title: 12

status: Public on Jul 26 2025

type: SRA

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
All reads were independently aligned with STAR_2.4.0f1 (Dobin et al, 2013) for sequence alignment against the human genome sequence build hg19, downloaded via the UCSC genome browser and SAMTOOLS v0.1.19 (Li et al, 2009) for sorting and indexing reads
Cufflinks (2.0.2) (Trapnell et al, 2012) was used to estimate the expression values (FPKMS), and GENCODE v19 (Derrien et al, 2012) GTF file for annotation.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
total RNA was extracted from samples by Trizol lysis and RNeasy Mini Kit (Qiagen, #74106) following the manufacturer’s protocols
cDNA libraries were generated using NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module) kit

tag: tissue

value: breast cancer

tag: cell line

tag: genotype

value: GPR52 KO


title: W1

value: WT


title: W2


title: PBMC DNA, High Blood Pressure, H10

status: Public on Jul 31 2024

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
After sequencing data was delivered, data filtering was carried out to remove low-quality data and obtain clean data or clean reads which are stored as FASTQ format. Then, clean data was mapped to the reference genome by BSMAP and the uniquely mapped data was used to gather the methylation information of the cytosine through the whole genome. The methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine which was also equal to the mC/C ratio at each reference cytosine.  Later, the cytosine information was used for standard bioinformatics analysis and personalized bioinformatics analysis. Rm average= [Nmall /(Nmall+Nnmall)]*100 %; Nm represents the reads number of mC, while Nnm represents the reads number of non-methylation reads. Putative DMRs were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5 CpG(CHG or CHH) sites with a 2- fold change in Methylation level and Fisher test p value <=0.05. Two nearby DMRs would be considered interdependent and joined into one continuous DMR if the genomic region from the start of an upstream DMR to the end of a downstream DMR also had 2- fold Methylation level differences between sample1 and sample2 with a p value <= 0.05. Otherwise, the two DMRs were viewed as independent. After iteratively merging interdependent DMRs, the final dataset of DMRs was made up of those that were independent from each other. The degree of difference of a methyl-cytosine ( mCG , mCHG , mCHH) between two samples was calculated, while comparing Methylationlevel of DMR in different  samples by CIRCOS. The following formula was used, degree of difference=log2 Rm1/log2Rm2; Rm1 and Rm2 represent the Methylation level of methyl-cytosine for sample1 and sample2 respectively. 0.001 will replace Rm1 (or Rm2) while it is 0.
Assembly: GRCh38.p14
Supplementary files format and content: excel, Log2 FC of significant DMRs between the sample comparisons

molecule: genomic DNA

source_name: Blood

extract_protocol:
Blood samples (2.5 ml) were drawn from each volunteer in a PAXgene tube (Qiagen cat# 762165) followed by genomic DNA isolation using a DNA isolation kit (Qiagen cat# 80204) according to the manufacturer instruction. DNA sample concentration and quality were evaluated using a nanodrop system (ThermoFisher Scientific). Samples were processed for global DNA methylation analysis via the whole-genome DNA methylation approach at BGI genomics core, USA.
For normal WGBS library constructing, the DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). After treatment with sodium bisulfite, unmethylated cytosine residues are converted to uracil whereas 5- methylcytosine (5mC) remains unaffected. Different Insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. After PCR amplification, uracil residues are converted to thymine. DNA methylation status was determined by direct PCR sequencing or cloning sequencing using the HighSeq4000 or other Illumina platforms.

value: Blood

tag: cell type

value: Peripheral blood mono nuclear cells


title: W3


title: PBMC DNA, High Blood Pressure, H5


title: PBMC DNA, High Blood Pressure, H8


title: PBMC DNA, High Blood Pressure, H6


title: PBMC DNA, High Blood Pressure, H2


title: PBMC DNA, High Blood Pressure, H4


title: OG


title: 11


title: PBMC DNA, Elevated/Mid Blood Pressure, M10


title: PBMC DNA, High Blood Pressure, H7


title: PBMC DNA, High Blood Pressure, H3


title: PBMC DNA, High Blood Pressure, H1


title: PBMC DNA, Elevated/Mid Blood Pressure, M5


title: PBMC DNA, Elevated/Mid Blood Pressure, M3


title: PBMC DNA, Elevated/Mid Blood Pressure, M4


title: PBMC DNA, Elevated/Mid Blood Pressure, M2


title: PBMC DNA, Elevated/Mid Blood Pressure, M9


title: PBMC DNA, Elevated/Mid Blood Pressure, M8


title: PBMC DNA, Elevated/Mid Blood Pressure, M7


title: PBMC DNA, High Blood Pressure, H9


title: PBMC DNA, Elevated/Mid Blood Pressure, M6


title: PBMC DNA, Low Blood Pressure, N6


title: PBMC DNA, Low Blood Pressure, N7


title: PBMC DNA, Low Blood Pressure, N3


title: PBMC DNA, Low Blood Pressure, N5


title: PBMC DNA, Low Blood Pressure, N8


title: PBMC DNA, Elevated/Mid Blood Pressure, M1


title: bacteria, OD1, subculture, adsa-Proline R1

city: NEW YORK

first: ALICE

last: PRINCE

state: NY

department: PEDIATRICS ID

institute: COLUMBIA UNIVERSITY

data_processing:
The raw counts were quantified using Subreads:FeatureCounts v1.6.3 and processed for differential gene expression using DEseq2 in R v3.5.3.
Analysis of sequencing for clinical isolates was performed by Windmüller and colleagues. Briefly, Data was stratified into ≥2f, ≥4f, ≥8f and into genes that were either not expressed in both isolates or not present on the genome level in both isolates. To exclude low abundant transcripts, a threshold of less than 3 reads per gene was used.
Assembly: NC_009641.1
Supplementary files format and content: processed data in txt files and csv

molecule: total RNA

organism: Staphylococcus aureus

source_name: Newman

growth_protocol: overnight in luria borth or luria broth + 100uM proline, subcultured and grown to OD1 ebfore extraction

extract_protocol:
Bacterial pellets were incubated in a cell wall lysis mixture TE buffer pH 8 (30 mMTris, 1mMEDTA, 15 mg/mL and 200μg/mL proteinase K) containing mutanolysin, lysostaphin and lysozyme at 37 °C for 30 minutes. TRK lysis buffer and 70% ethanol were added to each sample, prior to transferring to E.Z.N.A RNA isolation columns. RNA was isolated following the manufacturer’s instructions and DNA was selectively degraded using the DNA-free DNA removal kit.The RNA was precipitated with 0.1 volume 3 M sodium acetate (ThermoFisher #S209) and 3 volumes of 100% ethanol, recovered by centrifugation and washed with ice cold 70% ethanol. A ribosomal RNA-depleted cDNA library was prepared according to the manufacturer’s instructions using the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete kit (NuGEN #0363-32) and sequenced with Illumina HiSeq.
Raw base calls were converted to fatsq files using Bcl2fastqs. Filtered reads were aligned to the Newman (Refseq NC_009641.1) reference genome using STAR-Aligner v2.7.3a. The mapped reads were annotated for read groups and marked for duplicates using the Picard tools v2.22.3.

