remove the dermis. The cell suspensions were filtered through strainers (70-μm, BD Falcon), collected by centrifugation (300 × g, 5 min) and suspended in Dulbecco’s modified Eagle’s medium (Ca−). Cell suspensions were incubated with Pacific Blue anti-human/mouse CD49f (Biolegend) antibody and eFluor660 anti-mouse CD34 (Biolegend) antibody for 30 min on ice, washed twice with PBS and subjected to flow cytometric analysis. Cell isolation was performed on a FACSAria Ⅲ sorter. RNA was extracted from CD49f positive and CD34 negative cells using the RNeasy Micro Kit (Qiagen). Quality RNA samples were selected (RIN>7).  For scRNAseq, single cell suspensions of all samples were resuspended in PBS-1% BSA at 1000cells/μL and barcoded with a 10x Chromium Controller (10x Genomics).
RNA-seq libraries were generated using the TruSeq Stranded mRNA library prep kit (Illumina) and the libraries were sequenced on NextSeq 500 (Illumina). For scRNAseq, RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v2 reagent kit (10x Genomics). Sequencing was performed with Illumina NextSeq 500 .

value: Tbx3creERT2; R26H2B EGFP

value: post partum day 6


title: BrdU-Seq Early S SUPT5H siRNA

value: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8434

value: 16h timepoint siGENOME Human SUPT5H siRNA Pool,


title: H3 ChIP-Seq NELFA siRNA

value: Rabbit polyclonal anti-Histone H3, Abcam, Cat#ab1791

value: siGENOME Human NELFA siRNA Pool


title: Chr-RNA-Seq 28h R1

description: chromatin-bound RNA

value: hTERT-immortalized fibroblasts