title: PB_CD4plusCD45RAmin_D6_T72_ADA_ATAC

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

institute: King's College London

description: Genewiz

data_processing:
To obtain the open chromatin regions, reads were aligned to hg38 using Bowtie v2.3.42 with parameters [--maxins 175 --no-discordant --no-mixed]
Properly paired and uniquely mapped alignments were extracted using bamFilter v2.4.1 with parameters[ isMapped= true, isPaired= true,  isDuplicate= false, reference= !chrM]
Open chromatin regions were identified using from Homer v4.11 the findPeaks tool with parameters [-style factor -size 300 -minDist 50 -fdr 0.001 -norm 40000000 -tbp 0 -region -o]
Assembly: hg38
Supplementary files format and content: biwWig files of called peaks

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were obtained from healthy adult volunteers. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation using Lymphoprep (Axis-Shield, Oslo, Norway). CD4+ T-cells were isolated by magnetic-activated cell sorting (MACS) using the CD4+ T-cell Isolation Kit II (Miltenyi Biotec, Bergisch-Gladbach, Germany). Nuclei were isolated and ATAC-seq was performed according to published protocol (Buenrostro et al., Nature Methods, 2013)
Library was constructed according to published protocol (Buenrostro et al., Nature Methods, 2013).

treatment_protocol: Cells were cultured at 37°C with 5% CO2 in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 1% penicillin, streptomycin and L-glutamine (all from Gibco). MACS-isolated CD4+ T-cells were stimulated at 106/ml with 1.25 µg/ml of coated anti-CD3 (clone OKT3; BD Biosciences) and 1 µg/ml of soluble anti-CD28 (clone CD8.2; BD Biosciences) in the absence or presence of 1 µg/ml of adalimumab (ADA, Abbott Laboratories, Chicago, USA) for 3 days.

value: Peripheral blood

value: Healthy

value: CD45RA+ depleted CD4+ T cells


title: Donor3, Ctrl

status: Public on Sep 25 2024

type: SRA

city: Duarte

first: Debbie

last: Thurmond

state: CA

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

country: USA

institute: City of Hope

library_source: transcriptomic

data_processing:
RNA-seq raw fastq reads were aligned to the human hg19 genome using TopHat2.
Gene counts were obtained using htseq-count, with UCSC known gene annotations (TxDb.Hsapiens.UCSC.hg19.knownGene), and converted into counts per million (CPM) using edgeR.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with columns containing raw gene counts from each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic islets

extract_protocol:
RNA extraction was performed using QIAGEN RNase kit.
250ng of total RNA from each samples was used for sequencing library preperation with KAPA mRNA Hyperp Kit according to user manual. The library QC was checked with Agilent bioanalyzer DNA high sensitivity chip, and qubit was used for library quantification. The final libries were sequenced on Illumina Hiseq2500 wtih single read mode of 51 cyles, plus 7 cycles of index sequencing with V4 kit.

tag: tissue

value: Pancreatic islets

tag: individual

tag: disease state

value: ND

tag: genotype

value: Ctrl


title: UCB CD34+ cells_7-day expanded with SR1_Rep3

type: RNA

city: Pretoria

first: Juanita

last: Mellet

state: Gauteng

address: 5 Bophelo road

department: Immunology

country: South Africa

institute: University of Pretoria

hyb_protocol: Following fragmentation, cRNA were hybridized for 17 hours in an Affymetrix GeneChip® Hybridization Oven-645 at 45⁰C rotating at 60 rpm to the Affymetrix GeneChip® Human Gene 2.0 ST arrays. The hybridized chips were washed and stained in an Affymetrix GeneChip® Fluidics Station-450Dx.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip® Scanner-7G.

data_processing: The CEL files were imported into Affymetrix Transcriptome Analysis Console™ (TAC) Software 4.0 to perform background correction, summarization, normalization and calculation of expression values using default analysis settings.

label: Biotin

source_name: Umbilical cord blood CD34+ cells, expanded for 7 days with SR1

label_protocol: Biotinylated cRNA were prepared according to the manufacturer’s manual.

growth_protocol: StemSpan animal component free (ACF) medium supplemented with 2% penicillin (100 units/mL), streptomycin (0.1 mg/mL) and recombinant human growth factors, each at 100 ng/mL: Stem cell factor (SCF), thrombopoietin (TPO), FMS-like tyrosine kinase 3 ligand (FLT3L), granulocyte colony stimulating factor (G-CSF) and interleukin 3 (IL-3). Cultures were maintained at 37⁰C and 5% CO2 in a humidified atmosphere for 7 days.

extract_protocol: The Qiagen RNeasy Micro Plus kit was used to perform RNA extractions according to the manufacturer’s instructions.

treatment_protocol: SR1 was dissolved in dimethyl sulfoxide (DMSO) and further dilutions were made using StemSpan ACF to achieve a final concentrations of 1 µM.

value: Umbilical cord blood

tag: cell type

value: CD34+ cells

tag: time point

value: 7 days

value: yes


title: UCB CD34+ cells_freshly isolated_Rep2

source_name: Umbilical cord blood CD34+ cells, freshly isolated

value: 0 days

value: no


title: SLu10_3

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

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 mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

organism: Mus musculus

source_name: spleen

extract_protocol:
spleen were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

value: spleen

tag: age

value: 8 weeks


title: UCB CD34+ cells_freshly isolated_Rep3


title: UCB CD34+ cells_7-day expanded without SR1_Rep2

source_name: Umbilical cord blood CD34+ cells, expanded for 7 days without SR1


title: UCB CD34+ cells_7-day expanded without SR1_Rep1


title: PB_CD4plusCD45RAmin_D6_T72_NoADA_ATAC

country: United Kingdom

description: Genewiz

library_source: genomic

molecule: genomic DNA

tag: disease


title: RWPE1_Veh

city: Sacramento

first: yatian

last: yang

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

tag: cell line

value: normal prostate cell

value: WT

tag: treatment

value: veh

tag: time

value: 48 hours


title: SBLu10_3


title: UCB CD34+ cells_7-day expanded with SR1_Rep1


title: SBLu10_2


title: RWPE1_SR8278


title: PB_CD4plusCD45RAmin_D5_T72_ADA_ATAC

description: Genewiz

value: Peripheral blood

value: Healthy

value: CD45RA+ depleted CD4+ T cells


title: UCB CD34+ cells_freshly isolated_Rep1


title: RWPE1_input_Veh

data_processing:
Fastq files from ChIP-seq were processed by the pipeline of AQUAS Transcription Factor and Histone. Briefly, sequencing tags were mapped against the Homo sapiens (human) reference genome (hg19) using BWA 0.7.15. Uniquely mapped tags after filtering and deduping were used for peak calling by model-based analysis for ChIP-seq (MACS 2.1.0) to identify regions of enrichment over background.
Normalized genome-wide signal-coverage tracks from raw-read alignment files were built by MACS2, UCSC tools and bedTool.
Visualization of ChIP-seq signal at enriched genomic regions (avg profile and heatmap) was achieved by using deepTools.
Peak associated genes were identified using the annotatePeaks function of HOMER.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

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

extract_protocol:
samples were subject to crosslinking in 1% formaldehyde for 5 min followed by quenching with glycine for 5 min on ice. Cells were pelleted by centrifugation and resuspended in lysis buffer (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X100). The pellets were then resuspended in washing buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl), washed and resuspended in shearing buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8) before sonication using Covaris E220 following manufacturer’s instruction. Chromatin fragments were precipitated using specific antibodies and Protein G beads, washed and treated with Proteinase K and RNAse A.
The ChIP complexes were washed and eluted in 50 mM NaHCO3 and 1% SDS, followed by overnight reverse crosslinking. The recovered DNAs from ChIP and ChIP-reChIP were used for library generation. Libraries were quantified with the Bioanalyzer 2100.

tag: chip antibody

value: Vehicle 24hr


title: shScamp1 biol rep 2

city: Tianjin

first: Gang

last: Ma

email: horsegang@163.com, horsegang@tmu.edu.cn

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District

department: Department of Gastric Surgery

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Ge
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

growth_protocol: NCI-N87 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% of penicillin/streptomycin at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
When shNC and shScamp1 NCI-N87 cells grew to approximately 80% confluence, they were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NCI-N87 Cells were incubated with the shNC or shScamp1 lentivirus and polybrene (1 μl/ml) for 24 h. Puromycin (2 μg/ml) was used to establish stable cell populations.