treatment_protocol: treatment of cohort B and D in 100uM proline

value: Newman

value: delta-adsA

tag: treatment

value: luria broth + proline


title: bacteria, OD1, subculture, ADSA R1

value: luria broth


title: PBMC DNA, Low Blood Pressure, N9


title: PBMC DNA, Low Blood Pressure, N10


title: bacteria, OD1, subculture,WT-Proline R2


title: PBMC DNA, Low Blood Pressure, N4


title: PBMC DNA, Low Blood Pressure, N2


title: C.jejuni + DOM-1, 48h, C4

city: Vienna

first: Wageha

middle: A.

last: Awad

address: Veterinarplatz 1/23

department: Department for Farm Animals and Veterinary Public Health

country: Austria

institute: University of Veterinary Medicine

data_processing:
The resulting reads were demultiplexed (Illumina bcl2fastq 2.17.1.14 software), trimmed, and further filtered for rRNA sequences using RiboPicker 0.4.3
Alignment of RNA-Seq reads was performed with Bowtie 2, and against the annotated genome of C. jejuni 81-176 (NC_008787.1) showing 98.41% homology with our C. jejuni strain NCTC 12744 (microbial nucleotide BLAST, database prok_complete_genomes, NCBI)
HTSeq was used for counting of TopHat-aligned reads, and gene expression levels were normalized as reads per kilobase of transcript per million mapped reads (RPKM)
Supplementary files format and content: excel file including RPKM values for each sample

organism: Campylobacter jejuni

growth_protocol: C. jejuni was incubated in 100 µl of Mueller-Hinton-Broth on 96-well plates under microaerophilic conditions over 48h and at 41.5°C

extract_protocol:
Total RNA extractions were conducted with the RNAsnap method
RNA sampleswere treated with DNase and rRNA depletion was performed using the MICROBExpressTM bacterial mRNA enrichment kit (ThermoFisher Scientific). The RNA-Seq libraries were pooled and sequenced on Illumina NextSeq 500/550 V2 with 75 bp single reads.

treatment_protocol: Plates were inoculated with DON (5µg/mL) or DOM-1 (5µg/mL) and/or C. jejuni and incubated under microaerophilic conditions over 48h and at 41.5°C

tag: strain

value: Deepoxy-deoxynivalenol

tag: time

value: 48 hours


title: C.jejuni + DON, 48h, B4

value: Deoxynivalenol


title: PBMC DNA, Low Blood Pressure, N1


title: bacteria, OD1, subculture, adsa-Proline R2


title: bacteria, OD1, subculture,WT-Proline R1


title: bacteria, OD1, subculture, ADSA R2


title: C.jejuni + DON, 30h, B2

value: 30 hours


title: C.jejuni + DON, 30h, B1


title: bacteria, OD1, subculture,WT R2


title: C.jejuni, 48h, control A5

value: no treatment


title: C.jejuni, 30h, control A2


title: bacteria, OD1, subculture, WT R1


title: C.jejuni + DOM-1, 48h, C6


title: C.jejuni + DOM-1, 30h, C3


title: C.jejuni + DOM-1, 48h, C5


title: C.jejuni + DOM-1, 30h, C2


title: C.jejuni + DOM-1, 30h, C1


title: C.jejuni + DON, 48h, B6


title: C.jejuni + DON, 48h, B5


title: C.jejuni, 48h, control A6


title: C.jejuni, 48h, control A8


title: TA_MutMTstress_Rep1

city: BETHESDA

first: Derek

middle: Paul

last: Narendra

state: MD

address: 35 CONVENT DR, Rm. 2A-211

institute: NINDS, NIH

description: TA_Analysis_Results_20240604_ancova_adjusted_expression.csv

data_processing:
In R, counts per gene were normalized by gene length first, followed by normalization for differences in sequencing depth, using the counts per million procedure. Normalized values were pedestalled by (+2) then Log2 transformed. Cross-sample normalization was then performed to correct for differences in expression of distribution spread and location, using the “cyclicloess” procedure. After inspection of results in boxplots, noise was modeled to identify and remove noise-biased genes. Values for each gene were subset per cohort and fit via lowess to produce trend lines for each experiment group, in order to determine the dynamic range. Noise-cutoffs were defined where the trends deviated from linearity. Expression values less than cut-off were floored to the cut-off and genes not having at least one sample greater than the cut-off were removed as noise-biased and non-informative. A similar procedure was used for those genes with expression with values higher than the ceiling cut-off. ~12,870 genes remained after noise floor and filter processing. ANOVA (Expression ~ Group + Sex) was applied to these followed by posthoc testing.
Assembly: GRCh38/hg38
Supplementary files format and content: comma separated values file (.csv), ANCOVA adjusted (for biological sex) expression

organism: Mus musculus

source_name: Tibialis anterior muscle

extract_protocol:
RNA was extracted using the using the Direct-zol RNA Miniprep Kit (Zymo, catalog R2051)
RNA libraries for RNA sequencing were prepped with the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads using the manufacturer's protocol.

