title: Exp-T1K_4B_Cell-HaCaT_Treatment-exposed

type: genomic

city: Bremen

first: Jyoti

last: Jyoti

state: Bremen

address: Campus Ring 6

department: School of Science

country: Germany

institute: Constructor University

description:
S48
5gTemp_HaCat_Beta_detP.txt-S48
5gTemp_HaCat_Beta_detP.txt

hyb_protocol: The microarray hybridization was performed according to the Infinium HD Assay Methylation Protocol Guide (Illumina, Inc.). The bisulfite-converted DNA samples were hybridized at 48°C for 16 hrs on separate Illumina Infinium MethylationEPIC Arrays. DNA fragments anneal to locus-specific 50 mers which are covalently linked to different bead types. After hybridization and washing of the microarrays, the primers on the BeadChips were extended complementary to the binding DNA sample. This reaction incorporates labelled nucleotides. Incorporation of a G corresponds to the methylated state, A to the unmethylated state on the complementary strand. Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labelled nucleotide (C and G nucleotides are biotin labelled; A and T nucleotides are dinitrophenyl labelled.). Hybridized DNA was then removed and the labelled extended primers were stained and dried.

scan_protocol: Fluorescent signal intensities of the labelled and stained nucleotides on the BeadChips were detected with a dual color channel approach and the Illumina iScan™ System.

data_processing:
The software tool GenomeStudio V2011.1 (Illumina, Inc.) including the Methylation Module Version 1.9.0 was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed without normalization.
Beta Values with depection P values

label: Cy3 and Cy5

source_name: HaCaT

label_protocol: Illumina protocol

growth_protocol: Cells were cultured in DMEM, high glucose, supplemented with 10% FBS and 1% penicillin streptomycin in an incubator with 37°C, 5% CO2 and saturated humidity.

extract_protocol:
To keep the homogeneity of the transmitting power flux density or SAR as high as possible, the cells outside a defined area were excluded during harvesting. After exposure, the medium of the cell dishes was discarded and a template made with a 3D printer (at 27 GHz an ellipse with a radius of 24 mm/23 mm; at 40.5 GHz a capped circle with a radius of 24 mm and a distance of the capped area to the center of 19 mm) was applied to the outside of the bottom of the dish and the areas to be omitted were marked. The cells were removed according to the marking with a cell scraper and the cell monolayer was then rinsed twice with PBS.
Cells were harvested by washing the remaining cell monolayer once with PBS and transferring 350 ul lysis buffer to each of the dishes. The cell lysates were collected using a cell scraper and transferring them into reaction tubes. The lysates were frozen at -80C until further processing. DNA and RNA extraction was done using the DNA/RNA Allprep Mini Kit (Qiagen) or the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol:
For each exposure experiment 120,000 HDF or 200,000 HaCaT cells were seeded onto a 60 mm cell culture dish. Cells were used in passages 6-7 (HDF) and 35 (HaCaT). One day (48h experiments) or three days (2h experiments) after seeding, the dishes were transferred to the exposure incubators and cells were exposed or sham-exposed for 2h or 48h, with a frequency of 27 GHz or 40.5 GHz, and a power flux density of 1 mW/cm2 or 10 mW/cm2. In all experiments, the temperature was measured continuously using a fiber optic sensor. The internal temperature of the incubator in which the exposure takes place was reduced in the 10 mW/cm2 experiments manually, so that an average temperature of 37C could be maintained in the petri dishes and a lid heater was used to prevent condensation in the exposed petri dish and maintain blinding conditions.
Temperature controls: Cells were exposed or sham exposed at 40.5 GHz and 10 mW/cm2 for 48h without compensating for the temperature increase. The starting temperature of the medium was 37.0C in these experiments and increased to an average of 38.3C in the exposed samples. No lid heaters were used, so that the heating of the medium in the exposed samples led to medium condensation.
UV controls: Three replicates each of HaCaT and HDF cells were exposed or sham-exposed at a wavelength of 254 nm and an illuminance of 1 mW/cm2. The medium was removed and collected, rinsed twice with PBS and the cells were thinly coated with 600 ul PBS per dish. Exposure was performed without the dish lid for 20 sec, for sham exposure the dishes were stored in the dark at room temperature. The PBS was then aspirated, the cells were layered with the previously collected medium, and incubated for 2h at 37C and 5%CO2.

tag: cell line

value: HaCaT

value: exposed

tag: column header in matrix processed file

tag: date


title: DNA-ALB1-GST-Round4-Rep2

status: Public on May 01 2025

type: SRA

city: Boston

first: Luca

last: Mariani

state: ma

address: 77 Avenue Pasteur

department: Medicine

country: USA

institute: Harvard Medical School

description:
Library name: DNA-ALB1-GST-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GST for 4 rounds, Biological replicate 2

library_source: other

data_processing:
The forward (labeled ‘R1’) and reverse complement (labeled ‘R2’) 150-bp paired-end sequencing fastq reads were merged with PEAR in default setting (PMID: 24142950).
PCR duplicates were removed and the reads were trimmed at the 3’ end to remove the 6-bp UMIs. Since PIONEAR-seq libraries by design are 147-bp long, trimmed reads with different lengths were removed.
To extract the DNA sequence and the location of the tiles, the reads were aligned to the associated template  by the  R function pairwiseAlignment (default setting except: type='overlap’,  gapOpening=1000, gapExtension=0). This function furnishes an alignment score and the position of the base mismatches for each read. Given the template is 147-bp long and the random tile is 20-bp long, reads with an alignment score smaller than 127 were considered non-aligned and removed.
The position of the first and last mismatch were compared to assign the random tile position of each read
For each library, the read count of tiles at different position varies. To give the same weight to each tile position, the median read count of the library was used to resample the tiles at each psoition (Isotiling). To calculate motif enrichment the internal 16-bp of all the isotiles of the library were merged and compared to the associated input library by using the SELEX R package.
Assembly: Synthetic DNA
Supplementary files format and content: XXX_kmer_enrichment_table.txt' file is in txt format and contains a table showing:
Supplementary files format and content: the enrichment rank (Column 1: ID), the sequence of the enriched k-mer (column 2: Kmer), the k-mer count observed in the assessed library (column 3: ObservedCount), the expected k-mer count inferred from the associated input library used as background set (Column 4: ExpectedCount), their relative k-mer count increase, which is a measure of k-mer enrichment and is defined as the ration between the expected and observed counts (Column 5: Increase).
Library strategy: SELEX

molecule: other

organism: synthetic construct

source_name: synthetic DNA

extract_protocol:
Amplicon DNA
Sequencing libraries were prepared by adding to the selected libraries (1) 5' end Unique Molecular Identifies (UMIs), (2) llumina adaptors (IAs), (2) TRUseq dual barcodes (BCs) and (2) Illumina sequencing promoters P5 and P7 (P5/P7) by PCR amplification with custom primers.  10 ng of DNA was used as starting material samples. Libraries were with KAPA HiFi HotStart ReadyMix PCR Kit amplified by using 2 consecutive 6-cycle PCR runs (first cycle for UMIs and IAs, second cycle for BCs and P5/P7)  on the thermocycler. Post amplification libraries were size selected at ~3000bp in length by Azenta using AMPure XP beads. Libraries were validated by using both the Tapestation D1000 and  Qubit.

treatment_protocol: DNA Libraries were PCR amplified, assembled on in vitro reconstituted histone octamers to form nucleosome and incubated with GST-tagged transcription factors. TF-bound elements were selected by glutathione beads followed by PCR amplification. The treatment was repetead for 4 rounds.

tag: tissue

value: synthetic DNA

tag: treatment

value: Free DNA


title: tumour-infiltrating immune cells, not-treated, progressive, rep3

city: Lisboa

first: Nuno

middle: Luís

last: Barbosa-Morais

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 and v7.0.1.
Assembly: mm10
Supplementary files format and content: TSV files containing detected cellular barcodes (barcodes.tsv) and corresponding features (features.tsv) as returned by Cell Ranger.MTX sparse matrix containing counts as returned by Cell Ranger.
Supplementary files format and content: Tab-delimited text files containing count matrices in log2(counts+1) corrected for batch effect.