value: stomach

value: gastric cancer cell line

value: SCAMP1 Knockdown


title: RWPE1_input_SR8278


title: PB_CD4plusCD45RAmin_D5_T72_NoADA_ATAC

description: Genewiz


title: SB_3

description: busulfan


title: shScamp1 biol rep 1


title: SBLu10_1


title: SB_2

description: busulfan


title: shNC biol rep 3

value: Control


title: PB_CD4plusCD45RAmin_D2_T72_ADA_ATAC

description: Genewiz


title: SB_1

description: busulfan


title: PB_CD4plusCD45RAmin_D2_T72_NoADA_ATAC

description: Genewiz


title: shScamp1 biol rep 3


title: RWPE1_NR1D1_Veh

value: REV-ERBα (CST, #13418 and Proteintech, #14506-1-AP)


title: RWPE1_NR1D1_SR8278


title: shNC biol rep 2


title: LLu10_3

source_name: liver

extract_protocol:
liver were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: LLu10_2

value: ICR


title: Lucap35CR Vehicle

data_processing:
Fastq files from ATAC-seq were processed by the pipeline on Github (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Sequencing tags were mapped against the Homo sapiens (human) reference genome (hg19) using Bowtie 2.2.6. Mitochondrial and duplicated reads were filtered through SAMtools (v 1.2) and picard (v 2.1.1).
After filtering and deduping, uniquely mapped tags were used for peak calling by model-based analysis (MACS; 2.1.0) to identify regions of enrichment over background.
After normalization, genome-wide signal-coverage tracks from raw-read alignment files were built by MACS2, UCSC tools (bedGraphToBigWig/bedClip; http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/), and bedTools (https://github.com/arq5x/bedtools2).
The ATAC-seq signal visualization at enriched genomic regions (avgprofile and heatmap) was achieved by using deepTools (https://deeptools.readthedocs.io/en/develop/index.html).
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Briefly, 50,000 cells per condition were washed in cold PBS and resuspended in 50 μl of cold lysis buffer. Samples were centrifuged for 10 min at 500g, 4 °C and the cell pellet resuspended in the transposition reaction mix and incubated at 37 °C for 30 min. Samples were purified using the Qiagen MinElute PCR Purification Kit.
Transposed DNA was eluted in 10 μl of elution buffer,and subjected to PCR amplification using barcoded primers and NEBNext High Fidelity PCR Master Mix. ATAC-seq libraries were purified using 2× volumes of AMPure XP beads to remove fragments below 100 bp. Library quality was assessed using a Bioanalyser High Sensitivity DNA Analysis Kit

value: prostate cancer

value: Vehicle

value: 7 days


title: shNC biol rep 1


title: Lucap35CR SR8278

value: WT


title: Participant 3834-009 Post exercise

city: Itabashi-ku

first: Hiroshi

last: Nishimune

state: Tokyo

address: 35-2 Sakaecho

department: Neurobiology of Aging

country: Japan

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

data_processing:
The read quality was assessed using the FastQC software.
The reads were mapped to the human genome (GRCh38.rel92) using the STAR software, version 2.5.2b.
Transcript abundance estimates were calculated using the RSEM 32 (version 1.3.0) software.
Expression normalization and differential gene expression calculations were performed in edgeR (release 2.14) to identify statistically significant differentially expressed genes.
The significance p-vales were adjusted for multiple hypotheses testing by the Benjamini and Hochberg method establishing a false discovery rate (FDR) for each gene.
Assembly: GRCh38.rel92

source_name: Muscle

extract_protocol:
Patient muscle biopsies were homogenized in TRIzol reagent (Invitrogen) and transferred to 5 Prime - Phase Lock Gel - heavy 2ml tubes (Andwin Scientific) to purify total RNA.
Total RNA (500ng) was used to initiate the Stranded mRNA-Seq library preparation using the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina RS-122-2101/2102).

value: Muscle

value: Amyotrophic lateral sclerosis (ALS)

value: Exercise


title: Participant 3834-009 Pre exercise


title: PARAIL GapmeR 2, Rep1

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings (CD14+ monocytes)  or using HISAT (v2.1.0) for THP1-macrophages.
Gene expression level of Refseq coding genes or lncRNAs were quantified using an in-house method developed in Integrative Genomics Core. RNA-seq data were analyzed using edgeR.
Assembly: hg19
Supplementary files format and content: raw counts in text format

molecule: polyA RNA

growth_protocol: Human CD14+ monocytes (de-identified) from the blood of healthy volunteers were obtained from commercial sources (All Cells. Alameda, CA). CD14+ monocytes were cultured in RPMI containing 10% FBS, penicillin/streptomycin (Pen/Strp; 100 U/100 μg per ml), 2 mM glutamine, 5.5 mM glucose.  For lncRNA PARAIL characterization and mechanistic studies we used THP1 monocytic cell line (ATCC, Cat#TIB-202). THP1 cells were cultured in the same medium as described for monocytes plus 50 μM β-mercaptoethanol. THP1 cells were differentiated into macrophages using PMA (20 ng/mL, up to 48 hours) and treated as indicated.

extract_protocol:
Total RNA was isolated from CD14+ monocytes and THP1 macrophages using RNeasy mini kit and on-column DNase I digestion to eliminate genomic DNA (Qiagen).
RNA-Seq. Libraries were prepared according to instructions accompanying the Illumina® Illumina Stranded Total RNA Prep with Ribo-Zero kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols (CD14+ mnocytes).  For THP1 cells Libraries were prepared using KAPA mRNA HyperPrep with PolyA protocol.

treatment_protocol: CD14+ human monocytes were treated with NG for 72 hours (5.5mM), Palmitic acid (200 μM,PA) was added 48 hours after culturing in NG). THP-1 cells were differentiated into macrophages (PMA, 20 ng/mL, 24 hours) and transfected with antisense locked nucleic acid (LNA)-modified control GapmeRs (Qiagen) or GapmeRs targeting PARAIL (50 µM) using RNAiMAX reagent (Thermo Scientific). After 48 hours cells were treated with PA (200 µM) for 24 hours followed by RNA isolation.

value: Peripheral blood

value: monocyte

value: PARAIL GapmeR2

value: Palmitic acid treated


title: Lcon_3

description: Control

value: 8 weeks


title: Lcon_2

description: Control


title: PARAIL GapmeR 1, Rep2

value: PARAIL GapmeR1


title: Participant 3834-008 Pre exercise


title: Participant 3834-008 Post exercise


title: PARAIL GapmeR 1, Rep1


title: Lcon_1

description: Control


title: C42B, Vehicle

value: 48 hours


title: PB_CD4plusCD45RAmin_D1_T72_ADA_ATAC

description: Genewiz

value: Healthy

value: CD45RA+ depleted CD4+ T cells


title: Control GapmeR, Rep2

value: Control GapmeR


title: lucap35cr_REV-ERBα_Veh

value: prostate cancer

value: REV-ERBα (CST, #13418 and Proteintech, #14506-1-AP)

value: Vehicle 7days


title: Participant 3834-007 Pre exercise


title: C42B, SR8278

value: WT


title: PARAIL GapmeR 2, Rep2


title: LBLu10_3

value: ICR

value: liver


title: C42B,OE NR1D1

value: OE NR1D1


title: LLu10_1


title: Participant 3834-007 Post exercise

value: Muscle

value: Amyotrophic lateral sclerosis (ALS)

value: Exercise


title: PA, 24h, Rep2

value: Peripheral blood

value: CD14+ monocytes

value: Palmitic acid treated


title: Participant 3834-005 Pre exercise


title: LBLu10_1

value: 8 weeks


title: LBLu10_2


title: Control GapmeR, Rep1

value: monocyte


title: lucap35cr_Input_Veh


title: Participant 3834-005 Post exercise


title: lucap35cr_REV-ERBα_SR8278

value: 20mg/kg SR8278 7days


title: PA, 24h, Rep1


title: LB_3

description: busulfan


title: lucap35cr_Input_SR8278


title: C42B,empty

value: empty

value: 48 hours


title: Participant 3834-003 Pre exercise


title: Control, 24h, Rep2

value: Control (BSA)


title: LB_2

description: busulfan


title: Participant 3834-003 Post exercise


title: lucap35cr_FOXA1_Veh

value: prostate cancer

value: FOXA1(active motif, #39837 and abcam, #ab170933)

value: Vehicle 7days


title: Control, 24h, Rep1


title: LB_1

description: busulfan

value: ICR

value: liver


title: Gardnerella vaginalis single biofilms_biol rep3 (br3)

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

description: Gvaginae_Single vs Mixed biofilms_RPKM

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (v 2.17.1.14) starting from raw sequencing reads. The quality of individual sequences was evaluated using FastQC software after adapter trimming with cutadapt software (v 1.18).
Adapter trimmed data was further analysed by CLC Genomics Workbench v 21.99.
Sequence data were trimmed for low quality using CLC Genomics Workbench (parameter - quality limit: 0.05 and Maximum number of ambiguities allowed: 2).
Trimmed sequences read were mapped to either G. vaginalis NCTC 10287, F. vaginae FDAARGOS_934 or P. bivia DSM 20514 using CLC Genomics Workbench (parameters-Mismatch cost: 2, insertion cost; deletion cost: 3; length fraction 0.8, similarity fraction: 0.8 and maximum number of hits for a read: 10).
Differential expression analysis was performed using CLC Genomics Workbench, upon normalisation to RPKM. Baggerley statistical test was used to identify significant alterations in gene transcription. Only alterations with fold-changes > 2 and a false discovery rate (FDR)-adjusted P value < 0.05 were used for further bioinformatics analyses.
Assembly: G. vaginalis NCTC 10287 (NZ_LR134385.1), F. vaginae FDAARGOS_934 (CP065631.1) and P. bivia DSM 20514 (scaffolds NZ_JH660658.1; NZ_JH660659.1; NZ_JH660660.1)
Supplementary files format and content: The tab-delimited text file present RPKM values of either G.vaginalis, F. vaginae or P. bivia of the three replicas performed, for both single (S) and multispecies/mixed (M) biofilms.

organism: Gardnerella vaginalis

source_name: Gardnerella vaginalis (Gv)

growth_protocol: Single and triple-species biofilms of G. vaginalis, F. vaginae and P. bivia were formed on 24-well culture plates (Orange Scientific). First, an inoculum of each species was prepared in NYCIII medium [0.24% (w/v) HEPES (VWR), 1.5% (w/v) proteose peptone (Liofilchem), 0.38% (w/v) yeast extract (Liofilchem), 0.5% (w/v) NaCl (VWR), 0.5% (w/v) glucose (Fisher Scientific), and 10% (v/v) of inactivated horse serum (Sigma)] and incubated at 37˚C under anaerobic conditions for 24 h. Bacterial concentration was then adjusted to 1x107 CFU/mL and 1 mL of suspension was dispensed into 24-well plates. The plates were incubated for 48 h at 37˚C under anaerobic conditions. After 48 h, the medium was removed, and the biofilms were washed once with 1x phosphate-buffered saline (PBS) solution (Fisher Scientific). Biofilms were then detached from the bottom of the plate in RNA Protect bacteria reagent (QIAGEN), which was diluted 2:1 in PBS; and 12 biofilms (i.e. biofilms from 12 wells) were combined to obtain samples with enough RNA for further analysis. Finally, samples were centrifuged at 5000 xg for 10 min at room temperature.