value: Tibialis anterior muscle

value: Chchd10 G58R/+; Dele1+


title: TA_MutMTstress_Rep3


title: TA_Dele1neg_Rep2


title: TA_Dele1neg_Rep1


title: TA_Control_Rep2

value: Chchd10+/+; Dele1+


title: C.jejuni, 30h, control A4


title: C.jejuni, 30h, control A1


title: TA_Dele1neg_MutMTstress_Rep4

value: Chchd10 G58R/+; Dele1-/-


title: H_Dele1neg_MutMTstress_Rep6

description: H_Analysis_Results_20240604_ancova_adjusted_expression.csv

source_name: Heart

value: Heart


title: TA_Dele1neg_MutMTstress_Rep2


title: TA_Dele1neg_MutMTstress_Rep3


title: TA_Dele1neg_MutMTstress_Rep1


title: C.jejuni + DON, 30h, B3


title: H_Dele1neg_MutMTstress_Rep3


title: H_MutMTstress_Rep3


title: H_Dele1neg_Rep6


title: TA_MutMTstress_Rep4


title: H_MutMTstress_Rep2


title: TA_MutMTstress_Rep2


title: TA_Dele1neg_Rep4


title: C.jejuni, 48h, control A7


title: C.jejuni, 30h, control A3


title: TA_Control_Rep4


title: TA_Control_Rep3


title: H_Dele1neg_Rep4


title: H_Dele1neg_Rep2


title: H_Dele1neg_Rep1


title: H_Dele1neg_MutMTstress_Rep5


title: H_Dele1neg_Rep3


title: H_Dele1neg_MutMTstress_Rep2


title: H_Dele1neg_MutMTstress_Rep4


title: H_Control_Rep3


title: H_Dele1neg_MutMTstress_Rep1


title: H_MutMTstress_Rep5


title: H_MutMTstress_Rep4


title: H_MutMTstress_Rep1


title: TA_Control_Rep1


title: G_Dele1neg_MutMTstress_Rep6

description: G_Analysis_Results_20240604_ancova_adjusted_expression.csv

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle


title: H_Dele1neg_Rep5


title: G_MutMTstress_Rep3


title: H_Control_Rep5


title: H_Control_Rep4


title: H_Control_Rep6


title: H_Control_Rep2


title: G_MutMTstress_Rep1


title: G_Dele1neg_Rep5


title: G_Dele1neg_MutMTstress_Rep5


title: G_Dele1neg_MutMTstress_Rep4


title: H_Control_Rep1


title: G_Dele1neg_MutMTstress_Rep3


title: G_Dele1neg_MutMTstress_Rep2


title: G_Dele1neg_Rep2


title: G_Control_Rep5


title: G_Control_Rep4


title: G_MutMTstress_Rep5


title: G_MutMTstress_Rep6


title: G_Dele1neg_MutMTstress_Rep1


title: G_MutMTstress_Rep2


title: G_Control_Rep6


title: G_Control_Rep1


title: G_MutMTstress_Rep4


title: G_Dele1neg_Rep6


title: G_Dele1neg_Rep4


title: G_Dele1neg_Rep3


title: G_Dele1neg_Rep1


title: G_Control_Rep3


title: H_MutMTstress_Rep6


title: G_Control_Rep2


title: wt5_d21

city: St. Louis

first: Christina

last: Stallings

state: MO

address: 425 South Euclid ave

institute: Washington University in Saint Louis

data_processing:
Base calls and demultiplexing were performed using Illumina bcl2fast
Reads were aligned to Ensemble release 76 primary assembly with STAR 2.5.1a
Counts were obtained using Subread:featureCount and Salmon 0.8.2
Sequencing QC was performed using RSeQC 2.6.2
Assembly: GENCODE M3 (GRCm38.p3)
Supplementary files format and content: raw-delimeted text file includes raw counts for each sample

source_name: bone marrow

extract_protocol:
Cells were lysed using TRIzol reagent (Invitrogen) and RNA was isolated using a phenol/chloroform and isopropanol precipitation with high salt.
Library preparation conducted by the Washington University in St. Louis Genome Technology Access Center (GTAC).

value: bone marrow

value: WT

value: Mtb 21dpi


title: wt8_d21


title: wt4_d21


title: wt6_d21


title: wt1_d21


title: wt9_d21


title: wt3_naive

value: uninfected


title: wt3_d21


title: wt2_d21


title: wt1_naive


title: ko10_d21


title: ko9_d21


title: wt2_naive


title: ko5_d21


title: ko4_d21


title: ko7_d21


title: ko3_d21


title: ko8_d21


title: ko2_d21


title: ko6_d21


title: ko3_naive


title: ko1_d21


title: wt7_d21


title: ko1_naive


title: ko2_naive


title: Mouse testis TM4 Sertoli cells_control_rep2

city: Hubei

first: Cai

middle: Xia

last: Yang

address: Jingzhou

country: China

institute: yangtze Universty

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean Data were mapped to the reference genome using HISAT2. HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again--rna-strandness RF --dta–t–p 4.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

extract_protocol:
RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: control

value: Sertoli cell

tag: Sex

value: male


title: Mouse testis TM4 Sertoli cells_VC_rep3

value: valine


title: Mouse testis TM4 Sertoli cells_VC_rep2


title: Mouse testis TM4 Sertoli cells_VC_rep1


title: Cpt2_PKO_1

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S Russel St

department: Animal Sciences

institute: Purdue University

description:
mRNA
Cpt2_PKOvsWT_DEG.xlsx

data_processing:
The original raw data from Illumina HiSeq are transformed to sequenced reads by base calling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, then mapped to GRCm38/mm10 whole genome using TopHat2.
For the quantification of gene expression level, HTSeq V0.6.1 was used to analyze the read numbers mapped for each gene. The Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of each gene was calculated based on the gene read counts mapped to genes or exons.
A differential expression analysis was performed using the DESeq2 R/EdgeR R package with the threshold of significance set as adjusted p < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cpt2PKOvsWT_DEG.xlsx: Matrix table with raw gene counts and FPKM for every gene and every sample.

source_name: Muscle stem cell

extract_protocol:
mRNA from 1 ug of total RNA is enriched using oligo(dT) beads for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

tag: age

value: 2 months

value: Hind limb muscle stem cells


title: Cpt2_WT_2

description:
mRNA
Cpt2_PKOvsWT_DEG.xlsx


title: Mouse testis TM4 Sertoli cells_control_rep3


title: Cpt2_WT_1

description:
mRNA
Cpt2_PKOvsWT_DEG.xlsx


title: Mouse testis TM4 Sertoli cells_control_rep1


title: TA_Dele1neg_Rep3


title: Cpt2_PKO_2

description:
mRNA
Cpt2_PKOvsWT_DEG.xlsx


title: Sample 3B Infected EUK8 6 DPI

city: Philadelphia

first: Joseph

middle: W

last: Guarnieri

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hosptial of Philadelphia

description:
EUK8_IonCode_0128
EUK8_IonCode_0125-0132.xlsx

data_processing:
Sequencing data was aligned using the Ion Torrent S5 ampliSeqRNA and coverageAnalysis plugins.
Assembly: mm10
Supplementary files format and content: Excel files include raw counts for each sample

source_name: Lung

extract_protocol:
RNA was collected using TRIzol™ Reagent (Invitrogen, 15596026) from 5 infected and 3 uninfected hACE2 and hACE2-mCAT lung samples.
The RNA was assessed by NanoDrop spectrophotometer (ThermoFisher Scientific) and quantified by Qubit Flex (Thermofisher Scientific) using the Qubit RNA HS Assay Kit (Thermofisher Scientific, Q32855).
The RNA was diluted to 1.43 ng/ul and reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Cat. No. A45003). The RNA library was prepared using the Ion Torrent S5 Chef and Ion AmpliSeq Kit for Chef DL8 (Thermofisher Scientific, A29024) and sequenced using the Ion Torrent S5 Sequencer and Ion 540 Kit (Thermofisher Scientific, A30011).

treatment_protocol: RNA sequencing analysis on hACE2-transgenic (hACE2) and mitochondrial targeted catalase (mCAT)-transgenic hACE2 mice (hACE2-mCAT), intranasally infected with 2.5x10^4 PFU of the SARS-CoV-2 Washington Variant (WA1) or a mock-control.

value: Lung

value: C57BL6/J K18-hACE2

value: 2.5x10^4 PFU SARS-CoV-2 WA1

value: 4 DPI


title: Sample 4B Infected EUK8 6 DPI

description:
EUK8_IonCode_0130
EUK8_IonCode_0125-0132.xlsx


title: Sample 5B Infected EUK8 6 DPI

description:
EUK8_IonCode_0132
EUK8_IonCode_0125-0132.xlsx


title: Sample 5A Infected EUK8 6 DPI

description:
EUK8_IonCode_0131
EUK8_IonCode_0125-0132.xlsx


title: Sample 4A Infected EUK8 6 DPI

description:
EUK8_IonCode_0129
EUK8_IonCode_0125-0132.xlsx


title: Sample 2B Infected EUK8 6 DPI

description:
EUK8_IonCode_0126
EUK8_IonCode_0125-0132.xlsx


title: Sample 1B Infected EUK8 6 DPI

description:
EUK8_IonCode_0124
EUK8_IonCode_0117-0124.xlsx


title: Sample 3B Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0122
EUK8_IonCode_0117-0124.xlsx

value: 0 PFU SARS-CoV-2 WA1


title: Sample 1A Infected EUK8 6 DPI

description:
EUK8_IonCode_0123
EUK8_IonCode_0117-0124.xlsx


title: Sample 3A Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0121
EUK8_IonCode_0117-0124.xlsx


title: Sample 2A Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0119
EUK8_IonCode_0117-0124.xlsx


title: Sample 2B Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0120
EUK8_IonCode_0117-0124.xlsx


title: Sample 1B Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0118
EUK8_IonCode_0117-0124.xlsx