molecule: polyA RNA

organism: Mus musculus

source_name: tumor-infiltrating immune cells

extract_protocol:
Tumors resected from mice were cut in small pieces and digested with 1mg/mL collagenase Type I (Worthington), 0.4 mg/mL collagenase Type IV (Worthington) and 10μg/mL DNase I (Sigma-Aldrich) for 30 min at 37°C, in Eppendorf tubes. Cell suspensions were then filtered through a 100μm nylon cell strainer (Corning). Red blood cells were lysed using RBC Lysis Buffer (Biolegend) for 10 min at RT in the dark. Cells were centrifuged and resuspended in cRPMI (RPMI + Sodium Pyruvate (100x) + Non Essential Acids Amines (100x) + Hepes (100x) + Peni-Strep (100x) + bMercaptoethanol (1000x) + FCS 10%) and immediately processed for the specific readout.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10X Genomics).

value: tumor-infiltrating immune cells

tag: cell type

value: immune

tag: strain

tag: batch

tag: sample id

tag: age

value: 5-15 weeks


title: CREM fl/fl and CREM fl/fl Vil-CRE same sex littermates; Deletion, rep 1

city: Charlottesville

first: Audrey

last: Brown

state: Virginia

address: 345 Crispell Dr.

institute: The University of Virginia

description:
Sequencing Batch 1
CREM_Vil_CRE_WT_v_Deletion.csv
248

library_source: transcriptomic

data_processing:
Raw reads were checked for quality using FASTQC v0.11.5
Reads were trimmed to remove adapters using bbmap v39.01.
Salmon v.1.10.1 was used for ‘quasi-mapping’ and quantification
Assembly: mm10
Supplementary files format and content: CSV file with samples in columns and genes in rows. Contains normalized gene counts from Salmon

molecule: total RNA

source_name: Cecum

growth_protocol: Adult mice were challenege with E. histolytica by intra-cecal infection 72h prior to tissue collection.

extract_protocol:
Total RNA was extracted from cecal tissue snips using a Qiagen RNeasy Mini Kit followed by Invitrogen Turbo DNA-Free Kit DNase treatment according the manufacturer's instruction
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: At harvest, cecal tissue was collected and immediately placed in RNAlater at ambient temperature for 1 hour followed by storage in 4C until RNA extraction.

value: Cecum

tag: genotype

value: Deletion

value: E. histolytica challenge 72h prior


title: DNA-ALB1-GST-Round3-Rep2

description:
Library name: DNA-ALB1-GST-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GST for 3 rounds, Biological replicate 2


title: Exp-T1K_4A_Cell-HaCaT_Treatment-sham

description:
S47
5gTemp_HaCat_Beta_detP.txt-S47
5gTemp_HaCat_Beta_detP.txt

molecule: genomic DNA

organism: Homo sapiens

value: sham


title: Cancer associated fibroblast from NSCLC patient 20101221

type: RNA

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

description: Gene expression data of Cancer-associated fibroblast from NSCLC patient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization was utilized by the package affy in R.

label: biotin

source_name: Cancer-associated fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 800 cells per well were seeded to ultra-low adherent 24-wel plates (Corning) with MCDB201 medium (Invitrogen), and exposed to condition medium from cultured NFs and CAFs.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The medium was supplemented with epidermal growth factor (20ng/ml, Sigma) and bFGF (20ng/ml, Invitrogen).

value: Cancer-associated fibroblast

tag: smoking

value: Never

tag: gender

value: Female

tag: histology

value: Other

tag: Stage

value: Early


title: tumour-infiltrating immune cells, not-treated, progressive, rep2


title: Exp-T1K_2B_Cell-HaCaT_Treatment-sham

description:
S46
5gTemp_HaCat_Beta_detP.txt-S46
5gTemp_HaCat_Beta_detP.txt


title: Cancer associated fibroblast from NSCLC patient 20140411

value: Ever

value: Male


title: Cancer associated fibroblast from NSCLC patient 20150203_2

value: LUAD

value: Late


title: Cancer associated fibroblast from NSCLC patient 20100315


title: DNA-ALB1-OCT4-Round4-Rep2

description:
Library name: DNA-ALB1-OCT4-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of OCT4 for 4 rounds, Biological replicate 2

value: synthetic DNA

value: Free DNA


title: 1674_E1-2

city: Montreal

first: Daniel

last: Levesque

state: Qc

address: CP 6128, Succ. Centre-ville

department: Pharmacy

country: Canada

institute: University of Montreal

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the indexes.
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic and mapped to the reference genome using STAR version 2.5.1b.
Readcounts were computed by STAR during sequence alignment based on gene annotations from Ensembl release 84
Assembly: Rnor_6.0
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column), including expression values as expected counts, FPKM and TPM

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
Chloroform/isopropanol extraction and purification on RNeasy columns
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: Striatum

value: Wild type Fawn-Hooded hypertensive (FHH) rats

value: Haloperidol


title: DNA-ALB1-KLF4-Round4-Rep1

description:
Library name: DNA-ALB1-KLF4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of KLF4 for 4 rounds, Biological replicate 1


title: Exp-T1K_2A_Cell-HaCaT_Treatment-exposed

description:
S45
5gTemp_HaCat_Beta_detP.txt-S45
5gTemp_HaCat_Beta_detP.txt

value: HaCaT

value: exposed


title: DNA-ALB1-KLF4-Round3-Rep1

description:
Library name: DNA-ALB1-KLF4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of KLF4 for 3 rounds, Biological replicate 1


title: DNA-ALB1-GATA4-Round4-Rep1

description:
Library name: DNA-ALB1-GATA4-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA4 for 4 rounds, Biological replicate 1


title: DNA-ALB1-GATA4-Round3-Rep1

description:
Library name: DNA-ALB1-GATA4-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA4 for 3 rounds, Biological replicate 1


title: tumour-infiltrating immune cells, treated,72h, rep2

value: tumor-infiltrating immune cells

value: immune

value: 5-15 weeks

value: Treated


title: DNA-ALB1-GATA4-Round2-Rep1

description:
Library name: DNA-ALB1-GATA4-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA4 for 2 rounds, Biological replicate 1


title: Normal fibroblast from NSCLC patient 20151006

description: Gene expression data of normal fibroblast from NSCLC patient

source_name: Normal fibroblast

value: Normal fibroblast

value: Never

value: Female


title: Cancer associated fibroblast from NSCLC patient 20101228

value: Cancer-associated fibroblast

value: Ever

value: Male

value: LUSC

value: Early


title: tumour-infiltrating immune cells, not-treated, rep2


title: Cancer associated fibroblast from NSCLC patient 20101231

value: LUAD


title: Exp-T1K_1A_Cell-HaCaT_Treatment-sham

description:
S43
5gTemp_HaCat_Beta_detP.txt-S43
5gTemp_HaCat_Beta_detP.txt

value: sham


title: Cancer associated fibroblast from NSCLC patient 20150203_1


title: DNA-ALB1-GATA4-Round1-Rep1

description:
Library name: DNA-ALB1-GATA4-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA4 for 1 rounds, Biological replicate 1

value: synthetic DNA

value: Free DNA


title: Exp-UVC_K3S_Cell-HaCaT_Treatment-Control

description:
S42
UV_HaCat_Beta_detP.txt-S42
UV_HaCat_Beta_detP.txt

value: HaCaT

value: Control


title: tumour-infiltrating immune cells, treated,72h, rep1

value: tumor-infiltrating immune cells

value: immune


title: Normal fibroblast from NSCLC patient 20150930

value: Late


title: Exp-T1K_1B_Cell-HaCaT_Treatment-exposed

description:
S44
5gTemp_HaCat_Beta_detP.txt-S44
5gTemp_HaCat_Beta_detP.txt

value: exposed


title: tumour-infiltrating immune cells, not-treated, progressive, rep1

value: 5-15 weeks


title: DNA-ALB1-GATA1-Round4-Rep1

description:
Library name: DNA-ALB1-GATA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA1 for 4 rounds, Biological replicate 1


title: tumour-infiltrating immune cells, not-treated, rep1


title: Exp-UVC_K3V_Cell-HaCaT_Treatment-UV

description:
S41
UV_HaCat_Beta_detP.txt-S41
UV_HaCat_Beta_detP.txt

value: UV


title: DNA-ALB1-GATA1-Round3-Rep1

description:
Library name: DNA-ALB1-GATA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA1 for 3 rounds, Biological replicate 1


title: KO3

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the mm10 refSeq refFlat GTF file.
Genes with adjusted P-value < 0.05 and |foldChange| > 2 were defined as differentially expressed genes (DEGs).
Assembly: Mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Testis

extract_protocol:
The total RNA of mouse testis in each group was isolated using RNAiso Plus (TakaRa, 9108) and stored at -80℃.
The libraries were constructed using the Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (YEASEN), and sequenced on the NovaSeq sequencer (Illumina, San Diego, USA).