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (QIAGEN), according to the manufacturer's instructions with some brief modifications. First, cells were suspended in 600 μL of the lysis buffer RLT and the volume was transferred into a tube with 0.1 mm zirconium beads (Merck). Cells were lysed using the BeadBug 6 Microtube Homogenizer (Benchmark Scientific) at maximum speed for 35s. The cycle was repeated four times and the samples were kept on ice for 5 min between cycles. Then, the samples were centrifuged, and the supernatant was recovered into a new tube. Ethanol [70% (Thermo Fisher Scientific)] was added, in the same proportion (vol: vol), to the supernatant and the solution was transferred to an RNeasy Mini spin column. RNA was then eluted in RNase-free water (GRISP) and treated with Turbo DNase (Invitrogen) to degrade genomic DNA following the manufacturer's instructions for rigorous protocol. RNA quality was assessed using an Agilent 2100 Fragment Analyzer system (Agilent) and only samples with RNA quality indicators above 7 were used.
RNA-seq libraries were prepared by Lexogen (outsourced) using Lexogen’s CORALLTM Total RNA-seq kit with 100 ng of total RNA. Before RNA-seq, rRNA was removed using the RiboCop for Bacteria (Mixed Bacterial Samples META) rRNA Depletion kit (Lexogen). Sequencing libraries were evaluated for quality on a Fragment Analyzer System (Agilent) and quantified with QubitTM dsDNA HS Assay Kit (Invitrogen). Data were generated using Illumina NextSeq2000 Sequencing from single-end reads (SR100).


title: Participant 3834-002 Post exercise

value: Muscle


title: lucap35cr_FOXA1_SR8278


title: KLu10_3

source_name: kidney

extract_protocol:
Kidney were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney


title: Gardnerella vaginalis single biofilms_biol rep2 (br2)

description: Gvaginae_Single vs Mixed biofilms_RPKM


title: Participant 3834-002 Pre exercise

value: Amyotrophic lateral sclerosis (ALS)

value: Exercise


title: C42B_REV-ERBα_SR8278

value: REV-ERBα (CST, #13418 and Proteintech, #14506-1-AP)


title: KLu10_2


title: Participant 3834-001 Pre exercise


title: Kcon_3

description: Control


title: PB_CD4plusCD45RAmin_D1_T72_NoADA_ATAC

description: Genewiz

value: Peripheral blood

value: Healthy

value: CD45RA+ depleted CD4+ T cells


title: Gardnerella vaginalis single biofilms_biol rep1 (br1)

description: Gvaginae_Single vs Mixed biofilms_RPKM

source_name: Gardnerella vaginalis(Gv)


title: C42B_Input_oe_NR1D1

value: OE NR1D1


title: Participant 3834-001 Post exercise


title: C42B_REV-ERBα_Veh

value: Vehicle 24hr


title: SS-Grp8-R10

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

institute: NIDA

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol:
Training: Rats were randomly segregated into two groups of saline (n = 12) or METH (0.1 mg/kg /infusion) (n = 36). On each training day, rats were trained to lever press on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 22 days.
1st Footshock phase: Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the initial footshock at 0.18 mA and increased the foot-shock intensity by 0.06 mA up to a final current of 0.36 mA (with a total of 8 punishment days). After 8 days of foot-shock we identified two phenotypes. Some rats continued to take METH in presence of aversive stimuli (foot-shock 0.18 to 0.36 mA) we termed those rats shock-resistant (SR), whereas some rats decrease their reinforced lever responding and we called them shock-sensitive (SS)
The animals were withdrawal (force abstinent) from METH for 15 days, during which they are tested for METH seeking behavior on WD1 and WD15.
Rats were again allowed to self-administer METH-HCl and saline on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 12 days.
2nd Footshock phase: Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the foot-shock intensity to 0.30 mA, with a total of 3 punishment days. After 3 days of foot-shock we identified three phenotypes. We observed some SS rats from 1st punishment phase showed compulsive METH intake in presence of aversive stimuli (foot-shock, 0.30 mA), we called these rats resurgence shock-resistant (RSR), while remaining SS rats decrease their METH intake in presence of aversive stimuli. SR rats continued to self-administered METH during 2nd punishment phase.
The animals were withdrawal (force abstinent) from METH for 15 days, during which they are tested for METH seeking behavior on WD1 and WD15. The animals were euthanized 15 days later, the brain region was dissected, snap frozen on dry ice and then stored in the -70C freezer.

value: Long Evans

value: Dorsal striatum

value: adult

value: wild type

value: METH Shock Sensitive


title: Kcon_2

description: Control

value: ICR

value: 8 weeks


title: HC donor 5

city: Dublin

first: Conor

middle: M

last: Smith

address: TBSI

country: Ireland

institute: Trinity COllege Dublin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were generated through kallisto bustools (https://www.kallistobus.tools/)
The following command was applied to the fastq files of each sample: kallisto bus -x 10xv2 -o 10xv2 -i hg38.repeat_masked.gene.trans.exon.cds *R*fastq.gz
Each resulting bus file was corrected: bustools correct -w 737K-august-2016.txt -o output.correct.bus output.bus
Each corrected bus file was sorted: bustools sort -o output.correct.sort.bus output.correct.bus
Aggregation of reads: bustools count -o human_transcript_to_gene.tsv -e matrix.ec -t transcripts.txt --genecounts output.correct.sort.bus
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovial tissue (knee joint)

extract_protocol:
RA and PsA patients (defined by the ACR and CASPAR Criteria respectively) were recruited from the Rheumatology Department, St. Vincent’s University Hospital, UCD and Tallaght University Hospital, TCD.  RA and PsA patient synovial tissue samples from knee joints with active inflammation were obtained under local anaesthetic using Wolf 2.7 mm needle arthroscopy or ultrasound guided biopsy as previously described, please see table S1 for patient clinical characteristics 63.  RA and PsA patients had comparable moderate to high disease activity (DAS28 4.6 ± 1.1 and DAPSA 24.2 ± 4.9 respectively) and biopsies had lymphocyte infiltrates and lining layer hyperplasia as scored by a clinical pathologist. Healthy individuals undergoing arthroscopy during anterior cruciate ligament (ACL) reconstruction surgery were included in this study. Healthy subjects were defined as those who had no evidence of any form of arthritis on history or examination and had no cartilage damage or synovitis on knee arthroscopy. Furthermore, histological examination demonstrated normal synovium with no signs of inflammation. All patients gave fully informed written consent approved by the institutional Ethics Committee and research was performed in accordance with the Declaration of Helsinki.Synovial tissue single cell suspensions were generated following enzymatic and mechanical digestion of the synovial biopsies as described previously 27. Briefly, approximately 15 synovial biopsies per patient were digested using the GentleMACS Tumor Dissociation Kit, human (Miltenyi Biotech) as per manufacturers’ instructions. Immediately after isolation, biopsies are washed with RPMI (Merck) before being placed in 4.7 ml RPMI supplemented with 200 μl of enzyme H, 100 μl enzyme R and 25 µl enzyme A in a gentleMACS™ C Tube followed by initial mechanical disruption of the tissue using program h_tumor_01 on a gentleMACS™ Dissociator. Samples are enzymatically digested for a total of 1 h at 37 °C under continuous rotation using the MACSmix Tube Rotator with further applications of the gentleMACS™ Dissociator at the halfway point and at the end of the 1 h incubation. The cell suspension is then passed through a 70 µM cell strainer. Viability of the cells is assessed with trypan blue exclusion staining and immediately cryopreserved in sterile filtered 10% DMSO/FBS at a concentration of 1x10ˆ6 cells per ml.
Using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics), cells were loaded onto the GEM Chips.  The 10X Genomics Chromium Next GEM Single Cell 3’ user manual was followed for all steps to generate cDNA libraries for each sample. cDNA quantifications and quality control were determined using the Agilent TapeStation.
Final libraries were normalized, quantified (Illumina/ROX low, Kappa Biosystems), pooled based on 40k reads/sample.  Pooled libraries were sequenced on the Illumina NovaSeq using and S2 NovaSeq 6000 Reagents v1 kit and a 100-cycle sequencing run.