title: Sample 1A Uninfected EUK8 6 DPI

description:
EUK8_IonCode_0117
EUK8_IonCode_0117-0124.xlsx


title: Sample 5B Infected ddH20 6 DPI

description:
EUK8_IonCode_0116
EUK8_IonCode_0109-0116.xlsx

value: C57BL6/J K18-hACE2-mCAT


title: Sample 5A Infected ddH20 6 DPI

description:
EUK8_IonCode_0115
EUK8_IonCode_0109-0116.xlsx


title: Sample 4A Infected ddH20 6 DPI

description:
EUK8_IonCode_0113
EUK8_IonCode_0109-0116.xlsx


title: Sample 4B Infected ddH20 6 DPI

description:
EUK8_IonCode_0114
EUK8_IonCode_0109-0116.xlsx


title: Sample 3A Infected ddH20 6 DPI

description:
EUK8_IonCode_0111
EUK8_IonCode_0109-0116.xlsx


title: Sample 3B Infected ddH20 6 DPI

description:
EUK8_IonCode_0112
EUK8_IonCode_0109-0116.xlsx


title: Sample 2A Infected ddH20 6 DPI

description:
EUK8_IonCode_0109
EUK8_IonCode_0109-0116.xlsx


title: Sample 1B Infected ddH20 6 DPI

description:
EUK8_IonCode_0108
EUK8_IonCode_0101-0108.xlsx


title: Sample 1A Infected ddH20 6 DPI

description:
EUK8_IonCode_0107
EUK8_IonCode_0101-0108.xlsx


title: Sample 2B Infected ddH20 6 DPI

description:
EUK8_IonCode_0110
EUK8_IonCode_0109-0116.xlsx


title: Sample 3A Infected EUK8 6 DPI

description:
EUK8_IonCode_0127
EUK8_IonCode_0125-0132.xlsx


title: Sample 2A Infected EUK8 6 DPI

description:
EUK8_IonCode_0125
EUK8_IonCode_0125-0132.xlsx


title: Sample 3B Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0106
EUK8_IonCode_0101-0108.xlsx


title: Sample 2A Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0103
EUK8_IonCode_0101-0108.xlsx


title: Sample 3A Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0105
EUK8_IonCode_0101-0108.xlsx


title: Sample 1B Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0102
EUK8_IonCode_0101-0108.xlsx


title: Sample 2B Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0104
EUK8_IonCode_0101-0108.xlsx


title: Sample 1A Uninfected ddH20 6 DPI

description:
EUK8_IonCode_0101
EUK8_IonCode_0101-0108.xlsx


title: Sample 5A Infected hACE2 4 DPI

description:
IonCode_0107
IonCode_0101-0108.xlsx


title: Sample 5B Infected hACE2 4 DPI

description:
IonCode_0108
IonCode_0101-0108.xlsx


title: Sample 4B Infected hACE2 4 DPI

description:
IonCode_0106
IonCode_0101-0108.xlsx


title: Sample 4A Infected hACE2 4 DPI

description:
IonCode_0105
IonCode_0101-0108.xlsx


title: Sample 3B Infected hACE2 4 DPI

description:
IonCode_0104
IonCode_0101-0108.xlsx


title: Test-2

type: RNA

city: Bhubaneswar

first: Madhusmita

last: Panigrahy

state: Orissa

address: Siksha O Anusandhan University

country: India

institute: Government

description: Gene expression analysis from the carbon nanoparticle treated plant, flag leaves, replicate 2

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Oryza sativa

source_name: Oryza Sativa  (SWARNA (MTU7029)

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Rice plants were grown in 12 inch pots till 45 days. Carbon nanoparticle was given in the pot soil in 4 doses on 45th, 60th, 75th and 90th day of sowing, at a concentration 80mg/dose. After 4 treatements plants were left untreated for 1month before noting flowering time and reproductive data.

extract_protocol: Flag leaf were samples in the same light condition on the day of final emergence of the panicle from the main stem of the plant. Total RNA was extracted for genome-wide expression analysis using microarray.RNA was extracted from leaves using Qiagen RNAeasy Plant Mini kit (Cat#74904).

tag: cnp teratment

value: Treated with Carbon nanoparticle

tag: tissue sample

value: Flag leaves on the day of final emergence of the panicle


title: Tes-1

description: Gene expression analysis from the carbon nanoparticle treated plant, flag leaves, replicate 1


title: Sample 2B Infected hACE2 4 DPI

description:
IonCode_0102
IonCode_0101-0108.xlsx


title: Sample 2A Infected hACE2 4 DPI

description:
IonCode_0101
IonCode_0101-0108.xlsx


title: Control-2

description: Gene expression analysis from the untreated plant, flag leaves, replicate 2

value: Untreated


title: Sample 3A Infected hACE2 4 DPI

description:
IonCode_0103
IonCode_0101-0108.xlsx


title: Sample 3B Uninfected hACE2 4 DPI

description:
IonCode_0122
IonCode_0117-0124.xlsx


title: Sample 2B Uninfected hACE2 4 DPI

description:
IonCode_0120
IonCode_0117-0124.xlsx


title: Sample 2A Uninfected hACE2 4 DPI

description:
IonCode_0119
IonCode_0117-0124.xlsx


title: Sample 1A Infected hACE2 4 DPI

description:
IonCode_0123
IonCode_0117-0124.xlsx


title: Sample 1B Infected hACE2 4 DPI

description:
IonCode_0124
IonCode_0117-0124.xlsx


title: Sample 3A Uninfected hACE2 4 DPI

description:
IonCode_0121
IonCode_0117-0124.xlsx


title: Sample 1B Uninfected hACE2 4 DPI

description:
IonCode_0118
IonCode_0117-0124.xlsx


title: Sample 5A Infected mCAT 4 DPI

description:
IonCode_0115
IonCode_0109-0116.xlsx


title: Sample 4B Infected mCAT 4 DPI

description:
IonCode_0114
IonCode_0109-0116.xlsx


title: Sample 5B Infected mCAT 4 DPI

description:
IonCode_0116
IonCode_0109-0116.xlsx


title: Sample 1A Uninfected hACE2 4 DPI

description:
IonCode_0117
IonCode_0117-0124.xlsx


title: Sample 4A Infected mCAT 4 DPI

description:
IonCode_0113
IonCode_0109-0116.xlsx


title: Sample 1A Infected mCAT 4 DPI

description:
IonCode_0131
IonCode_0125-0132.xlsx


title: Sample 3B Infected mCAT 4 DPI

description:
IonCode_0112
IonCode_0109-0116.xlsx


title: Sample 2A Infected mCAT 4 DPI

description:
IonCode_0109
IonCode_0109-0116.xlsx


title: Sample 3A Infected mCAT 4 DPI

description:
IonCode_0111
IonCode_0109-0116.xlsx


title: Sample 2B Infected mCAT 4 DPI

description:
IonCode_0110
IonCode_0109-0116.xlsx


title: Sample 2B Uninfected mCAT 4 DPI

description:
IonCode_0128
IonCode_0125-0132.xlsx


title: Sample 3B Uninfected mCAT 4 DPI

description:
IonCode_0130
IonCode_0125-0132.xlsx


title: Sample 1B Uninfected mCAT 4 DPI

description:
IonCode_0126
IonCode_0125-0132.xlsx


title: Sample 1B Infected mCAT 4 DPI

description:
IonCode_0132
IonCode_0125-0132.xlsx


title: Sample 2A Uninfected mCAT 4 DPI

description:
IonCode_0127
IonCode_0125-0132.xlsx


title: Sample 1A Uninfected mCAT 4 DPI

description:
IonCode_0125
IonCode_0125-0132.xlsx


title: Control-1

description: Gene expression analysis from the untreated plant, flag leaves, replicate 1