value: Testis

value: KIFC1 knockout


title: Exp-UVC_K2S_Cell-HaCaT_Treatment-Control

description:
S40
UV_HaCat_Beta_detP.txt-S40
UV_HaCat_Beta_detP.txt


title: Normal fibroblast from NSCLC patient 20150826

value: Normal fibroblast

value: Never

value: Female


title: Normal fibroblast from NSCLC patient 20150812

value: LUAD

value: Early


title: KO2


title: DNA-ALB1-GATA1-Round2-Rep1

description:
Library name: DNA-ALB1-GATA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA1 for 2 rounds, Biological replicate 1

value: synthetic DNA


title: KO1


title: DNA-ALB1-GATA1-Round1-Rep1

description:
Library name: DNA-ALB1-GATA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of GATA1 for 1 rounds, Biological replicate 1

value: Free DNA


title: DNA-ALB1-FOXA1-Round4-Rep2

description:
Library name: DNA-ALB1-FOXA1-Round4-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 4 rounds, Biological replicate 2


title: Exp-UVC_K1S_Cell-HaCaT_Treatment-Control

description:
S38
UV_HaCat_Beta_detP.txt-S38
UV_HaCat_Beta_detP.txt

value: HaCaT


title: Normal fibroblast from NSCLC patient 0304


title: WT3

value: wild-type


title: Normal fibroblast from NSCLC patient 20150707

value: Ever

value: Male


title: DNA-ALB1-FOXA1-Round4-Rep1

description:
Library name: DNA-ALB1-FOXA1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 4 rounds, Biological replicate 1


title: Exp-UVC_K1V_Cell-HaCaT_Treatment-UV

description:
S37
UV_HaCat_Beta_detP.txt-S37
UV_HaCat_Beta_detP.txt


title: Exp-T1F_3B_Cell-HDF_Treatment-sham

description:
S36
5gTemp_HDF_Beta_detP.txt-S36
5gTemp_HDF_Beta_detP.txt

source_name: HDF

value: HDF

value: sham


title: WT2


title: Normal fibroblast from NSCLC patient 1213


title: Exp-T1F_3A_Cell-HDF_Treatment-exposed

description:
S35
5gTemp_HDF_Beta_detP.txt-S35
5gTemp_HDF_Beta_detP.txt

value: exposed


title: DNA-ALB1-FOXA1-Round3-Rep1

description:
Library name: DNA-ALB1-FOXA1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 3 rounds, Biological replicate 1


title: DNA-ALB1-FOXA1-Round3-Rep2

description:
Library name: DNA-ALB1-FOXA1-Round3-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 3 rounds, Biological replicate 2


title: Exp-T1F_2B_Cell-HDF_Treatment-exposed

description:
S34
5gTemp_HDF_Beta_detP.txt-S34
5gTemp_HDF_Beta_detP.txt


title: Normal fibroblast from NSCLC patient 20150902

description: Gene expression data of normal fibroblast from NSCLC patient


title: Normal fibroblast from NSCLC patient 20150818

value: Late


title: DNA-ALB1-FOXA1-Round2-Rep2

description:
Library name: DNA-ALB1-FOXA1-Round2-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 2 rounds, Biological replicate 2


title: JHHCGX_148，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days

city: Hangzhou

first: Yingying

state: Zhejiang

address: No. 260, Baichuan Street, Fuyang District, Hangzhou City

institute: Zhejiang Chinese Medical University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: tissue

value: ICR mice

value: Jinhua Hecha administration


title: Exp-UVC_K2V_Cell-HaCaT_Treatment-UV

description:
S39
UV_HaCat_Beta_detP.txt-S39
UV_HaCat_Beta_detP.txt

value: UV


title: Normal fibroblast from NSCLC patient 20100510

value: Normal fibroblast

value: Female

value: LUSC


title: Normal fibroblast from NSCLC patient 20150519

value: Never

value: LUAD

value: Early


title: Normal fibroblast from NSCLC patient 0330


title: Exp-T1F_2A_Cell-HDF_Treatment-sham

description:
S33
5gTemp_HDF_Beta_detP.txt-S33
5gTemp_HDF_Beta_detP.txt


title: DNA-ALB1-FOXA1-Round2-Rep1

description:
Library name: DNA-ALB1-FOXA1-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 2 rounds, Biological replicate 1

value: synthetic DNA

value: Free DNA


title: JHHCGX_129，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days


title: Exp-T1F_1A_Cell-HDF_Treatment-exposed

description:
S31
5gTemp_HDF_Beta_detP.txt-S31
5gTemp_HDF_Beta_detP.txt


title: DNA-ALB1-FOXA1-Round1-Rep2

description:
Library name: DNA-ALB1-FOXA1-Round1-Rep2
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 1 rounds, Biological replicate 2


title: Exp-T1F_1B_Cell-HDF_Treatment-sham

description:
S32
5gTemp_HDF_Beta_detP.txt-S32
5gTemp_HDF_Beta_detP.txt


title: WT1

value: Testis

value: wild-type


title: JHHCGC_19，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days


title: Exp-UVC_F3S_Cell-HDF_Treatment-Control

description:
S30
UV_HDF_Beta_detP.txt-S30
UV_HDF_Beta_detP.txt

value: HDF

value: Control


title: JHHCGC_48，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days


title: JHHCGX_256JHHCGX，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days


title: Normal fibroblast from NSCLC patient 20150505

value: Ever

value: Male

value: Late


title: DNA-ALB1-CEBPB-Round4-Rep1

description:
Library name: DNA-ALB1-CEBPB-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of CEBPB for 4 rounds, Biological replicate 1


title: Exp-UVC_F3V_Cell-HDF_Treatment-UV

description:
S29
UV_HDF_Beta_detP.txt-S29
UV_HDF_Beta_detP.txt


title: Normal fibroblast from NSCLC patient 20150428


title: JHHCGC_7，Colon tissue, intragastric administration of Jinhua Hecha-a fermented green tea for 44 days

value: tissue

value: ICR mice

value: Jinhua Hecha administration


title: Normal fibroblast from NSCLC patient 20150303

value: Normal fibroblast

value: Female

value: Other


title: DNA-ALB1-CEBPB-Round3-Rep1

description:
Library name: DNA-ALB1-CEBPB-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of CEBPB for 3 rounds, Biological replicate 1


title: Exp-UVC_F2S_Cell-HDF_Treatment-Control

description:
S28
UV_HDF_Beta_detP.txt-S28
UV_HDF_Beta_detP.txt


title: FFZRX_268，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days

value: Compound jujube kernel administration


title: FFZRX_238，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days


title: DNA-ALB1-CEBPB-Round2-Rep1

description:
Library name: DNA-ALB1-CEBPB-Round2-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of CEBPB for 2 rounds, Biological replicate 1


title: Exp-UVC_F2V_Cell-HDF_Treatment-UV

description:
S27
UV_HDF_Beta_detP.txt-S27
UV_HDF_Beta_detP.txt

value: UV


title: FFZRX_139，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days


title: DNA-ALB1-FOXA1-Round1-Rep1

description:
Library name: DNA-ALB1-FOXA1-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of FOXA1 for 1 rounds, Biological replicate 1

value: synthetic DNA


title: Normal fibroblast from NSCLC patient 20150318

value: Never

value: LUAD

value: Early


title: Normal fibroblast from NSCLC patient 20100426_1


title: Exp-UVC_F1S_Cell-HDF_Treatment-Control

description:
S26
UV_HDF_Beta_detP.txt-S26
UV_HDF_Beta_detP.txt

value: HDF


title: Normal fibroblast from NSCLC patient 20101221

description: Gene expression data of normal fibroblast from NSCLC patient


title: Exp-UVC_F1V_Cell-HDF_Treatment-UV

description:
S25
UV_HDF_Beta_detP.txt-S25
UV_HDF_Beta_detP.txt


title: FFZRC_24，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days


title: FFZRC_12，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days


title: DNA-ALB1-ASCL1-Round4-Rep1

description:
Library name: DNA-ALB1-ASCL1-Round4-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of ASCL1 for 4 rounds, Biological replicate 1

value: Free DNA


title: Exp-V6F_4BWdh_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S106
P10_HDF_Beta_detP.txt-S106
P10_HDF_Beta_detP.txt

value: sham

tag: trial

tag: incubator

value: B

tag: frequency [ghz]