value: single cell suspension

tag: Sex

value: Male

value: synovial tissue (knee joint)


title: C42B_Input_empty

value: prostate cancer

value: empty


title: SS-Grp8-L5


title: C42B_Input_Veh


title: HC donor 4

description: 10x Genomics


title: SS-Grp7-R9


title: HC donor 3

description: 10x Genomics


title: Kcon_1

description: Control

value: kidney


title: C42B_Input_SR8278


title: SS-Grp7-R2


title: KLu10_1


title: C42B_H3K27ac_Veh


title: HC donor 2

description: 10x Genomics

value: Healthy


title: KBLu10_2


title: SS-Grp7-R1


title: HC donor 1

description: 10x Genomics


title: SS-Grp7-L10


title: C42B_FOXA1_oe_NR1D1

value: FOXA1(active motif, #39837 and abcam, #ab170933)


title: U87 cells fire-fly luciferase silencing rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description:
U87_siCTRL_rep3
count.matrix.txt.gz

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
Genes quantification was conducted with HT-seq count tool as implemented in STAR (v2.7.10b) mapped to Homo sapiens genome version GRCh38 and with reference gtf annotation version 109.
Batch effect was removed using Combat-Seq R package
Read counts generated by STAR were analysed by using DESeq2 package (Love, 2014) for detecting genes that were differentially expressed. An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Assembly: Homo sapiens genome version GRCh38 and with reference annotation gtf version 109.
Supplementary files format and content: tab delimited csv file contains raw counts for each sample.

growth_protocol: U87 were cultured up to 20 passages in DMEM (1x), high glucose, GlutaMAX Supplement, pyruvate (Life-Technologies) supplemented with 10% fetal bovine serum (FBS from Life-Technologies) and 1% Antibiotic-Antimycotic-stabilized suspension (Sigma-Aldrich), at 37°C with humidified atmosphere of 5% CO2.

extract_protocol:
RNA was extracted using miRNeasy Kit (QIAGEN)
Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: 300 µl of Opti-MEM (Life-Technologies), 6 μl of 40 μM control siRNA, 18 µl of Lipofectamine RNAiMAX reagent

value: Glioblastoma/astrocytoma cell line

value: WT


title: C42B_H3K27ac_SR8278


title: SR-Grp8-R7

value: Long Evans

value: METH Shock Resistant


title: U87 cells fire-fly luciferase silencing rep2

description:
U87_siCTRL_rep2
count.matrix.txt.gz


title: C42B_FOXA1_empty


title: SR-Grp8-R8

value: Dorsal striatum

value: adult


title: U87 cells fire-fly luciferase silencing rep1

description:
U87_siCTRL_rep1
count.matrix.txt.gz


title: C42B_FOXA1_Veh

value: Vehicle 24hr


title: KBLu10_1

value: ICR


title: C42B_FOXA1-oe-NR1D1-veh


title: C42B_FOXA1_SR8278


title: U87 cells TDP-43 silencing rep3

description:
U87_siTDP-43_rep3
count.matrix.txt.gz

treatment_protocol: 300 µl of Opti-MEM (Life-Technologies), 6 μl of 40 μM siRNA against TDP-43, 18 µl of Lipofectamine RNAiMAX reagent

value: TDP-43 silencing


title: KBLu10_3

value: 8 weeks


title: SR-Grp7-R10

value: wild type


title: KB_1

description: busulfan


title: SR-Grp7-R4


title: KB_3

description: busulfan


title: KB_2

description: busulfan


title: SR-Grp8-R4


title: C42B_FOXA1-oe-NR1D1-azd5153


title: U87 cells TDP-43 silencing rep1

description:
U87_siTDP-43_rep1
count.matrix.txt.gz


title: SR-Grp7-L4


title: C42B_BRD4_oe_NR1D1

value: BRD4 (Diagenode, #c15410337)

value: OE NR1D1


title: SH-SY5Y cells TDP-43 silencing rep3

description:
SH-SY5Y_siTDP-43_rep3
count.matrix.txt.gz

growth_protocol: SH-SY5Y were cultured was cultured up to 20 passages in Dulbecco’s modified Eagle’s medium Nutrient Mixture F-12 Ham (Sigma-Aldrich), supplemented with 15% fetal bovine serum (FBS) (Life-Technologies), 1% MEM Non-essential Amino Acid Solution (100X) (Sigma-Aldrich), and 1% Antibiotic-Antimycotic-stabilized suspension (Sigma-Aldrich) at 37°C with humidified atmosphere of 5% CO2.

extract_protocol:
RNA was extracted using miRNeasy Kit (QIAGEN)
Libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: 150 µl of Opti-MEM (Life-Technologies), 3 μl of 40 μM siRNA against TDP-43, 9 µl of Lipofectamine RNAiMAX reagent

value: Neuroblastoma cell line


title: 2-5845, NS

city: China

first: Qian

last: Zhang

address: No.119 South 4th Ring West Road

institute: Beijing Tiantan Hospital

description: miRNA expression in asymptomtic ICAS patients without stroke

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: serum

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using Qiagen serum/Plasma Kit(Qiagen#217184), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: serum

tag: group

value: without stroke

tag: gender

value: male


title: 2-5528, NS


title: RSR-Grp8-R1

value: Resurgence METH Shock Resistant


title: RSR-Grp8-L9


title: SH-SY5Y cells TDP-43 silencing rep2

description:
SH-SY5Y_siTDP-43_rep2
count.matrix.txt.gz


title: C42B_BRD4_empty

value: prostate cancer

value: empty


title: C42B_BRD4_Veh


title: SH-SY5Y cells TDP-43 silencing rep1

description:
SH-SY5Y_siTDP-43_rep1
count.matrix.txt.gz


title: U87 cells TDP-43 silencing rep2

description:
U87_siTDP-43_rep2
count.matrix.txt.gz

value: Glioblastoma/astrocytoma cell line


title: RSR-Grp8-L4

value: Long Evans

value: Dorsal striatum


title: 2-4617, NS

value: female


title: C42B_BRD4_SR8278


title: 2-4565, NS


title: 2-4578, NS


title: Patient platelets wt rep2

description:
platelets_CTRL_rep2
count.matrix.txt.gz

source_name: Blood

growth_protocol: no growth

extract_protocol:
RNA extraction was performed from 10mL of human platelet-rich-plasma (PRP) bag from 5 healthy donors
Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: no treatment

value: Blood

value: Platelets

value: WT


title: RSR-Grp7-R7

value: adult

value: wild type


title: RSR-Grp7-L2


title: Patient platelets wt rep3

description:
platelets_CTRL_rep3
count.matrix.txt.gz


title: C42B_AR_Veh

value: AR(Millipore sigma, #06-680)

value: Vehicle 24hr


title: Patient platelets wt rep1

description:
platelets_CTRL_rep1
count.matrix.txt.gz


title: C42B_AR_SR8278


title: Ct-Grp8-R11

value: Control


title: 2-3125, NS

value: serum

value: without stroke


title: 2-3804, NS

value: male


title: SH-SY5Y cells wt rep3

description:
SH-SY5Y_CTRL_rep3
count.matrix.txt.gz

treatment_protocol: 150 µl of Opti-MEM (Life-Technologies), 3 μl of 40 μM control siRNA, 9 µl of Lipofectamine RNAiMAX reagent

value: Neuroblastoma cell line


title: Ct-Grp8-L11


title: SH-SY5Y cells wt rep2

description:
SH-SY5Y_CTRL_rep2
count.matrix.txt.gz


title: lucap35cr_sr8278

value: prostate cancer

value: 7 days


title: Ct-Grp7-R12

value: Long Evans


title: lucap35cr_jq1


title: SH-SY5Y cells wt rep1

description:
SH-SY5Y_CTRL_rep1
count.matrix.txt.gz


title: Ct-Grp7-R6

value: Dorsal striatum


title: lucap35cr_comb1


title: HCC_165T

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq v2.20.0.422 used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools). Gene expression quantification were obtained using HTSeq-count with Gencode v7. RSEM quantification at gene level was produced with NCBI Refseq (2011).
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  For HTSeq, the first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. For RSEM, the results are combined to three output files: expected read counts, RPKM and TPM value for each gene for all 3 samples in each column.