title: CD3_008_V0

type: genomic

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

hyb_protocol: Bisulfite converted DNAs were amplified, fragmented, and hybridized to Inf MethylationEPIC Beadchips according to the standard Illumina HD Methylation Assay Protocol

scan_protocol: Arrays were imaged using an Illumina iScan with the Methylation NXT scan setting

data_processing: Average Beta values after quantile normalization with minfi

source_name: whole blood

label_protocol: Standard Illumina Infinium HD Methylation Assay Protocol

extract_protocol: CD3+ T cells were isolated from peripheral blood using anti-CD3 magnetic nanoparticles (Cat. No. 552593, BD Biosciences), DNA was isolated using QlAmp DNA Micro Kit (Cat No. 56304, QIAGEN). 250 ng DNA underwent bisulfite conversion using Zymo EZ DNA Methylation kit before hybridization to the Infinium MethylationEPIC BeadChip array

tag: gender

value: M

tag: height

tag: weight

value: No

tag: co


title: CD3_007_V6

value: Yes


title: CD3_015_V12

value: F


title: CD3_032_V12


title: CD3_005_V0


title: CD3_015_V6


title: CD3_026_V3


title: CD3_033_V0


title: CD3_036_V9


title: CD3_030_V9


title: CD3_012_V3


title: Sample 3A Uninfected mCAT 4 DPI

description:
IonCode_0129
IonCode_0125-0132.xlsx

tag: tissue


title: CD3_005_V6


title: CD3_033_V7


title: CD3_008_V6


title: CD3_018_V0


title: CD3_028_V0


title: CD3_002_V12


title: CD3_025_V3


title: CD3_024_V12


title: CD3_017_V12


title: CD3_030_V3


title: CD3_016_V6


title: CD3_022_V12


title: CD3_015_V3


title: CD3_029_V3


title: CD3_032_V0


title: CD3_035_V3


title: CD3_011_V0


title: CD3_006_V0


title: CD3_036_V6


title: CD3_013_V12


title: CD3_027_V12


title: CD3_032_V3


title: CD3_008_V9


title: CD3_004_V3


title: CD3_018_V6


title: CD3_006_V12


title: CD3_025_V0


title: CD3_022_V4


title: CD3_011_V3


title: CD3_022_V6


title: CD3_025_V6


title: CD3_001_V3


title: CD3_002_V9


title: CD3_001_V9


title: CD3_031_V0


title: CD3_035_V6


title: CD3_021_V12


title: CD3_016_V12


title: CD3_007_V0


title: CD3_037_V4


title: CD3_019_V6


title: CD3_004_V12


title: CD3_027_V6


title: CD3_013_V6


title: CD3_035_V0


title: CD3_032_V7


title: CD3_020_V6


title: CD3_012_V0


title: CD3_029_V12


title: CD3_019_V3


title: CD3_020_V3


title: CD3_027_V3


title: CD3_036_V4


title: CD3_024_V3


title: CD3_033_V9


title: CD3_019_V12


title: CD3_030_V0


title: CD3_002_V6


title: CD3_028_V6


title: CD3_013_V0


title: CD3_021_V9


title: CD3_027_V9


title: CD3_012_V12


title: CD3_011_V12


title: CD3_017_V6


title: CD3_025_V9


title: CD3_030_V12


title: CD3_034_V6


title: CD3_026_V0


title: CD3_008_V3


title: CD3_037_V0


title: CD3_024_V0


title: CD3_023_V0


title: CD3_025_V12


title: CD3_026_V6


title: CD3_005_V4


title: CD3_023_V3


title: CD3_022_V0


title: CD3_016_V3


title: CD3_001_V12


title: CD3_030_V6


title: CD3_011_V9


title: CD3_021_V6


title: CD3_001_V6


title: CD3_020_V9


title: CD3_015_V9


title: CD3_033_V3


title: CD3_028_V9


title: CD3_016_V9


title: CD3_010_V9


title: CD3_013_V9


title: CD3_013_V3


title: CD3_017_V0


title: CD3_023_V6


title: CD3_008_V12


title: CD3_006_V6


title: CD3_031_V3


title: CD3_004_V6


title: CD3_017_V9


title: CD3_007_V3


title: CD3_015_V0


title: CD3_028_V3


title: CD3_020_V0


title: CD3_037_V6


title: CD3_010_V12


title: CD3_032_V9


title: CD3_006_V9


title: CD3_024_V6


title: CD3_031_V9


title: CD3_021_V3


title: CD3_009_V3


title: CD3_029_V0


title: CD3_019_V0


title: CD3_034_V0


title: CD3_026_V9


title: Chr12_Q_R2

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

data_processing:
Start site counts generated from alignment files using a script.
Assembly: YPS1009
Supplementary files format and content: Matix Count tables, text file.
Library strategy: Ribosome profiling

organism: Saccharomyces cerevisiae YPS1009

growth_protocol: Strains used in the study are all haploids of the YPS1009 background. Cultures were started from colonies on YPD agar plates at a starting OD600 of 0.05, then grown in shake flasks at 30°C with shaking. Log-phase samples were harvested after 3 generations. Stationary phase samples were harvested 4 days from start of culturing. Cells were harvested by rapid vacuum filtration, scraped into eppendorf tubes, and immediately flash frozen in liquid N2, then stored at −80°C.

extract_protocol:
Ribosome profiling was performed commercially by EzraBio using Ezra-Seq method (PMID: 37957305).
Library construction was performed commercially by EzraBio using Ezra-Seq method (PMID: 37957305).

tag: genetic lineage

value: North American

value: day 4

tag: media

value: YPD

tag: stress

value: stationary phase


title: Euploid_Q_R2


title: Chr12_LOG_R2

value: log-phase


title: Euploid_LOG_R2


title: Chr12_Q_R1


title: Chr12_LOG_R1


title: CD3_007_V12


title: Euploid_LOG_R1


title: AGY1845_D7_R2

description: Gasch 1326

data_processing:
Trimmed reads with Trimmomatic 0.39
Reading mapping to YPS1009 genome with BWA mem (Version: 0.7.12-r1039)
Read counts calculated with HTSeq-count version 0.7.2
Assembly: YPS1009
Supplementary files format and content: raw HTSeq counts

source_name: Saccharomyces cerevisiae with Schizosaccharomyces pombe spike-in

growth_protocol: Strains used in the study are all haploids of the YPS1009 background. Cultures were started from colonies on YPD agar plates at a starting OD600 of 0.05, then grown in shake flasks at 30°C with shaking. Log-phase samples were harvested after 3 generations. Day 1, 3, and 7 samples were harvested 24, 72, and 168 hours, respectively, from start of culturing. Cells were harvested by centrifugation, flash frozen in liquid N2, and stored at −80°C.

extract_protocol:
RNA was extracted using hot acid-phenol RNA extraction, with the following modification for quiescent samples: 500uM glass beads were added to each sample and vortexed every 10' for 1' during the hot acid-phenol incubation.
rRNA depletion was performed using the Ribo-Zero (Yeast) rRNA Removal Kit (Illumina). Libraries were prepared with TruSeq Stranded Total RNA kit (illumina) and purified using a Axygen AxyPrep MAG PCR Clean-Up Kit (Axygen).