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: aliquot

tag: passage

value: b

value: c

value: a


title: INPUT-W601-part2

description:
Library name: INPUT-W601-part2
Input DNA Library based on the tiling of the nucleosome positioning sequence W601, Techincal Replicate 2

tag: tissue

tag: treatment

value: Input DNA


title: FFZRC_5，Colon tissue was intragastric administration of compound Suanzoren capsule for 44 days

value: tissue

value: ICR mice


title: Normal fibroblast from NSCLC patient 20150203_1

tag: cell type

value: Normal fibroblast

value: Male


title: Normal fibroblast from NSCLC patient 20140411

value: Ever

value: Other


title: Normal fibroblast from NSCLC patient 20100315

value: Never


title: Exp-V6F_4AWdh_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S105
P10_HDF_Beta_detP.txt-S105
P10_HDF_Beta_detP.txt

value: exposed

tag: column header in matrix processed file

tag: date

value: A

tag: batch


title: INPUT-NRCAM-part2

description:
Library name: INPUT-NRCAM-part2
Input DNA Library based on the tiling of the nucleosome positioning sequence NRCAM, Techincal Replicate 2

value: synthetic DNA


title: INPUT-W601-part1

description:
Library name: INPUT-W601-part1
Input DNA Library based on the tiling of the nucleosome positioning sequence W601, Techincal Replicate 1


title: Normal fibroblast from NSCLC patient 20150331_1

tag: age

tag: smoking

value: LUAD

value: Early


title: DNA-ALB1-CEBPB-Round1-Rep1

description:
Library name: DNA-ALB1-CEBPB-Round1-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of CEBPB for 1 rounds, Biological replicate 1

value: Free DNA


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 knockdown - 3

city: Leuven

first: Sam

last: Bryce-Smith

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

description:
Library name: i3Neuron_CTRL_UPF1_3
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).

data_processing:
Raw reads in FASTQ format were quality trimmed for a minimum Phred score of 10 and otherwise default parameters using fastp (v0.20.1). Quality trimmed reads were aligned to the GRCh38 genome build using gene models from GENCODE v40 with STAR (v2.7.8a).  The  alignment  pipeline is implemented in Snakemake and is available at  https://github.com/frattalab/rna_seq_snakemake  .
Gencode v40 transcripts were quantified by Salmon using a decoy-aware transcriptome index (hg38 genome sequence as decoys, default parameters). Salmon v1.4.0 was used with the --gcBias and --seqBias flags enabled (otherwise default parameters). Tximport (default parameters) was used to summarise estimated transcript counts to the gene-level and produce raw count matrices.
Assembly: hg38
Supplementary files format and content: comma-delimited text file containing raw gene counts for each sample

extract_protocol:
RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription.
Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (iPSC-derived cortical neurons = 2x150bp, > 40 million reads per sample).

tag: cell line

value: iPSC-derived cortical neuron


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 knockdown - 1

description:
Library name: i3Neuron_CTRL_UPF1_1
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 knockdown - 2

description:
Library name: i3Neuron_CTRL_UPF1_2
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).


title: Normal fibroblast from NSCLC patient 20101231

tag: gender

value: Female

tag: histology

tag: Stage


title: Exp-V8F_3B_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S92
P10_HDF_Beta_detP.txt-S92
P10_HDF_Beta_detP.txt

value: HDF

tag: trial

tag: incubator

value: B

tag: frequency [ghz]

value: b

value: c


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 knockdown - 4

description:
Library name: i3Neuron_CTRL_UPF1_4
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).


title: INPUT-NRCAM-part1

description:
Library name: INPUT-NRCAM-part1
Input DNA Library based on the tiling of the nucleosome positioning sequence NRCAM, Techincal Replicate 1

value: Input DNA


title: NCX_124，Colon tissue, administered saline for 44 days

value: tissue

tag: genotype

value: ICR mice

value: control


title: Exp-V5F_6A_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S95
P10_HDF_Beta_detP.txt-S95
P10_HDF_Beta_detP.txt

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: aliquot

tag: passage

value: a


title: NCX_147，Colon tissue, administered saline for 44 days

tag: tissue

tag: treatment


title: NCX_134，Colon tissue, administered saline for 44 days


title: INPUT-CX3-part2

description:
Library name: INPUT-CX3-part2
Input DNA Library based on the tiling of the nucleosome positioning sequence CX3, Techincal Replicate 2


title: INPUT-CX3-part1

description:
Library name: INPUT-CX3-part1
Input DNA Library based on the tiling of the nucleosome positioning sequence CX3, Techincal Replicate 1


title: Exp-V5F_5A_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S93
P10_HDF_Beta_detP.txt-S93
P10_HDF_Beta_detP.txt

tag: cell type

value: exposed

tag: column header in matrix processed file

tag: date

tag: batch


title: DNA-ALB1-ASCL1-Round3-Rep1

description:
Library name: DNA-ALB1-ASCL1-Round3-Rep1
SELEX for the binding of seq of the DNA library based on the tiling of nucleosome positioning sequence ALB1 for the binding of ASCL1 for 3 rounds, Biological replicate 1


title: Exp-V5F_5B_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-sham

description:
S94
P10_HDF_Beta_detP.txt-S94
P10_HDF_Beta_detP.txt

value: sham


title: NCC_17，Colon tissue, administered saline for 44 days


title: ，NCC_8Colon tissue, administered saline for 44 days


title: NCC_2，Colon tissue, administered saline for 44 days


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 control - 4

description:
Library name: i3Neuron_CTRL_CTRL_4
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).

tag: cell line


title: Normal fibroblast from NSCLC patient 20101228

description: Gene expression data of normal fibroblast from NSCLC patient

value: Normal fibroblast

tag: age

tag: smoking

value: Ever

tag: gender

value: Male

tag: histology

value: LUSC


title: Exp-V8F_3A_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S91
P10_HDF_Beta_detP.txt-S91
P10_HDF_Beta_detP.txt

tag: trial

tag: incubator

value: A

tag: frequency [ghz]


title: Normal fibroblast from NSCLC patient 20150203_2

value: Never

value: Female

value: LUAD

tag: Stage

value: Late


title: INPUT-ALB1-part1

description:
Library name: INPUT-ALB1-part1
Input DNA Library based on the tiling of the nucleosome positioning sequence ALB1, Techincal Replicate 1

value: synthetic DNA


title: Cd24a-Pax9+ anti-IgG Cut&Tag_rep1

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

description: Sample 19

library_source: genomic

data_processing:
Sample 1-2  Raw data was processed using the Cell Ranger pipeline (cellranger-7.1.0) to generate gene-barcode matrices. Quality control was performed using Seurat (version 5.1.0) to filter out cells with low gene counts, high mitochondrial gene content, and potential doublets. Sample 3-6  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1.FeatureCounts version 2.0.1 was used to add a gene tag to each alignment. The feature-barcode matrix was processed using Seurat (V5.0.1) package. Sample 7-11  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1. FeatureCounts version 2.0.1 was used to add a gene tag to each alignment.  Sample 12-27  Paired-end reads were aligned to the mm10 reference genome using Bowtie2 version 2.3.5.1.Peak calling was executed using SEACR 1.3.
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz,features tsv.gz,matrix.mtx.gZ gene counts expression matrix file gene expression matrix file .bw
Assembly: bw
Library strategy: Cut&Tag