source_name: liver tumor

extract_protocol:
Total RNA was isolated from the tissues using RNA Mini Spin Column of Enzy Max LLC (Lexington, KY) according to the manufacturer’s instructions. DNase (Thermo Scientific, Rockford, IL, Cat.# EN0521) was added to the first wash solution at 10µg/70µl and incubated for 15 min at room temperature to remove genomic DNA contamination
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

tag: tumor

value: Hepatocellular carcinoma


title: HCC_165N

source_name: normal liver tissue adjacent to tumor

value: normal


title: Ct-Grp7-R5

tag: tissue


title: Ct-Grp7-L7


title: 2-406, NS

value: female


title: HCC_164T


title: HCC_164N


title: lucap35cr_veh

value: WT

value: veh


title: SDC2

first: Huan

last: Yu

address: Weijin Road Campus: No. 92 Weijin Road, Nankai District, Tianjin

department: School of Chemical Engineering and Technology

institute: Tianjin University

data_processing:
Raw data were filtered by the folowing standards, 1) removing reads with ≥ 10 % unidentified nucleotides (N); 2) removing reads with > 50 % bases having phred quality scores of ≤  20; 3) removing reads aligned to the barcode adapter using FASTP (version 0.18.0)[9]. Quality trimmed reads were mapped to the refference genome using Bowtie2[1](version 2.2.8) allowing no mismatches, reads mapped to ribosome RNA were removed. Retainted reads were aligned with the the refference genome using Bowtie2[1](version 2.2.8) to identify known genes and calculated gene expression by RSEM[2].
Reference genome(https://www.ncbi.nlm.nih.gov/nuccore/CP053946.1) and gene model annotation files (https://www.ncbi.nlm.nih.gov/nuccore/CP053946.1) were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.(Langmead, B. and S.L. Salzberg, 2012)
To evaluate reproducibility between samples, the correlation coefficient among replicas was calculated. Values closer to one indicated better reproducibility. Principle component analysis (PCA) was performed with the R package gmodels (http://www.rproject.org) to reveal the relationship between samples
The gene expression level was further normalized by using the fragments per kilobase of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression. The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05. DEGs were then subjected to an enrichment analysis of GO function and KEGG pathways, and q values < 0.05 were using as threshold.
The prediction of sRNA was conducted using Rockhopper[3] (version 2.0.3) with the removal of sequences less than 50 bp. Candidate sRNAs were then screened against the sRNAMap database[10] （ version2009） and Rfam database[6] （ version13） for annotation. Secondary structures of sRNA were predicted by Vienna RNA packages[4](version 2.3.5). The sRNA expression level was normalized by using TPM values (transcripts per million). The edgeR package (http://www.r-project.org/) was used to identify differentially expressed sRNAs across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05.
New Transcripts were predicted using Rockhopper[3](version 2.0.3). Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. According to the features, cis-NATs with overlap length to the known genes more than 30 bp were identified. Candidate cis-NATs were further verified using RNAplex[5](version 2.0.3) and cis-NATs with minimum free energy more than -30 kcal/mol were removed. Transcription start site (TSS), transcription termination site (TTS) and operons were revealed using Rockhopper[3]. After the identification of Untranslated Regions (UTR), Shine-Dalgarno sequence was predicted using RBSfinder[7] with the parameter of rbs region length of 20 bp. ρ -independent terminator was identified using TransTermHP[8](version 2.09)
Assembly: CP053946.1
Supplementary files format and content: Excel file includes RPKM values for each sample.

organism: Shewanella oneidensis MR-1

extract_protocol:
Total RNA was extracted by TRIzol-based method (Life Technologies, CA, USA). RNA quality control was performed under several steps: (1) RNA degradation degree and potential contamination was monitored on 1% agarose gels. (2) RNA purity (OD260/OD280, OD260/OD230) was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). (3) RNA integrity was measured using Bioanalyzer 2100 (Agilent, Santa Clara, CA) .
Firstly, the rRNA was depleted from 1 microgram of total RNA using illumina MRZB12424 Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, San Diego, CA, USA ). Then, the first-strand cDNA was synthesized using ProtoScript Ⅱ Reverse Transcriptase (New England BioLabs, Ipswich, MA, USA) at 25 °C for 10 min; 42 °C for 15 min; 70 °C for 15 min. The second-strand cDNA was synthesized using NEBNext Second Strand Synthesis Reaction Buffer and dATP, dGTP, dCTP, dUTP mix (New England BioLabs, Ipswich, MA, USA) at 16 °C for 1 h. Resulted cDNA was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA) and end repaired with NEBNext End Repair Reaction Buffer and Enzyme Mix (New England BioLabs, Ipswich, MA, USA) at 20 °C for 30 min; 65 °C for 30 min. Sequencing adapters were ligated using NEBNext Adaptor for Illumina (New England BioLabs, Ipswich, MA, USA) at 20 °C for 15 min. The second-strand cDNA was then degraded using the USER enzyme mix (New England BioLabs, Ipswich, MA, USA) at 37 °C for 15 min and the product was purified by Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Finally, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using NEBNext Q5 Hot Start HiFi PCR Master Mix(New England Biolabs, Ipswich, MA, USA). After cluster generation, sequencing was performed using the Illumina Novaseq 6000 platform with pair-end 150 base reads.

tag: developmental stage

value: the late logarithmic phase

value: SDC


title: HCC_33T


title: SDC1


title: C42B_oe_NR1D1_sictrl

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

value: oe NR1D1-sicontrol

value: 48 hours


title: HCC_33N


title: 2-3090, NS

value: serum


title: 2-1191, NS

value: without stroke


title: 2-1337, NS

value: male


title: 1-5609, NS

description: miRNA expression in asymptomtic ICAS patients with incident stroke

value: incident ischemic stroke


title: 1-5501, NS


title: 2-1354, NS


title: SD3

value: SD


title: C42B_oe_NR1D1_siFOXA1

value: prostate cancer

value: oe NR1D1-siFOXA1


title: 1-3198, NS


title: SD2


title: PB, CD4plusCD45RAmin, D6, T72, NoADA

description:
D6_T72_NoADA
Genewiz

data_processing:
The reads were mapped against genome using STAR on default parameters against the human hg38 reference genome release 32.
Assembly: hg38
Supplementary files format and content: Tab-separated matrix file of raw counts

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were obtained from healthy adult volunteers. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation using Lymphoprep (Axis-Shield, Oslo, Norway). CD4+ T-cells were isolated by magnetic-activated cell sorting (MACS) using the CD4+ T-cell Isolation Kit II (Miltenyi Biotec, Bergisch-Gladbach, Germany). RNA was isolated using RNeasy Mini kit (Qiagen) following manufacturer's instructions.
cDNA synthesis and amplification were performed using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Massachuestts, USA) following the manufacturer’s protocol. Dual-indexed libraries were prepared using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) following the manufacturer’s protocol.

value: Peripheral blood

tag: disease state

value: Healthy

value: CD45RA+ depleted CD4+ T cells

value: NoADA

tag: individual

value: donor 6


title: PB, CD4plusCD45RAmin, D6, T72, ADA

description:
D6_T72_ADA
Genewiz

tag: cell type

value: ADA


title: SDC3

value: the late logarithmic phase

tag: genotype


title: SD1

tag: strain


title: 1-2521, NS

value: female

tag: age


title: PB, CD4plusCD45RAmin, D5, T72, ADA

description:
D5_T72_ADA
Genewiz

value: donor 5


title: SulA3

value: SulA


title: PB, CD4plusCD45RAmin, D5, T72, NoADA

description:
D5_T72_NoADA
Genewiz


title: 1-4531, NS

value: serum


title: SulA2


title: C42B_Veh_for_ENZ

value: WT

value: Veh

value: 48 hours


title: 1-2142, NS

value: incident ischemic stroke

value: male


title: 1-3131, NS


title: PB, CD4plusCD45RAmin, D2, T72, ADA

description:
D2_T72_ADA
Genewiz

value: donor 2


title: 1-1894, NS


title: 1-1551, NS


title: 1-1814, NS


title: SulA1


title: C42B_ENZ

value: prostate cancer

value: 20uM ENZ


title: PB, CD4plusCD45RAmin, D1, T72, ADA

description:
D1_T72_ADA
Genewiz

value: Peripheral blood

value: Healthy

value: CD45RA+ depleted CD4+ T cells

value: donor 1


title: PB, CD4plusCD45RAmin, D2, T72, NoADA

description:
D2_T72_NoADA
Genewiz

value: NoADA


title: siSMPD1_48h

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
Gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

growth_protocol: A673 cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum. 10 microgram/ml insulin, and 55 microM beta-mercaptoethanol. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Invitrogen).
Total RNA samples were used for sequencing library preparation with KAPA RNA HyperPrep kit with RiboErase (HMR) following KAPA RNA library preparation protocol. Each library was bar-coded and then pooled for sequencing run paired-end sequencing protocol.

treatment_protocol: A673 cells were transfected with either scrambled-siRNA or SMPD1-siRNAs or GPR64-siRNA for 48 hours. Transfection was carried out  using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol.

value: Muscle

value: A673 cell line

value: Ewing Sarcxoma

value: SMPD1 knockdown


title: WT3

value: the late logarithmic phase

value: WT


title: WT2


title: PB, CD4plusCD45RAmin, D1, T72, NoADA

description:
D1_T72_NoADA
Genewiz


title: Control_siRNA_48h

value: scrambled-siRNA control


title: WT1


title: 1-1150, NS

value: serum

value: incident ischemic stroke

value: female


title: 22RV1_shNR1D1

value: prostate cancer

value: 48 hours


title: 1-1498, NS

value: male


title: 22RV1_shctrl

value: shctrl


title: ChIP-seq on mutant CH12 cells, ectopically expressing human BORIS (mutCH12_BORIS) with Snf2h Antibodies

status: Public on Sep 24 2024

city: Bethesda

first: Elena

last: Pugacheva

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

data_processing:
ChIP-seq, ATAC-seq, MNase-ChIP-seq, MeDIP-seq, and ATAC-seq data: single-end or paired-end reads were aligned to the UCSC mm9 genome using Bowtie version 2 under default parameters with options “–very-sensitive -X 2000” .
Bowtie output files (SAM) were converted into BAM files using the "samtools view" option in Samtools,
ChIP-seq, MeDIP-seq, and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
For ChIP-seq, MeDIP-seq, Mnase-ChIP-seq, and ATAC-seq data, output BAM files were converted into bedgraph track files using MACS2 with default settings
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bedgraph, bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM)).
Supplementary files format and content: For ATAC-seq data processing, we generated bigwig files using DeepTools' bamCoverage option to sort BAM files based on the size of the sequenced fragments. To identify CTCF footprints, we applied the following parameters: --Mnase --minFragmentLength 40 --maxFragmentLength 130 --normalizeUsing RPKM. For nucleosome positioning, we used the parameters: --Mnase --minFragmentLength 160 --maxFragmentLength 200 --normalizeUsing RPKM. This allowed us to distinguish between the small fragments associated with CTCF binding and the larger fragments representative of nucleosome positioning.
Supplementary files format and content: For MNase-Seq assisted H3 ChIP-seq data processing, we generated bigwig files using DeepTools' bamCoverage option with the parameters --Mnase --normalizeUsing RPKM to accurately determine nucleosome positions.