value: day 7


title: CD3_002_V3


title: Euploid_Q_R1


title: CD3_036_V0


title: AGY1845_D3_R2

description: Gasch 1325

value: day 3


title: AGY1845_D1_R2

description: Gasch 1324

value: day 1


title: AGY1845_LOG_R2

description: Gasch 1322


title: AGY1839_D1_R2

description: Gasch 1319


title: AGY1835_D7_R2

description: Gasch 1316


title: AGY1839_D3_R2

description: Gasch 1320


title: CD3_027_V0


title: AGY1835_D3_R2

description: Gasch 1315


title: AGY1839_D7_R2

description: Gasch 1321


title: AGY1835_D1_R2

description: Gasch 1314


title: AGY1839_LOG_R2

description: Gasch 1317


title: AGY1835_LOG_R2

description: Gasch 1312


title: AGY735_D1_R2

description: Gasch 1309


title: AGY735_LOG_R2

description: Gasch 1306


title: AGY731_D7_R2

description: Gasch 1305


title: AGY731_D3_R2

description: Gasch 1304


title: AGY731_LOG_R2

description: Gasch 1300


title: AGY731_D1_R2

description: Gasch 1303


title: AGY1845_D7_R1

description: Gasch 1299


title: AGY1845_D3_R1

description: Gasch 1298


title: AGY1845_LOG_R1

description: Gasch 1295


title: AGY1845_D1_R1

description: Gasch 1297


title: AGY1839_D7_R1

description: Gasch 1294


title: AGY1839_LOG_R1

description: Gasch 1290


title: AGY1835_D7_R1

description: Gasch 1289


title: AGY1839_D1_R1

description: Gasch 1292


title: AGY1839_D3_R1

description: Gasch 1293


title: AGY1835_D3_R1

description: Gasch 1288


title: AGY735_D7_R1

description: Gasch 1284


title: AGY1835_D1_R1

description: Gasch 1287


title: AGY731_D1_R1

description: Gasch 1276


title: AGY735_D3_R2

description: Gasch 1310


title: PN nonlesional 4812

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

library_source: transcriptomic single cell

data_processing:
Sequencing analysis was carried out using 10X Genomics’ CellRanger software. Fastq files were generated using the CellRanger mkfastq pipeline.
Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger count pipeline. The expression matrices from different samples were concatenated.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: skin

extract_protocol:
Generation of single-cell suspensions for scRNA-seq was performed as follows: Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies, Thermo Fisher Scientific, Waltham, Mass) in HBSS (Gibco, Thermo Fisher Scientific) at 4°C. The epidermis and dermis were separated. The epidermis was digested in 0.25% trypsin-EDTA (Gibco) with 10 U/mL DNase I (Thermo Fisher Scientific) for 1 hour at 37°C, quenched with FBS (R&D Systems [formerly Atlanta Biologicals], Bio-Techne, Minneapolis, Minn), and strained through a 70-μmol/L mesh. The dermis was minced, digested in 0.2% collagenase II (Life Technologies) and 0.2% collagenase V (Sigma-Aldrich, St Louis, Mo) in a plain medium for 1.5 hours at 37°C, and strained through a 70-μmol/L mesh. Epidermal and dermal cells were combined in a 1:1 ratio.
The libraries were constructed by the University of Michigan Advanced Genomics Core on the 10x Chromium system with chemistry (version 3; 10x Genomics, Pleasanton, Calif). Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer (Illumina Inc, San Diego, Calif) to generate 150-bp paired-end reads.

value: skin

tag: disease state

value: Prurigo nodularis nonlesional

tag: cell type

value: skin cells


title: AGY735_D7_R2

description: Gasch 1311

tag: strain

tag: time


title: AGY735_LOG_R1

description: Gasch 1279


title: AGY731_D7_R1

description: Gasch 1278


title: PN lesional 4630

value: Prurigo nodularis lesional


title: AGY731_D3_R1

description: Gasch 1277


title: PN lesional 4812


title: AGY731_LOG_R1

description: Gasch 1273


title: PN nonlesional 4546


title: PN nonlesional 4630


title: PN lesional 4546


title: PN nonlesional 4533


title: PN nonlesional 3734


title: PN lesional 4533


title: PN lesional 3734


title: PN nonlesional 3228


title: AGY735_D3_R1

description: Gasch 1283


title: AGY735_D1_R1

description: Gasch 1282


title: AGY1835_LOG_R1

description: Gasch 1285


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, DDX4+ iOLCs

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

data_processing:
Reads from our samples were aligned to the human reference genome (GRCh38) using STAR (version 2.7.6), to construct count matrices aligning sequencing reads to the known set of human genes. For samples with 2 x 150 bp reads, the STAR options --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 were used in order to keep the minimum match length equivalent between the different samples.
Assembly: hg38
Supplementary files format and content: Counts matrix (STAR aligner output)

growth_protocol: Human iPSCs were dissociated using Accutase and seeded onto Matrigel coated plates at a density of 50,000/cm2 in cold mTESR1 supplemented with 2% Cultrex (R&D Systems), 10 µM Y-27632, 5 µM GSK-3484862, and 1 µg/mL doxycycline. After 24 hours, cells were washed with RPMI and the medium was changed to aRB27 with 25 ng/mL hBMP4, 2% Cultrex, 5 µM GSK-3484862, and 1 µg/mL doxycycline. After 24 hours, the cells were fed with fresh medium. After 24 hours, the medium was changed to aRB27 with 50 ng/mL SCF, 50 ng/ml EGF, 10 ng/mL hLIF, 5 µM GSK-3484862, and 1 µg/mL doxycycline. After 24 hours, the cells were fed with fresh medium. After 24 hours, cells were harvested with Accutase for downstream analysis.

extract_protocol:
Qiagen Rneasy Plus micro kit
Cells were induced according to the above protocols and isolated for bulk RNA-sequencing. Library preparation was performed using the NEB Next ultra-low input RNA-sequencing library preparation kit with PolyA capture module for samples containing less than 10,000 cells. For samples with greater than 10,000 cells the NEBNext Ultra II RNA-sequencing library preparation kit with PolyA mRNA capture module was utilized. Sequencing was performed on Illumina Next-Seq 500 and NovaSeq platforms with 2 x 100bp or 2 x 150bp paired end reads, respectively. Only samples with RNA quality RIN scores of greater than 8 were utilized for analysis.

treatment_protocol: Two of the samples were processed using an alternate protocol which did not include DNMT1 inhibitor (GSK-3484862)

tag: cell line

value: DDX4+ induced oogonia-like cells

tag: genotype

value: DDX4-tdTomato / DAZL-mGreenLantern

tag: treatment


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, unsorted cells from iOLC induction

value: unsorted cells from oogonia-like cell induction


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, transient naive reset, DDX4+ iOLCs

value: DDX4-tdTomato / REC8-mGreenLantern


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, DDX4+ iOLCs, replicate 2


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, transient naive reset, DDX4+ iOLCs

value: DDX4-tdTomato / SYCP3-mGreenLantern


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, unsorted cells from iOLC induction


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+AR-V7, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, unsorted cells from iOLC induction


title: ATCC-BXS0115 DDX4-tdTomato/DAZL-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, transient naive reset, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+AR-V7, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, DDX4+ iOLCs, replicate 2