source_name: Cells isolated from primary tissues

extract_protocol:
Sample1-2 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.  Sample3-6 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.  Sample7-11 Following euthanasia of mice and tooth extraction, PN3 molar tissue was embedded in OCT compound. Laser capture microdissection (LCM) was conducted following an established protocol using Cresyl violet staining (Merck, C5042) for enhanced visualization of cellular morphology on PEN Membrane slides (MMI, 50102). Five regions were dissected: "Center," "Direct Below," "Side," "Pax9 Positive," and "Pax9 Negative." Samples were collected on IsolationCaps (MMI, 50206). Sample12-27 Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.
Sample1-2 Cell counting and viability confirmation were performed using the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). Samples were then utilized for single-cell RNA sequencing with the 10x Genomics system.By using laser capture microdissection and odified SMART-seq3 library preparation methods, the relationships between different tissue regions were compared. Sample 3-6 Smart-seq3 was conducted with slight modifications. Single cells were sorted into 96-well plates with lysis buffer, then incubated at 72°C. Reverse transcription was performed with a mix containing RNase inhibitor and Maxima H-minus RT enzyme at 42°C. PCR pre-amplification followed, using KAPA HiFi HotStart buffer and specific primers. Samples were purified using homemade PEG beads and quantified. Tagmentation was done with homemade Tn5 and the libraries were amplified using the TruePrep Index Kit V2. Finally, samples were pooled, purified, and sequenced with 150-bp paired end using NovaSeq6000 Sample 7-11 The LCM samples collected on the IsolationCaps (MMI, 50206) were checked before further lysis with 50µl of 4M Guanidine isothiocyanate (GuSCN) solution (Invitrogen, 15577-018). RNA precipitation was conducted by adding a 771µl buffer composed of 600µl anhydrous ethanol (Fisher Chemical, A995-4), 20µl of 1.5M sodium acetate (Invitrogen, AM9740), 1µl glycogen (Thermo Fisher, AM9516), and 150µl of DNase/RNase-Free Distilled Water (Thermo Fisher, 10977015). The mixture was then incubated at -80°C for 30min, followed by centrifugation at 4°C at 12,000g for 30min to recover RNAs. The obtained RNA was processed for library construction utilizing the smart-Seq3 protocol (2) with slight modifications: The lysis buffer comprised 0.5U/μl of recombinant RNase inhibitor (RRI) (Takara, 2313A), 0.5mM dNTP (Thermo Scientific, R0192), and 0.5μM Smart-seq3 oligo-dT primer (5′-biotin-ACGAGCATCAGCAGCATACGAT30VN-3′; HPLC) (Takara). Following lysis, 10μl of reverse transcription mix was added to each sample, comprising 25mM Tris-HCl, pH 8.0 (Thermo Fisher, AM9855G), 30mM NaCl (Thermo Fisher, AM9760G), 1mM GTP (Thermo Fisher, R1461), 2.5mM MgCl2 (Thermo Fisher, AM9530G), 8mM DTT (Thermo Fisher, 707265ML), 0.5U/μl RRI, 2μM of Smart-seq3 TSOs (5′-biotin-AGAGACAGATTGCGCAATGNNNNNNNNrGrGrG-3′; HPLC) (Takara), and 2U/μl of Maxima H-minus RT enzyme (Thermo Fisher, EP0751). This integrated approach facilitates the detailed transcriptomic profiling of discrete anatomical regions. Sample 12-27 After harvesting, cells were counted and centrifuged for 3 minutes at 600g at room temperature, followed by resuspension in 4ml PBS and another centrifugation. Cells were then resuspended in 2ml ice-cold NE1 buffer with Pierce Protease Inhibitor Tablets (Thermo Fisher, A32965) and left on ice for 10 minutes. After centrifugation at 1,300g for 4 minutes at 4°C, cells were resuspended in 2ml PBS and centrifuged again. Nuclei were resuspended in wash buffer to approximately 1 million cells/ml, frozen in cryogenic vials with 10% DMSO, and stored at -80°C. Upon thawing, nuclei were incubated with Concanavalin A-coated magnetic beads (Bangs Laboratories, BP531), and then with primary antibody (α-H3K4me3 rabbit polyclonal antibody (Diagenode, C15410003)) and negative control (guinea pig α-rabbit IgG antibody (Antibodies online, ABIN101961)) overnight at 4°C. Secondary antibody (guinea pig α-rabbit IgG antibody (Antibodies online, ABIN101961)) was added and incubated for 1 hour. pA-Tn5 transposon was then added, and tagmentation was performed for 1 hour at 37°C. DNA was extracted, amplified by PCR for 17 cycles, purified using VAHTS DNA Clean Beads (Vazyme, N411), and sequenced at 150-bp paired end by Novaseq6000

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

tag: genotype

tag: antibody

value: IgG

value: 9days old


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 control - 3

description:
Library name: i3Neuron_CTRL_CTRL_3
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).

value: iPSC-derived cortical neuron


title: Exp-V8F_2B_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S90
P10_HDF_Beta_detP.txt-S90
P10_HDF_Beta_detP.txt

value: HDF

value: exposed

value: B

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: aliquot

tag: passage

value: b

value: c


title: INPUT-ALB1-part2

description:
Library name: INPUT-ALB1-part2
Input DNA Library based on the tiling of the nucleosome positioning sequence ALB1, Techincal Replicate 2

tag: tissue

tag: treatment

value: Input DNA


title: Cd24a+Pax9+anti-IgG Cut&Tag_rep1

description: Sample 18

tag: cell type


title: Exp-V8F_2A_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S89
P10_HDF_Beta_detP.txt-S89
P10_HDF_Beta_detP.txt

value: sham

tag: column header in matrix processed file

tag: date

value: A

tag: batch


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 control - 2

description:
Library name: i3Neuron_CTRL_CTRL_2
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).

tag: cell line


title: H1-NCP_Libraries-2-MNase

description:
Library name: H1-WANC-2-MNase
Mnase-digested Input PIONEAR-seq NCP Library containing  nucleosome positioning sequences ALBN1, CX3CR1, NRCAM and W601 tiled with 20-mers, Biological replicate 2

data_processing:
The forward (labeled ‘R1’) and reverse complement (labeled ‘R2’) 150-bp paired-end sequencing Fastq reads were merged with PEAR using default setting (PMID: 24142950).
Analysis of MNase cuts on single sequence NCPs ( Libraries: F3-203-1-MNase, G3-203-2-Mnase, E2-337-2-MNase, F2-338-1-MNase): Reads whose lengths were between 80 and 147 bp were aligned back to their expected 147-bo sequences with the R function pairwiseAlignment (default setting except: type='overlap’) and dismissed if there were any gaps or more than 5 mismatches, and if the alignment was less than 80 bp. Since the reads were filtered to be longer than 80 bases, the 5’ end of the fragments always occurred at position between 1 and 67 bases, and the 3’ end occurred at position between 81 and 147 bases, within the 147-bp DNA. The read counts of the cut position at the 5’ end (at position between bases 2 to 67) and 3’ end (at position between bases 81 to 146) were used separately to find 5' and 3'-end cuts.
Analysis of MNase cuts on PIONEAR-seq NCP input libraries (Part1 ): alignment to the libraries template of the Libraries C1-WANC-1-Input, G1-WANC-1-Input, D1-WANC-1-MNase and H1-WANC-2-MNase.  To remove PCR duplicates, datasets of ‘unique reads’ were created by excluding duplicated reads, so that filtered reads with both identical tiles and identical end cuts were considered just once. Unique reads whose length was between 80 and 147 bp were assigned to the template (W601, ALBN1, CX3CR1 or NRCAM) that exhibited the best alignment. Reads with no mismatched were dismissed, since they represented fragments where the N20 tile had been cut out and its position could not be identified. The remaining reads are the “QCed reads” that can be used to quantify relative subsequences abundances and to identify the position of the N20 tile within the template according to the original sublibraries (see Part 2).
Analysis of MNase cuts on PIONEAR-seq NCP input libraries (Part 2): location of MNase cuts along the libraries template of the Libraries D1-WANC-1-MNase and H1-WANC-2-MNase. From the 'QCed reads' obtained at the end of Part 1, two groups of reads were selected. The first group represented fragments where the MNase cut happened on the left and right of the N20 tile and included reads containing mismatches within an internal region no longer than 20-bp, which informed on the position of the N20 tile in the reads. The second group represented fragments where the MNase cut happened within the N20 tile and included reads that at one end contained up to 20 mismatches, which were also within the N20 tile. These two read groups were merged, and then sorted according to their N20 sublibrary of origin.
Assembly: Synthetic DNA
Supplementary files format and content: tab-delimited text file, eventually merged in tar archives, includes count of fragment end positions