growth_protocol: CH12 wild type (wt) and mutant (mut) cells were maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol.

extract_protocol:
MNase-ChIP-seq was performed on fixed cells using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, Cat #9003) following the manufacturer’s protocol. Briefly, after obtaining MNase-digested lysates as described in the MNase-seq method, chromatin lysates were incubated with 5 μg of Histone H3 (Cell Signaling, #D2B12) XP® Rabbit mAb and rotated overnight at 4°C. Following this incubation, 30 µL of Protein G Magnetic Beads were added to the mixture and rotated for 2 hours at 4°C. The Protein G magnetic beads were then pelleted using a magnetic separation rack for 1–2 minutes. The supernatant was carefully removed, and the beads were washed three times with 1 mL of low salt wash buffer, incubating each wash for 5 minutes at 4°C with rotation. After the final low salt wash, 1 mL of high salt wash buffer was added, and the beads were incubated again for 5 minutes at 4°C with rotation. The beads were pelleted, and the supernatant was removed. Next, 150 µL of 1X ChIP Elution Buffer was added, and the chromatin was eluted from the antibody/Protein G magnetic beads by placing the tubes on a thermomixer at 65°C for 30 minutes with gentle shaking (1,000 rpm). The eluted chromatin supernatant was transferred to a new tube, and the immunoprecipitated DNA was purified according to the kit protocol. Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (Illumina, Inc., USA).
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol: CH12  cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
MeDIP-seq protocol: Genomic DNA (gDNA) was extracted from freshly growing CH12 cells and sonicated using a Covaris ultrasonicator to obtain a mean fragment size of 200 bp. For library preparation, 5 μg of sonicated gDNA was end-repaired and ligated with adaptors using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA). The reaction mixture was then purified with AMPure XP beads (Beckman-Coulter, CA, USA). For precise size selection, half of the sample was run on a 1.5% agarose gel, and DNA fragments of 150-250 bp were extracted from the gel. Both the size-selected and non-size-selected libraries were denatured at 95°C for 10 minutes, followed by incubation on ice for 10 minutes. The denatured DNA was subjected to immunoprecipitation with 5-Methylcytosine antibody (Catalog #: 61479, Active Motif) by incubating the reaction mixture at 4°C for 15 hours. The immunoprecipitated DNA was size-selected again using AMPure XP beads and amplified using Q5 High-Fidelity DNA Polymerase (NEB, M0491). The amplification products were purified with AMPure XP beads. Finally, the purity and fragment length distribution were assessed using a Bioanalyzer 2100 (Agilent Technologies), and the libraries were subjected to deep sequencing on the Illumina HiSeq 2000 platform.
MNase-ChIP-seq and MeDIP-seq libraries were prepared using  NEBNext® Ultra™ II DNA Library Prep Kit (Illumina, Inc., USA)
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler.

tag: expressed vector

value: mut_CH12 stably expressed human BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: Mouse B lymphoma cell

value: CH12 cells were CAS9-modified to introduce a homozygous deletion of ZF9-11 in CTCF gene

value: Snf2h (Abcam, #ab3749)


title: ChIP-seq on mutant CH12 cells, ectopically expressing deltaC-CTCF (mutCH12_deltaC) with Snf2h Antibodies

tag: cell line

value: mut_CH12 stably expressed deltaC-CTCF from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: homozygous deletion of ZF9-11 in CTCF gene


title: ChIP-seq on NIH3T3+BORIS (cl.2) cells with SMC3  Antibodies

source_name: NIH3T3+BORIS (clone2)

value: NIH3T3+BORIS (clone2)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2

value: Mouse immortalized embryonic fibroblast cell line

tag: treatment

value: NIH3T3 stably expressing BORIS

value: SMC3 (Abcam, ab#9263)


title: ChIP-seq on NIH3T3+BORIS (cl.2) cells with SMC1  Antibodies

value: SMC1 (Bethyl Laboratories, #A300-055A)


title: ChIP-seq on mutCH12 cells with H3K9me3 antibodies

value: H3K9me3 (Abcam, ab#8898)


title: ChIP-seq on mutant CH12 cells, ectopically expressing Full-Length (FL)-CTCF (mutCH12_FLCTCF) with Snf2h Antibodies

value: mut_CH12 stably expressed FL-CTCF from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: ChIP-seq on NIH3T3+EV cells with SMC3 Antibodies

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: ChIP-seq on mutCH12 cells with Snf2h antibodies


title: ChIP-seq on wtCH12 cells with Snf2h antibodies

value: wild type


title: Input for meDIP-seq with 5mC Abs on wtCH12 cells


title: Input for meDIP-seq with 5mC Abs on mutCH12 cells


title: ChIP-seq on wtCH12 cells with H3K9me3 antibodies


title: ChIP-seq on mutant CH12 cells, ectopically expressing deltaN-CTCF (mutCH12_deltaN) with Snf2h Antibodies

value: mut_CH12 stably expressed deltaN-CTCF from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: meDIP-seq with 5mC Abs on mutCH12 cells

value: Mouse B lymphoma cell

value: 5-Methylcytosine antibody (Catalog #:61479, Active Motif)


title: ChIP-seq on NIH3T3+EV cells with SMC1  Antibodies


title: ATAC-seq on mutant CH12 cells, ectopically expressing human BORIS (mutCH12_BORIS)

value: mut_CH12 stably expressed human BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: CH12 cells were CAS9-modified to introduce a homozygous deletion of ZF9-11 in CTCF gene


title: ATAC-seq on mutant CH12 cells, ectopically expressing deltaN-CTCF (mutCH12_deltaN)

value: homozygous deletion of ZF9-11 in CTCF gene


title: ATAC-seq on mutant CH12 cells, ectopically expressing deltaC-CTCF (mutCH12_deltaC)

value: mut_CH12 stably expressed deltaC-CTCF from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: meDIP-seq with 5mC Abs on wtCH12 cells


title: ChIP-seq on NIH3T3+BORIS (cl.2) cells with RAD21  Antibodies

value: NIH3T3+BORIS (clone2)

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2


title: ChIP-seq on NIH3T3+EV cells with RAD21  Antibodies

value: Mouse immortalized embryonic fibroblast cell line


title: ATAC-seq on mutant CH12 cells, ectopically expressing Full-Length (FL)-CTCF (mutCH12_FLCTCF)


title: MNase-Seq Assisted H3 ChIP-seq in mutCH12+BORIS cells


title: ATAC-seq on wtCH12 cells


title: ATAC-seq on mutant CH12 cells (mutCH12)


title: MNase-Seq Assisted H3 ChIP-seq in wtCH12 cells


title: BMS-ASCs 2_RNAseq

city: Hiroshima

first: Yoshiki

last: Tanaka

address: 1-2-3 Kasumi, Minami-ku

department: Department of Nephrology

institute: Hiroshima University Hospital

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to Homo sapiens (GRCh38) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Read count were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: subcutaneous adipose tissues

growth_protocol: ASCs were cultured in STK2 medium (Kanto Chemical).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 70% confluence, ASCs were treated with different concentrations of an inhibitory kappa-B kinase-β (IKKβ) inhibitor, BMS-345541 (Sigma-Aldrich, St. Louis, MO, USA). After 24 hours, cells stimulated by BMS-345541 as “BMS-ASCs” and non-stimulated as “NS-ASCs” were collected to be used in vitro experiments

value: subcutaneous adipose tissues

value: mesenchymal stem cells


title: BMS-ASCs 3_RNAseq


title: MNase-Seq Assisted H3 ChIP-seq in mutCH12+deltaC-CTCF cells


title: MNase-Seq Assisted H3 ChIP-seq in mutCH12+deltaN-CTCF cells


title: MNase-Seq Assisted H3 ChIP-seq in mutCH12 cells


title: BMS-ASCs 1_RNAseq


title: NS-ASCs 2_RNAseq

value: control


title: hTERT1, 32kPa, timepoint 7, ATAC-Seq, replicate 1

city: South San Francisco

first: J

middle: Graham

last: Ruby

address: 1170 Veterans Blvd

institute: Calico Life Sciences

description:
ATAC-seq
35

data_processing:
FASTQ files were trimmed and low quality reads were filtered using cutadapt (v.4.9.0   , https://github.com/marcelm/cutadapt) to remove primer sequences. Trimmed FASTQ files were then aligned to the genome using bowtie2 (v.2.3.4, https://github.com/BenLangmead/bowtie2), and sorted based on genomic location and indexed using Samtools (v.1.14.0, https://github.com/samtools/samtools). Quality control, peak calling, differential peak analysis, and principal component analyses were performed using ChrAccR (v.0.9.17, https://github.com/GreenleafLab/ChrAccR) in R (v.4.3.0).  The setConfigElement doPeakCalling() was used with annotationPeakGroupAgreePerc() = 1 to generate the genome-wide peaks list (peaksCons) via MACS2 (v.2.2.9.1, https://pypi.org/project/MACS2).
Assembly: hg38
Supplementary files format and content: Normalized bigWig file for each sample