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+AR-V7+ANHX, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+AR-V7, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ANHX, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+ANHX, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+AR-V7, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1+AR-V7+ANHX, DDX4+ iOLCs


title: PN lesional 3228


title: ATCC-BXS0115 DDX4-tdTomato, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs

value: LHX8+ZNF281+SOHLH1, iOLC induction without DNMT1 inhibition


title: ATCC-BXS0116 DDX4-tdTomato/SYCP3-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1, DDX4+ iOLCs


title: PGP1 DDX4-tdTomato/REC8-mGreenLantern, LHX8+ZNF281+SOHLH1+ZGLP1, DDX4+ iOLCs


title: ATCC-BXS0116 DDX4-tdTomato, LHX8+ZNF281+SOHLH1, DDX4+ iOLCs


title: ATCC-BXS0116 hiPSC

value: hiPSC


title: 2795,SI-GA-A3

first: Samia

last: Ali

state: Massachusetts

address: 800 Washington Street

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: 10x Genomics, S4 Flow Cell

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, and matrix files

molecule: nuclear RNA

source_name: Septal Tissue

extract_protocol:
Cryopreserved tissue was thawed in a 37°C water bath for 75 seconds. Nuclei were released from the tissue via dounce homogenization using a buffer containing Triton X-100 (0.1 v/v). The homogenate was filtered through a 10µM cell strainer and nuclei were pelleted (500 x g for 5 minutes at 4°C) and washed before being resuspended in 1% w/v BSA, 1X PBS, and  0.2 U/µL RNase inhibitor
Library was constructed according to manufacturers instructions (single cell 3' v3.1, 10x Genomics).

value: Septal Tissue

value: Heart Tissue

value: POS


title: ATCC-BXS0115 hiPSC


title: GTC259-G2-HepG2_NR1H3_2021_15

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
STAR 2.5.0a was used to map and perform gene level count against GRCh38/Ensembl 104
Assembly: GRCh38
Supplementary files format and content: Raw read count in tab-delimited format

extract_protocol:
Direct-zol RNA Miniprep Kit (Zymo Research)
RNA-Seq libraries were prepared using the TruSeq RNA CD Indexes and the Illumina Standard mRNA Prep kit according to Illumina protocol. Multiplexed libraries were validated using the Agilent TapeStation system, normalised and pooled for sequencing.

value: DN

value: Vehicle-Dox


title: GTC259-C3-HepG2_NR1H3_2021_19

value: WT


title: GTC259-C2-HepG2_NR1H3_2021_11


title: GTC259-F3-HepG2_NR1H3_2021_22


title: GTC259-F2-HepG2_NR1H3_2021_14


title: GTC259-H3-HepG2_NR1H3_2021_24


title: GTC259-G3-HepG2_NR1H3_2021_23


title: GTC259-H2-HepG2_NR1H3_2021_16


title: GTC259-A3-HepG2_NR1H3_2021_17

value: Vehicle-DMSO


title: GTC259-E3-HepG2_NR1H3_2021_21


title: GTC259-D3-HepG2_NR1H3_2021_20


title: GTC259-A2-HepG2_NR1H3_2021_9


title: GTC259-G1-HepG2_NR1H3_2021_7


title: GTC259-H1-HepG2_NR1H3_2021_8


title: GTC259-E1-HepG2_NR1H3_2021_5


title: GTC259-E2-HepG2_NR1H3_2021_13


title: GTC259-B2-HepG2_NR1H3_2021_10


title: GTC259-D1-HepG2_NR1H3_2021_4


title: GTC259-F1-HepG2_NR1H3_2021_6


title: GTC259-D2-HepG2_NR1H3_2021_12


title: GTC259-C1-HepG2_NR1H3_2021_3


title: GTC259-B1-HepG2_NR1H3_2021_2


title: GTC259-A1-HepG2_NR1H3_2021_1


title: Collagen 1 and DDR1i Treated (4)

first: Colin

last: Trepicchio

address: 136 Harrison Ave

department: GSBS

institute: Tufts University

data_processing:
Read Alignment to the human genome was performed using STAR (Dobin et al., 2013)
Assembly: CRCh37/hg19 assembly
Supplementary files format and content: CSV file containing the the raw counts of all samples
Supplementary files format and content: .XLSX file containing all extracted data from each of the individual samples fastq file

source_name: Breast

growth_protocol: MCF10A Cells were maintained in DMEM/F12 Media containing   10 μg/mL insulin, 20 ng/mL hEGF, 500 ng/mL hydrocortisone, 100 ng/mL cholera toxin, 5% Horse Serum, and 1x Antibiotic/antimitotic in incubator at 37C and 5% CO2

extract_protocol:
RNA was harvested using Rneasy minikit
Standard Illumina Primer Library used

treatment_protocol: Cells were seeded at a density of 1e6 cells in a 10 cm plate and were treated with DMSO or inhibitor for 24 hours. At this point media was removed and replaced with a media containing 0.05mg/mL collagen and NaOH for polymerization, as well as DMSO or inhibitor. Control received two normal media changes and no collagen.

value: Breast

value: Epithelial Cell

value: Diploid

value: Collagen 1 + DDR1i


title: Collagen 1 Treated (4)

value: Collagen 1 + DMSO


title: Collagen 1 and RUNXi Treated (4)

value: Collagen 1 + RUNXi


title: Control (4)

value: DMSO


title: Collagen 1 and RUNXi Treated (3)


title: GTC259-B3-HepG2_NR1H3_2021_18


title: Collagen 1 and DDR1i Treated (3)


title: Collagen 1 and DDR1i Treated (2)


title: Collagen 1 Treated (3)


title: Collagen 1 and RUNXi Treated (2)


title: Collagen 1 Treated (1)


title: Control (3)


title: Control (1)


title: Control (2)


title: Collagen 1 Treated (2)


title: Collagen 1 and RUNXi Treated (1)


title: Collagen 1 and DDR1i Treated (1)


title: Pool3Supermere2

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Reads were processed using the TIGER informatics pipeline doi: 10.1080/20013078.2018.1506198
Reads were trimmed to remove adapter sequences with Cutadapt v2.10
Reads were aligned to GRCh38 using Bowtie1 v1.3.1
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: Colorectal cancer

extract_protocol:
Total small RNA was extracted fromextracellular samples using the miRNeasy kit (QIAGEN, 217004) according to the manufacturer’s protocol.
Total RNA from each sample was taken into small RNA library preparation protocol using NEXTflex® Small RNA-Seq Kit (Bioo Scientific, PerkinElmer) according to manufacturer’s protocol.