source_name: Syntehtic DNA

extract_protocol:
Amplicon DNA
Sequencing libraries were prepared by ligating to the digested libraries adding to the selected libraries (1) 5' end Unique Molecular Identifies (UMIs), (2) llumina adaptors (IAs), (2) TRUseq dual barcodes (BCs) and (2) Illumina sequencing promoters P5 and P7 (P5/P7) by PCR amplification with custom primers.  10 ng of DNA was used as starting material samples. Libraries were PCR amplified with KAPA HiFi HotStart ReadyMix PCR Kit by using 2 consecutive 6-cycle PCR runs (first cycle for UMIs and IAs, second cycle for BCs and P5/P7)  on the thermocycler. Post amplification libraries were size selected at ~300bp in length by Azenta using AMPure XP beads. Libraries were validated by using both the Tapestation D1000 and  Qubit.

treatment_protocol: DNA Libraries were PCR amplified, assembled on in vitro reconstituted histone octamers to form nucleosome and mildly digested mith MNase.

value: Syntehtic DNA

value: MNASE DIGESTION


title: Cd24a+Pax9- anti-IgG Cut&Tag_rep1

description: Sample 17

tag: age


title: G3-NRCAM-2-MNase

description:
Library name: G3-203-2-MNase
MNase-digested NCPs assembled with the nucleosome positioning sequence NRCAM, Biological replicate 2


title: Exp-V8F_1B_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-exposed

description:
S88
P10_HDF_Beta_detP.txt-S88
P10_HDF_Beta_detP.txt

tag: trial

tag: incubator


title: G1-NCP_Libraries-2-Input

description:
Library name: G1-WANC-2-Input
Input PIONEAR-seq NCP Library containing  nucleosome positioning sequences ALBN1, CX3CR1, NRCAM and W601 tiled with 20-mers, Biological replicate 2

value: UNTREATED CONTROL


title: Cd24a-Pax9- anti-IgG Cut&Tag_rep1

description: Sample 16


title: HEL-shCD84-2-nw_S14

city: Duarte

first: Mariam

last: Murtadha

state: CA

address: 1500 E. Duarte Rd

institute: City of Hope

description:
Library name: Sample8
column name in  log2_fpkm.txt: HEL-shCD84-2-nw_S14

data_processing:
trimmomatic
STAR
Assembly: hg38
Supplementary files format and content: log2 FPKM, expression matrix

source_name: Bone marrow

extract_protocol:
Cells were collected and resuspended in Trizol reagent (Invitrogen Corporation) following the manufacturer’s instructions.
RNA sequencing libraries were prepared with Kapa RNA HyperPrep kit with polyA kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. Sequencing run was performed in the single read mode using Illumina HiSeq 2500

value: Bone marrow

value: erythroblast

value: HEL cell line was transduced with shCD84-2 lentivirus (MOI=5) for 72 hours


title: Exp-V8F_1A_Cell-HDF_Power-10_Frequency-27_Time-48_Treatment-sham

description:
S87
P10_HDF_Beta_detP.txt-S87
P10_HDF_Beta_detP.txt

tag: frequency [ghz]


title: F3-NRCAM-1-MNase

description:
Library name: F3-203-1-MNase
MNase-digested NCPs assembled with the nucleosome positioning sequence NRCAM, Biological replicate 1


title: Exp-V5F_6B_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-sham

description:
S96
P10_HDF_Beta_detP.txt-S96
P10_HDF_Beta_detP.txt

value: a


title: HEL-shCD84-1-new_S13

description:
Library name: Sample7
column name in  log2_fpkm.txt: HEL-shCD84-1-new_S13


title: Cd24a-Pax9+ anti-H3K4me3 Cut&Tag_rep1

description: Sample 15

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

tag: genotype

value: 9days old


title: Exp-V5F_3B_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-sham

description:
S86
P10_HDF_Beta_detP.txt-S86
P10_HDF_Beta_detP.txt

value: HDF


title: Cd24a+Pax9+ anti-H3K4me3 Cut&Tag_rep1

description: Sample 14

tag: antibody


title: F2-NRCAM_TFBS_CEBPB_Right-MNase

description:
Library name: F2-338-1-MNase
MNase-digested NCPs assembled with the nucleosome positioning sequence NRCAM and containing the CEBPB binding motif (TTGCGCAA) at basepairs 114-121


title: Exp-V5F_3A_Cell-HDF_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S85
P10_HDF_Beta_detP.txt-S85
P10_HDF_Beta_detP.txt

value: exposed

tag: power [mw/cm2]


title: Exp-V7F_6B_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S84
P10_HDF_Beta_detP.txt-S84
P10_HDF_Beta_detP.txt

value: B

tag: exposuretime [hr]

value: b


title: HEL-shCtrl-1-new_S11

description:
Library name: Sample5
column name in  log2_fpkm.txt: HEL-shCtrl-1-new_S11

value: HEL cell line was transduced with shCtrl lentivirus (MOI=5) for 72 hours


title: Cd24a+Pax9- anti-H3K4me3 Cut&Tag_rep1

description: Sample 13


title: E2-NRCAM_TFBS_CEBPB_Left-MNase

description:
Library name: E2-337-2-MNase
MNase-digested NCPs assembled with the nucleosome positioning sequence NRCAM and containing the CEBPB binding motif (TTGCGCAA) at basepairs 32-39


title: D1-NCP_Libraries-1-MNase

description:
Library name: D1-WANC-1-MNase
Mnase-digested Input PIONEAR-seq NCP Library containing  nucleosome positioning sequences ALBN1, CX3CR1, NRCAM and W601 tiled with 20-mers, Biological replicate 1


title: THP1-shCD84_S10

description:
Library name: Sample4
column name in  log2_fpkm.txt: THP1-shCD84_S10

source_name: Peripheral blood

value: Peripheral blood

value: Monocyte

value: THP1 cell line was transduced with shCD84-2 lentivirus (MOI=5) for 72 hours


title: Exp-V7F_6A_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S83
P10_HDF_Beta_detP.txt-S83
P10_HDF_Beta_detP.txt

value: sham

value: A

tag: aliquot


title: Cd24a-Pax9- anti-H3K4me3 Cut&Tag_rep1

description: Sample 12


title: C1-NCP_Libraries-1-Input

description:
Library name: C1-WANC-1-Input
Input PIONEAR-seq NCP Library containing  nucleosome positioning sequences ALBN1, CX3CR1, NRCAM and W601 tiled with 20-mers, Biological replicate 1