source_name: WI-38 cell line

extract_protocol:
Cells were harvested from plates using TrypLE Express Enzyme as described above and stored frozen in liquid nitrogen in Recovery Cell Culture Freezing Medium (Gibco).
Once all samples were collected, ATAC-sequencing was performed as previously described. In brief, frozen cells were thawed rapidly in a 37°C water bath and 75,000 cells were aliquoted and washed once with PBS. Nuclei were isolated, lysed, and incubated with Tn5 transposase (Illumina) as described. Transposed DNA was isolated with the MinElute Reaction Cleanup Kit (Qiagen). Libraries were prepared by amplifying DNA for 5 cycles with NEBNext 2x MasterMix (New England Biolabs). After performing qPCR to determine additional cycles needed, libraries were amplified for an additional 6 cycles. Double sided bead purification was performed using AMPure XP beads (Beckman) to remove primers and large (>1000 bp) fragments using standard protocols. Quality and concentration of libraries were determined using a Qubit 4 Fluorometer (Invitrogen) and a 2100 Bioanalyzer Instrument (Agilent). Samples were sequenced on a NovaSeq 6000 (Illumina).

value: WI-38 cell line

value: hTERT


title: WT2, 32kPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
34

value: Wild-type


title: hTERT2, 0.5kPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
32


title: MNase-Seq Assisted H3 ChIP-seq in mutCH12+FL-CTCF cells

value: mut_CH12 stably expressed FL-CTCF from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: hTERT1, 0.5kPa, timepoint 7, ATAC-Seq, replicate 1

description:
ATAC-seq
31


title: NS-ASCs 3_RNAseq


title: NS-ASCs 1_RNAseq


title: fetal lung cells in culture

description:
sci-RNA-seq3
1

library_source: transcriptomic single cell

data_processing:
The resulting FASTQ files were processed using cellranger count (10x Genomics). The resulting expression matrices were loaded into R (v.4.3.0) and processed using Seurat (v4.3.0, https://github.com/satijalab/seurat) for downstream analyses.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells were harvested from plates using TrypLE Express Enzyme as described above and stored frozen in liquid nitrogen in Recovery Cell Culture Freezing Medium (Gibco).
Once all samples were collected, single-cell combinatorial indexing RNA-sequencing (sci-RNA-seq3) was performed as previously described.


title: hTERT2, 32kPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
36


title: WT1, 32kPa, timepoint 7, ATAC-Seq, replicate 1

description:
ATAC-seq
33


title: WT2, 0.5kPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
30


title: High grade serous ovarian carcinoma FF1

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing:
Data was extracted from the TIFF files using Agilent FE 11.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.
Log2(Cy5/Cy3)

source_name: Surgical resection

label_protocol: DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes while DNAs. In each case 1 µl of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols (22). All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA)

growth_protocol: Fresh tumor samples were flash-frozen and maintained at -80 degrees C.

extract_protocol: Frozen tissue samples were minced in the presence of NST buffer and DAPI according to published protocols. Nuclei from each sample were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Aria III cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm.

tag: tissue source

value: Resection

tag: tissue type

value: frozen tissue

tag: flow sort content

value: Human tumor

tag: t n

value: Tumor

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: High grade serous ovarian carcinoma FF8


title: WT1, 0.5kPa, timepoint 7, ATAC-Seq, replicate 1

description:
ATAC-seq
29


title: Endometriod carcinoma FF6


title: High grade serous ovarian carcinoma FF7


title: hTERT2, 2.3GPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
28


title: hTERT1, 2.3GPa, timepoint 7, ATAC-Seq, replicate 1

description:
ATAC-seq
27


title: WT1, 32kPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
21


title: WT2, 2.3GPa, timepoint 7, ATAC-Seq, replicate 2

description:
ATAC-seq
26


title: hTERT2, 32kPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
24


title: hTERT1, 32kPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
23


title: hTERT2, 0.5kPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
20


title: High grade serous ovarian carcinoma FF2


title: hTERT2, 2.3GPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
16


title: WT2, 0.5kPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
18


title: WT1, 0.5kPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
17


title: WT1, 2.3GPa, timepoint 7, ATAC-Seq, replicate 1

description:
ATAC-seq
25


title: WT2, 32kPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
22


title: WT1, 2.3GPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
13


title: WT2, 2.3GPa, timepoint 4, ATAC-Seq, replicate 2

description:
ATAC-seq
14


title: High grade serous ovarian carcinoma FF5


title: hTERT1, 0.5kPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
19


title: WT2, 32kPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
10


title: hTERT1, 2.3GPa, timepoint 4, ATAC-Seq, replicate 1

description:
ATAC-seq
15


title: hTERT2, 32kPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
12


title: WT1, 32kPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
9


title: hTERT1, 32kPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
11


title: hTERT2, 0.5kPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
8


title: High grade serous ovarian carcinoma FF4


title: hTERT1, 0.5kPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
7


title: hTERT1, 2.3GPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
3


title: Low grade serous ovarian carcinoma FF3


title: WT1, 0.5kPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
5


title: WT, 0.4MPa, timepoint 3, RNA-Seq 2, replicate 2

description:
RNA-seq
14B

data_processing:
FASTQ files were aligned to the human genome (hg38) and sorted by genomic location using STAR (v2.5.3, https://github.com/alexdobin/STAR). Sorted BAM files were counted and mapped to each gene using HTSeq-Count (v.0.11.3, https://github.com/simon-anders/htseq). Differentially expressed genes (DEGs) were identified using DESeq2 (v.1.44.0, https://github.com/thelovelab/DESeq2) in R (v.4.2.2) with a cutoff of P-adjusted < 0.05. Wald test was used to calculate fold change and P values using the model: ~condition, where condition is a variable capturing time point, genotype, and substrate stiffness.
Assembly: hg38
Supplementary files format and content: Raw counts file, each column in a sample

extract_protocol:
Cells were lysed directly on cell culture plates in Buffer RLT Plus (Qiagen). The lysate was homogenized using Qiashredder columns (Qiagen) and stored at -80°C. Once all samples were collected, RNA was isolated using a RNeasy mini kit (Qiagen).
Quality and concentration of RNA were determined using a 2100 Bioanalyzer Instrument (Agilent). cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina polyA mRNA workflow (New England Biolabs). Samples were sequenced on a NovaSeq 6000 (Illumina).