value: Syntehtic DNA

value: UNTREATED CONTROL


title: i3Neuron TDP-43/UPF1 knockdown - TDP-43 control UPF1 control - 1

description:
Library name: i3Neuron_CTRL_CTRL_1
Human iPS cells used in this study were engineered (Fernandopulle et al., 2018; Wang et al., 2017) to express mouse or human neurogenin-2 under a doxycycline-inducible promoter, as well as an enzymatically dead Cas9 (+/− CAG-dCas9-BFP-KRAB) (Tian et al., 2019). To achieve knockdown, sgRNAs targeting either a non-targeting control guide (GTCCACCCTTATCTAGGCTA), UPF1 (GGCCAGACGCAGACGCCCCC), or TARDBP (GGGAAGTCAGCCGTGAGACC) were delivered to iPS cells by lentiviral transduction (Lois et al., 2002), for a total of 4 groups: Control for TDP-43 and UPF1 knockdown (control/control), Control for TDP-43 knockdown and positive for UPF1 knockdown (control/UPF1KD), Positive for TDP-43 knockdown and control for UPF1 knockdown (TDP43KD/control), Positive for TDP-43 and UPF1 knockdown (TDP43KD/UPF1KD). After lentiviral transduction, cells were plated in tissue culture dishes coated with human embryonic stem cell-qualified Matrigel (Corning). The following morning, cells were washed with PBS and the media was changed to E8 alone or (depending on cell number) E8 supplemented with 10 µM ROCK inhibitor in a 37°C, 5% CO2 incubator. Cells were passaged with accutase (Life Technologies) for 5–10 min at 37 °C and then washed with PBS before re-plating. Two days after lentiviral delivery, cells were selected overnight with either puromycin (10 µg/ml) or blasticidin (50–100 µg/ml). iPS cells were then expanded for 2 days before initiating neuronal differentiation. To initiate neuronal differentiation, 20–25 million iPS cells per 15 cm plate were individualised using accutase on day 0 and re-plated onto Matrigel-coated tissue culture dishes in N2 differentiation media containing: knockout DMEM/F12 media (Life Technologies Corporation) with N2 supplement (Life Technologies Corporation), 1× GlutaMAX (Thermofisher Scientific), 1× MEM nonessential amino acids (Thermofisher Scientific), 10 µM ROCK inhibitor (Selleckchem) and 2 µg/ml doxycycline (Clontech). Media was changed daily during this stage. On day 3 pre-neuron cells were replated onto dishes coated with freshly made poly-L-ornithine (0.1 mg/ml; Sigma), 6-well dishes (2 million per well), in i3Neuron Culture Media: Brain-Phys media (Stemcell Technologies) supplemented with 1× B27 Plus Supplement (ThermoFisher Scientific), 10 ng/ml BDNF (PeproTech), 10 ng/ml NT-3 (PeproTech), 1 µg/ml mouse laminin (Sigma), and 2 µg/ml doxycycline (Clontech). i3Neurons were then fed three times a week by half media changes. i3Neurons were then collected on day 7 after the addition of doxycycline. RNA  was  extracted using  the  RNeasy  mini  kit  (Qiagen)  following  the  manufacturer’s  protocol,  including  the on-column  DNA  digestion  step.  RNA  concentrations  were  measured  by  Nanodrop  and  1,000  ng of  RNA  was  used  for  reverse  transcription. Sequencing libraries were prepared with polyA enrichment using a TruSeq Stranded mRNA Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 or NovaSeq 6000 machine at UCL Genomics (2x150bp,  > 40 million reads per sample).

value: iPSC-derived cortical neuron


title: PN3 mouse M1 Laser Capture Microdissection Center domain

description:
Modified SMARTseq3
Sample 11

data_processing:
Sample 1-2  Raw data was processed using the Cell Ranger pipeline (cellranger-7.1.0) to generate gene-barcode matrices. Quality control was performed using Seurat (version 5.1.0) to filter out cells with low gene counts, high mitochondrial gene content, and potential doublets. Sample 3-6  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1.FeatureCounts version 2.0.1 was used to add a gene tag to each alignment. The feature-barcode matrix was processed using Seurat (V5.0.1) package. Sample 7-11  Paired-end reads were aligned to the mm10 reference genome using HISAT2 version 2.2.1. FeatureCounts version 2.0.1 was used to add a gene tag to each alignment.  Sample 12-27  Paired-end reads were aligned to the mm10 reference genome using Bowtie2 version 2.3.5.1.Peak calling was executed using SEACR 1.3.
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz,features tsv.gz,matrix.mtx.gZ gene counts expression matrix file gene expression matrix file .bw
Assembly: bw

source_name: Dental Tissue

value: Dental Tissue

value: 3days old


title: Exp-V7F_5B_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S82
P10_HDF_Beta_detP.txt-S82
P10_HDF_Beta_detP.txt

tag: passage

value: a


title: THP1-shCD84-2-new_S9

description:
Library name: Sample3
column name in  log2_fpkm.txt: THP1-shCD84-2-new_S9

tag: tissue


title: PN3 mouse M1 Laser Capture Microdissection Side domain

description:
Modified SMARTseq3
Sample 10


title: THP1-shCtrl-2-new_S8

description:
Library name: Sample2
column name in  log2_fpkm.txt: THP1-shCtrl-2-new_S8

tag: treatment

value: THP1 cell line was transduced with shCtrl lentivirus (MOI=5) for 72 hours


title: WN3,NaNO3,3d

city: nanjing

first: xiaoyu

last: guo

address: xuanwu district

institute: nanjing agricultural university

description:
Library name: sample 6
FPKM (WN3)

data_processing:
1. data evaluation and quality control, 2. transcriptome splicing, 3. gene annotation, 4. RNAseq sequencing evaluation, 5. gene structure analysis, 6. expression level analysis, 7. expression difference analysis, 8. gene enrichment analysis
Assembly: Ganoderma lucidum
Supplementary files format and content: gene_expression.addAnno.txt

organism: Ganoderma lucidum

source_name: mycelia

extract_protocol:
1. Leave the lysed sample or homogenate at room temperature for 5-10min to allow complete separation of the nucleoprotein from the nucleic acid. 2. Add 0.2ml of chloroform and shake vigorously for 15sec for 3min._x000D_ 2. Add 0.2 ml of chloroform, shake vigorously for 15 sec and leave at room temperature for 3 min. centrifuge at 12000 rpm at 4°C for 10 min._x000D_ 3. Aspirate the upper aqueous phase and transfer to a clean centrifuge tube, add an equal volume of isopropanol, mix well and leave at room temperature for 20min._x000D_  4. 12000rpm 4°C centrifuge for 10min._x000D_ 4. Centrifuge at 12000rpm for 10min at 4°C and discard the supernatant. 5. Add 1ml of 75% ethanol._x000D_ 5. Add 1ml of 75% ethanol to wash the precipitate. 12000rpm 4°C centrifugation for 3min, discard the supernatant. Dry at room temperature_x000D_ Dry at room temperature for 5-10min. 6._x000D_ 6. Add appropriate amount of RNase-free ddH2O to fully dissolve the RNA, and store the resulting RNA solution at -70°C or use immediately for subsequent experiments._x000D_ Store the obtained RNA solution at -70°C or use it immediately for subsequent experiments._x000D_ 7. Qubit2.0 was used to measure RNA concentration, and agarose gel was used to measure RNA integrity and genomic contamination._x000D_ _x000D_ Translated with DeepL.com (free version)
Total RNA is subjected to mRNA isolation, fragmentation, double-stranded cDNA synthesis, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting, and library amplification._x000D_ cDNA fragmentation, cDNA fragmentation modification, magnetic bead purification and fragmentation sorting, library amplification and other processes. After testing and quality control, the sequencing libraries can be applied to the Illumina platform._x000D_ The final result is a sequencing library that can be used on the Illumina platform after testing and quality control._x000D_ _x000D_ Translated with DeepL.com (free version)

value: mycelia


title: WN2,NaNO3,3d

description:
Library name: sample 5
FPKM (WN2)


title: PN3 mouse M1 Laser Capture Microdissection  Direct_below domain

description:
Modified SMARTseq3
Sample 9

tag: cell type


title: Exp-V7F_4B_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-exposed

description:
S80
P10_HDF_Beta_detP.txt-S80
P10_HDF_Beta_detP.txt

value: HDF

value: exposed

tag: column header in matrix processed file


title: THP1-shCtrl-1-new_S7

description:
Library name: Sample1
column name in  log2_fpkm.txt: THP1-shCtrl-1-new_S7


title: Exp-V7F_4A_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S79
P10_HDF_Beta_detP.txt-S79
P10_HDF_Beta_detP.txt

tag: date

value: b


title: HEL-shCtrl-2-new_S12

description:
Library name: Sample6
column name in  log2_fpkm.txt: HEL-shCtrl-2-new_S12

value: Bone marrow

value: erythroblast

value: HEL cell line was transduced with shCtrl lentivirus (MOI=5) for 72 hours


title: W3,(NH4)2SO4,3d

description:
Library name: sample 3
FPKM (W3)


title: PN3 mouse M1 Laser Capture Microdissection Pax9_positive domain

description:
Modified SMARTseq3
Sample 7


title: PN3 mouse M1 Laser Capture Microdissection Pax9_negative domain

description:
Modified SMARTseq3
Sample 8


title: HGC-27 cell, E2 treated

city: Wuhan

first: sheng

last: tian

address: 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province.

institute: zhongnan hospital

description: Library name: E2_2

data_processing:
HISAT2 for mapping, featureCounts for count the reads.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts data for each sample

extract_protocol:
Total RNA from HGC-27 and AGS cells and those treated with 10 nM estradiol for 1 day was extracted using TRIzol. The RNA samples underwent stringent quality control through measure the purity and concentration, include agarose gel electrophoresis, NanoPhotometer spectrophotometer, Qubit2.0 Fluorometer, and Agilent 2100 bioanalyzer
Libraries were constructed according to the NEB normal method.

value: gastric cancer cell

value: WT

value: 10 nM E2, 1 day


title: AGS cell, control

description: Library name: NC_1

source_name: AGS

value: AGS

value: nc


title: Exp-V6F_3A_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S75
P10_HDF_Beta_detP.txt-S75
P10_HDF_Beta_detP.txt

value: A

tag: batch


title: W2,(NH4)2SO4,3d

description:
Library name: sample 2
FPKM (W2)


title: Exp-V6F_3B_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S76
P10_HDF_Beta_detP.txt-S76
P10_HDF_Beta_detP.txt

value: sham

value: B


title: Cd24a- SMARTseq3 scRNAseq

description:
SMARTseq3
Sample 6

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

value: Cd24a-CreERT2; tdT mice

value: 9days old


title: HGC-27 cell, control

description: Library name: NC_2

tag: cell line


title: W1,(NH4)2SO4,3d

description:
Library name: sample 1
FPKM (W1)

value: mycelia


title: Cd24a+ SMARTseq3 scRNAseq

description:
SMARTseq3
Sample 5

tag: age


title: Exp-V6F_2B_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-sham

description:
S74
P10_HDF_Beta_detP.txt-S74
P10_HDF_Beta_detP.txt

value: HDF

tag: trial

value: b

value: a


title: Bovine,RNA-seq,MII,rep2

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
We aligned all RNA-seq datasets to distinct genomes (bovine, bosTau9) utilizing Hisat2 v2.1.1. The quantification of gene expression was subsequently performed using StringTie 2.2.1.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

organism: Bos taurus

source_name: MII

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 96 hpi (16-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of MII oocytes, zygotes, and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant. ICMs were placed in a 1:4 dilution of rabbit anti- bovine serum (Sigma-Aldrich, B-8270) for 40 minutes, washed twice in DPBS-0.001% BSA, and incubated for 40 minutes in a 1:4 dilution of guinea pig Complement Serum (Sigma-Aldrich, S1639). The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
For the generation of Smart-seq2 libraries, zona pellucida-free oocytes or embryos lysis in a 708 buffer containing RNase inhibitor, following the Smart-seq2 protocol as described (Picelli,2013). After completion of purification and fragmentation, the library was quantificatied and sequenced.

value: MII


title: Exp-V7F_5A_Cell-HDF_Power-10_Frequency-27_Time-2_Treatment-sham

description:
S81
P10_HDF_Beta_detP.txt-S81
P10_HDF_Beta_detP.txt

tag: incubator


title: Pax9- SMARTseq3 scRNAseq

description:
SMARTseq3
Sample 4

value: Pax9-CreERT2; tdT mice


title: Exp-V6F_2A_Cell-HDF_Power-10_Frequency-40.5_Time-2_Treatment-exposed

description:
S73
P10_HDF_Beta_detP.txt-S73
P10_HDF_Beta_detP.txt

value: exposed

tag: frequency [ghz]


title: TRANSATRA Patient 05-001 EOT

city: Freiburg im Breisgau

first: Michael

last: Kruszewski

state: Baden-Württemberg

address: Hugstetter Str. 55

institute: Universitätsklinikum Freiburg

data_processing:
Read quality was checked with FastQC (≥95% >Q30), alignment to the reference genome GRCh38/hg38 was performed with STAR aligner and read-counting was performed with featureCounts.
Each sample counts file was then fed to DESeq2 (16) to obtain the results file for treated samples vs screening timepoint. Differentially expressed genes (DEG)s were found by filtering genes with adjusted p value <0.05 and Log2 fold change >abs (0.6).
The result file is ranked using sign[log2fold]*Log10[p-adj] as suggested by Galaxy FGSEA tutorial before using them as input for FGSEA on the MSigDB Hallmark pathways database.
All analysis steps till here are calculated on the European Galaxy instance (https://usegalaxy.eu/) (17). The results files were further sorted, filtered, and plotted (Heatmap and Volcano plot) using Pandas, scikit, Matplotlib and the Seaborn library of Python.
Assembly: reference genome GRCh38/hg38
Supplementary files format and content: text file contianing raw counts for each sample

source_name: peripheral blood

extract_protocol:
enrichment of blasts: aMACS sort for CD34 and CD117 positive cells, (Miltenyi: CD34 MicroBead Kit, human, #130-046-702, CD117 MicroBead Kit, human, # 130-091-332)total RNA isolation: Machery&Nagel Kit, NucleoSpin RNA, #740955.250
Library prep: Illumina, TruSeq Stranded Total RNA Library Prep Gold, Read: length 2x75, Depth 100 M

value: peripheral blood

value: non-M3 acute myeloid leukemia blasts


title: Bovine,RNA-seq,MII,rep1


title: Exp-V6K_8B_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-exposed

description:
S72
P10_HaCat_Beta_detP.txt-S72
P10_HaCat_Beta_detP.txt

data_processing:
The software tool GenomeStudio V2011.1 (Illumina, Inc.) including the Methylation Module Version 1.9.0 was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed without normalization.
Beta Values with depection P values

source_name: HaCaT

value: HaCaT

value: c


title: WN1,NaNO3,3d

description:
Library name: sample 4
FPKM (WN1)


title: Pax9+ SMARTseq3 scRNAseq

description:
SMARTseq3
Sample 3

tag: genotype


title: Bovine,RNA-seq,GV,rep2

source_name: GV

value: GV


title: AGS cell, E2 treated

description: Library name: E2_1

value: AGS

value: gastric cancer cell

value: WT

value: 10 nM E2, 1 day


title: TRANSATRA Patient 05-001 day 28


title: Exp-V6K_8A_Cell-HaCaT_Power-10_Frequency-40.5_Time-48_Treatment-sham

description:
S71
P10_HaCat_Beta_detP.txt-S71
P10_HaCat_Beta_detP.txt

value: sham

value: A


title: Pax9+ 10X Genomics scRNAseq

description: 10x Genomics

data_processing:
Raw data was processed using the Cell Ranger pipeline (cellranger-7.1.0) to generate gene-barcode matrices. Quality control was performed using Seurat (version 5.1.0) to filter out cells with low gene counts, high mitochondrial gene content, and potential doublets.
Assembly: mm10
Supplementary files format and content: barcodes tsv.gz,features tsv.gz,matrix.mtx.gz

extract_protocol:
Following euthanasia of mice and tooth extraction, dental pulp was subsequently obtained using a syringe needle to remove epithelial tissue while preserve the mesenchymal part. The collected specimens were then placed into 1.5ml centrifuge tubes, finely minced for 3min, and subjected to a 5min enzymatic dissociation in 0.5ml of 0.25% trypsin-EDTA (ThermoFisher, 25200072). Neutralization was achieved with 1ml of culture medium (DMEM basal medium (Gibco, C11995500BT) supplemented with 10% fetal bovine serum (Lonsera, S711-001)). The medium was further supplemented with 20μl of 5mg/ml DNase I (Roche, 10104159001) and thoroughly mixed. After straining through a 70µm strainer and resuspension in 1x PBS, flow cytometry was employed for the isolation of the targeted cell populations.
Cell counting and viability confirmation were performed using the Countess II Automated Cell Counter (Thermo Fisher, AMQAX1000). Samples were then utilized for single-cell RNA sequencing with the 10x Genomics system

value: dental mesenchymal stem cells

value: Cells isolated from primary tissues

tag: strain

value: 9days old