title: WT, 0.4MPa, timepoint 3, RNA-Seq 2, replicate 1

description:
RNA-seq
14A


title: WT, 0.7MPa, timepoint 3, RNA-Seq 2, replicate 2

description:
RNA-seq
13B


title: WT2, 2.3GPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
2


title: WT, 6.6MPa, timepoint 3, RNA-Seq 2, replicate 2

description:
RNA-seq
12B


title: WT1, 2.3GPa, timepoint 1, ATAC-Seq, replicate 1

description:
ATAC-seq
1


title: WT, 0.4MPa, timepoint 2, RNA-Seq 2, replicate 2

description:
RNA-seq
10B


title: WT, 6.6MPa, timepoint 2, RNA-Seq 2, replicate 2

description:
RNA-seq
8B


title: WT, 2kPa, timepoint 2, RNA-Seq 2, replicate 2

description:
RNA-seq
7B


title: WT, 6.6MPa, timepoint 3, RNA-Seq 2, replicate 1

description:
RNA-seq
12A


title: WT, 0.7MPa, timepoint 2, RNA-Seq 2, replicate 1

description:
RNA-seq
9A


title: WT, 6.6MPa, timepoint 2, RNA-Seq 2, replicate 1

description:
RNA-seq
8A


title: WT, 0.4MPa, timepoint 2, RNA-Seq 2, replicate 1

description:
RNA-seq
10A


title: WT, 0.7MPa, timepoint 2, RNA-Seq 2, replicate 2

description:
RNA-seq
9B


title: WT, 2kPa, timepoint 2, RNA-Seq 2, replicate 1

description:
RNA-seq
7A


title: WT2, 0.5kPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
6


title: WT, 2.3GPa, timepoint 2, RNA-Seq 2, replicate 2

description:
RNA-seq
6B


title: WT, 2.3GPa, timepoint 2, RNA-Seq 2, replicate 1

description:
RNA-seq
6A


title: hTERT2, 2.3GPa, timepoint 1, ATAC-Seq, replicate 2

description:
ATAC-seq
4


title: WT, 0.4MPa, timepoint 1, RNA-Seq 2, replicate 1

description:
RNA-seq
5A


title: WT, 0.4MPa, timepoint 1, RNA-Seq 2, replicate 2

description:
RNA-seq
5B


title: WT, 0.7MPa, timepoint 3, RNA-Seq 2, replicate 1

description:
RNA-seq
13A


title: WT, 0.7MPa, timepoint 1, RNA-Seq 2, replicate 1

description:
RNA-seq
4A


title: WT, 6.6MPa, timepoint 1, RNA-Seq 2, replicate 2

description:
RNA-seq
3B


title: WT, 2kPa, timepoint 1, RNA-Seq 2, replicate 2

description:
RNA-seq
2B


title: WT, 0.7MPa, timepoint 1, RNA-Seq 2, replicate 2

description:
RNA-seq
4B


title: WT, 2.3GPa, timepoint 1, RNA-Seq 2, replicate 1

description:
RNA-seq
1A


title: WT, 6.6MPa, timepoint 1, RNA-Seq 2, replicate 1

description:
RNA-seq
3A


title: WT, 2.3GPa, timepoint 3, RNA-Seq 2, replicate 1

description:
RNA-seq
11A


title: WT, 2kPa, timepoint 1, RNA-Seq 2, replicate 1

description:
RNA-seq
2A


title: WT, 2.3GPa, timepoint 1, RNA-Seq 2, replicate 2

description:
RNA-seq
1B


title: hTERT, 32kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
186

extract_protocol:
Cells were lysed directly on cell culture plates in Buffer RLT Plus (Qiagen). The lysate was homogenized using Qiashredder columns (Qiagen) and stored at -80°C. Once all samples were collected, RNA was isolated using a RNeasy mini kit (Qiagen).
Quality and concentration of RNA were determined using a 2100 Bioanalyzer Instrument (Agilent). cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina rRNA depletion workflow (New England Biolabs). Samples were sequenced on a NovaSeq 6000 (Illumina).


title: hTERT, 32kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
184


title: hTERT, 16kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
181


title: WT, 32kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
183


title: WT, 32kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
182


title: hTERT, 32kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
185


title: hTERT, 16kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
180


title: hTERT, 16kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
179


title: WT, 16kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
178


title: WT, 16kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
177


title: hTERT, 2kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
176


title: WT, 2kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
173


title: hTERT, 2kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
174


title: WT, 2kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
171


title: hTERT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
170


title: hTERT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
169


title: WT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
167


title: WT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
165


title: WT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
166


title: hTERT, 0.5kPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
168


title: WT, 2.3GPa, timepoint 7, RNA-Seq 1, replicate 2

description:
RNA-seq
158


title: WT, 2.3GPa, timepoint 3, RNA-Seq 2, replicate 2

description:
RNA-seq
11B


title: WT, 2.3GPa, timepoint 7, RNA-Seq 1, replicate 1

description:
RNA-seq
157


title: WT, 2kPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
172


title: WT, 2.3GPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
164


title: hTERT, 2.3GPa, timepoint 8, RNA-Seq 1, replicate 2

description:
RNA-seq
161


title: WT, 2.3GPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
163


title: hTERT, 2.3GPa, timepoint 8, RNA-Seq 1, replicate 1

description:
RNA-seq
160


title: hTERT, 32kPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
147


title: hTERT, 16kPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
144


title: WT, 32kPa, timepoint 7, RNA-Seq 1, replicate 3

description:
RNA-seq
153


title: hTERT, 2.3GPa, timepoint 8, RNA-Seq 1, replicate 3

description:
RNA-seq
162


title: hTERT, 16kPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
143


title: hTERT, 2kPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
139


title: hTERT, 0.5kPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
138


title: hTERT, 0.5kPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
137


title: WT, 32kPa, timepoint 7, RNA-Seq 1, replicate 1

description:
RNA-seq
151


title: hTERT, 32kPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
145


title: hTERT, 2kPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
140


title: hTERT, 0.5kPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
136


title: hTERT, 2kPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
141


title: hTERT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
135


title: hTERT, 32kPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
146


title: hTERT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
133


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 4

description:
RNA-seq
130


title: WT, 32kPa, timepoint 7, RNA-Seq 1, replicate 2

description:
RNA-seq
152


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 3

description:
RNA-seq
129


title: hTERT, 16kPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
142


title: hTERT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
134


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 6

description:
RNA-seq
132


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 5

description:
RNA-seq
131


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 1

description:
RNA-seq
127


title: hTERT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 3

description:
RNA-seq
126


title: WT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 2

description:
RNA-seq
122


title: hTERT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 1

description:
RNA-seq
124


title: hTERT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 2

description:
RNA-seq
125


title: WT, 32kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
116


title: hTERT, 32kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
119


title: WT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 1

description:
RNA-seq
121


title: hTERT, 16kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
114


title: WT, 2.3GPa, timepoint 5, RNA-Seq 1, replicate 3

description:
RNA-seq
123


title: WT, 2.3GPa, timepoint 6, RNA-Seq 1, replicate 2

description:
RNA-seq
128


title: hTERT, 32kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
120


title: WT, 16kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
111


title: WT, 16kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
109


title: hTERT, 16kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
112


title: WT, 2kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
104


title: WT, 2kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
103


title: hTERT, 32kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
118


title: WT, 32kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
117


title: WT, 32kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
115


title: hTERT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
101


title: hTERT, 16kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
113


title: WT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
99


title: WT, 16kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
110


title: WT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
98


title: hTERT, 2kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
108


title: hTERT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
96


title: hTERT, 2kPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
107


title: WT, 2kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
105


title: hTERT, 32kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
90


title: hTERT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
102


title: hTERT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
100


title: WT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
92


title: WT, 32kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
87


title: WT, 0.5kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
97


title: WT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 3

description:
RNA-seq
93


title: hTERT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
94


title: hTERT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 2

description:
RNA-seq
95


title: WT, 2.3GPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
91


title: WT, 32kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
86


title: hTERT, 16kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
83


title: hTERT, 16kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
82


title: hTERT, 32kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
89


title: hTERT, 2kPa, timepoint 4, RNA-Seq 1, replicate 1

description:
RNA-seq
106


title: WT, 16kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
80


title: hTERT, 2kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
78


title: hTERT, 16kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
84


title: WT, 32kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
85


title: hTERT, 2kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
76


title: WT, 16kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
81


title: WT, 2kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
73


title: hTERT, 2kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
77


title: hTERT, 32kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
88


title: hTERT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
71


title: hTERT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
72


title: hTERT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
70


title: WT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
68


title: WT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
67


title: hTERT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
66


title: WT, 0.5kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
69


title: hTERT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
65


title: WT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
63


title: hTERT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
64


title: hTERT, 32kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
59


title: WT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
61


title: WT, 2.3GPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
62


title: hTERT, 32kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
58


title: hTERT, 32kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
60


title: WT, 2kPa, timepoint 3, RNA-Seq 1, replicate 3

description:
RNA-seq
75


title: WT, 16kPa, timepoint 3, RNA-Seq 1, replicate 1

description:
RNA-seq
79


title: WT, 32kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
56


title: WT, 32kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
57


title: WT, 32kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
55


title: WT, 2kPa, timepoint 3, RNA-Seq 1, replicate 2

description:
RNA-seq
74


title: hTERT, 16kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
54


title: hTERT, 16kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
52


title: hTERT, 16kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
53


title: WT, 16kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
50


title: WT, 16kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
51


title: hTERT, 2kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
48


title: WT, 16kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
49


title: hTERT, 2kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
47


title: hTERT, 2kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
46


title: WT, 2kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
45


title: WT, 2kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
44


title: hTERT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
41


title: hTERT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
42


title: hTERT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
40


title: WT, 2kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
43


title: WT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
38


title: WT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
37


title: hTERT, 2.3GPa, timepoint 2, RNA-Seq 1, replicate 1

description:
RNA-seq
34


title: hTERT, 2.3GPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
36


title: hTERT, 2.3GPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
35


title: WT, 2.3GPa, timepoint 2, RNA-Seq 1, replicate1

description:
RNA-seq
31


title: WT, 2.3GPa, timepoint 2, RNA-Seq 1, replicate 2

description:
RNA-seq
33


title: hTERT, 32kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
30


title: hTERT, 32kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
28


title: WT, 32kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
27


title: WT, 32kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
25


title: hTERT, 32kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
29


title: WT, 32kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
26


title: hTERT, 16kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
23


title: hTERT, 16kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
22


title: WT, 16kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
20


title: WT, 16kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
21


title: WT, 16kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
19


title: hTERT, 2kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
17


title: hTERT, 2kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
18


title: WT, 2kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
14


title: hTERT, 2kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
16


title: WT, 2kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
15


title: hTERT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
12


title: WT, 0.5kPa, timepoint 2, RNA-Seq 1, replicate 3

description:
RNA-seq
39


title: WT, 2kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
13


title: hTERT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
10


title: hTERT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
11


title: WT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
9


title: hTERT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
6


title: WT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
8


title: hTERT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
4


title: WT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
3


title: hTERT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
5


title: WT, 0.5kPa, timepoint 1, RNA-Seq 1, replicate 1

description:
RNA-seq
7


title: hTERT, 16kPa, timepoint 1, RNA-Seq 1, replicate 3

description:
RNA-seq
24


title: WT, 2.3GPa, timepoint 1, RNA-Seq 1, replicate 2

description:
RNA-seq
2