value: Colorectal cancer

value: DiFi


title: Pool3Supermere3


title: Pool3Media1


title: Pool3Media2


title: Pool2Exomere2


title: Pool2Media3


title: Pool2Exomere1


title: Pool1Media2


title: Pool1Media1


title: Regular_Media


title: Unfiltered_HF7_HDM


title: HF7_Plate_2_Cells


title: Unfiltered_HF6_HDM


title: Pool1Exomere1


title: Pool1Exomere3


title: Pool1Exomere2


title: HF7_Plate_3_Cells


title: Pool2Media1


title: HF6_Plate_3_Cells


title: Pool2Media2


title: Pool2Exomere3


title: HF7_Cell_Pellet


title: HF7_Plate_1_Cells


title: HF6_Plate_2_Cells


title: Filtered_HF7_HDM


title: HF6_Plate_1_Cells


title: HF6_Cell_Pellet


title: Filtered_HF6_HDM


title: HDM_Media


title: HDM_Media_noCells


title: GBM39 cells, Sup4

source_name: Brain

extract_protocol:
Total small RNA was extracted fromextracellular samples using the miRNeasy kit (QIAGEN, 217004) according to the manufacturer’s protocol.
Total RNA from each sample was taken into small RNA library preparation protocol using NEXTflex® Small RNA-Seq Kit (Bioo Scientific, PerkinElmer) according to manufacturer’s protocol.
smallRNA-Seq

value: Brain

tag: group

value: Sup


title: GBM39 cells, Exo4

value: Exo


title: GBM39 cells, Sup1


title: GBM39 cells, SmallEV4

value: SmallEV


title: GBM39 cells, Exo1


title: GBM39 cells, Sup2


title: GBM39 cells, Exo2


title: GBM39 cells, Exo3


title: GBM39 cells, Sup3


title: GBM39 cells, SmallEV3


title: GBM39 cells, LargeEV1

value: LargeEV


title: GBM39 cells, Control1

value: Control


title: GBM39 cells, Control3


title: GBM39 cells, Control2


title: GBM39 cells, LargeEV3


title: GBM39 cells, Control4


title: GBM39 cells, SmallEV2


title: Sample_28

city: Indianapolis

first: Ashiq

last: Masood

address: Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine

department: Hematology & Oncology

institute: IU School Of Medicine

description: FFPE Spatial Transcriptome Sequencing

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed using 10X genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to human reference genome (GRCh38) using Space Ranger's default settings
Gene expression level of RefSeq genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv : file in CSV format that contains table of Moran's I values for each feature when specific conditions are met
Supplementary files format and content: tissue_hires_image.png: high-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: tissue_positions.csv : list of spatial barcodes and the co-ordinates specfying spots

source_name: Lymph node

extract_protocol:
Visium spatial gene expression data for FFPE tissue were obtained following the protocols CG000408, CG000409, and CG000407 provided by 10X Genomics for tissue preparation and library construction. The tissues were then deparaffinized, stained, and decrosslinked.
Human whole transcriptome probe panels were added to the deparaffinized, stained, and decrosslinked tissues. After hybridization, the probes were ligated, and the ligation products were released from the tissue upon RNase treatment and permeabilization. The ligated probe products were captured by spatially barcoded oligonucleotides, and the probes were extended. Libraries were generated from the extended probes. The quantity and quality of each resulting library were assessed with a Qubit and Agilent TapeStation. The final libraries were sequenced on Illumina NovaSeq 6000 28-bp reads, including spatial barcode and UMI sequences, and 50-bp probe reads were generated

value: Lymph node

tag: tissue/specimen type

value: Lymph node(LN)


title: Sample_26

description: FFPE Spatial Transcriptome Sequencing

source_name: Pancreas

value: Pancreas

value: Normal Pancreas


title: Sample_23

description: FFPE Spatial Transcriptome Sequencing

value: Primary Tumor (PT)


title: Sample_22

description: FFPE Spatial Transcriptome Sequencing


title: Sample_27

description: FFPE Spatial Transcriptome Sequencing

source_name: Liver

value: Liver

value: Hepatic Mets (HM)


title: Sample_25

description: FFPE Spatial Transcriptome Sequencing


title: Sample_21

description: FFPE Spatial Transcriptome Sequencing


title: Sample_24

description: FFPE Spatial Transcriptome Sequencing


title: Sample_30

description: FFPE Spatial Transcriptome Sequencing


title: Sample_18

description: FFPE Spatial Transcriptome Sequencing


title: Sample_19

description: FFPE Spatial Transcriptome Sequencing


title: Sample_13

description: FFPE Spatial Transcriptome Sequencing


title: Sample_9

description: FFPE Spatial Transcriptome Sequencing


title: Sample_12

description: FFPE Spatial Transcriptome Sequencing


title: Sample_17

description: FFPE Spatial Transcriptome Sequencing


title: Sample_15

description: FFPE Spatial Transcriptome Sequencing


title: Sample_11

description: FFPE Spatial Transcriptome Sequencing


title: Sample_10

description: FFPE Spatial Transcriptome Sequencing


title: Sample_29

description: FFPE Spatial Transcriptome Sequencing


title: Sample_16

description: FFPE Spatial Transcriptome Sequencing


title: Sample_8

description: FFPE Spatial Transcriptome Sequencing


title: Sample_14

description: FFPE Spatial Transcriptome Sequencing


title: Sample_2

description: FFPE Spatial Transcriptome Sequencing


title: Sample_3

description: FFPE Spatial Transcriptome Sequencing


title: Sample_7

description: FFPE Spatial Transcriptome Sequencing


title: Sample_4

description: FFPE Spatial Transcriptome Sequencing


title: Sample_6

description: FFPE Spatial Transcriptome Sequencing


title: Sample_1

description: FFPE Spatial Transcriptome Sequencing


title: Sample_5

description: FFPE Spatial Transcriptome Sequencing


title: Sample_20

description: FFPE Spatial Transcriptome Sequencing


title: DSS5, scRNAseq

city: Shanghai

first: Yulong

last: Tang

state: --- Select One ---

address: Songhu Road 2005

institute: Fudan University

description: 10X Genomics

data_processing:
The gene-barcode matrices were generated using the Cell Ranger toolkit (version 3.1), aligning sequences to the GRCh38 human reference genome and counting unique molecular identifiers (UMIs) for each cell. Quality control and downstream analysis employed the R package Seurat (version 3.1.4). Initially, cells with mitochondrial gene counts exceeding 10% and UMIs < 500 or > 5000 were filtered. Potential doublets were identified and removed using the R package DoubletFinder (version 2.0) with default settings. Subsequently, we normalized feature expression for each cell using “LogNormalize” and log-transformed the results with the NormalizeData() function. Batch effects were corrected utilizing the R package Harmony (version 0.1.1). The scaled and batch effect-corrected expression profiles of all samples were utilized for subsequent analyses.
Assembly: hg38
Supplementary files format and content: rds files containing QC processed dataset

source_name: degenerative ligament

extract_protocol:
Tissue samples, including bone (spinous process, facet, and lamina) and ligaments (ligamentum flavum, interspinous ligament, and supraspinal ligament) from Homo Sapiens were obtained during spinal canal decompression surgery. They were then sorted by Fluorescence-activated cell sorting using BD FACS Aria III (BD Biosciences) into CD45+ and CD45-, followed by applying CD45+ and CD45- cells at 3:7 ratio to the 10X Genomics system.
Library preparation utilized Gel Bead Kit V3 (10X Genomics, Pleasanton, CA) following standard protocols. The resulting single-cell libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing mode under default settings.

value: degenerative ligament

value: Primary ligament cell

value: Surgery


title: HEK293T_RNAseq_LINC00662_ASO_rep2

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

description:
HEK293T_LINC00662_ASO_rep2
HEK293T_ASO_RNAseq_samples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19/mm10 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HCT116 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in NIH3T3 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in Neuro-2a cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HEK293T cells
Supplementary files format and content: tab-delimited text file include ASO_RNA-seq three biological replicates raw counts for each sample in HEK293T cells

growth_protocol: Plate cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the Smart-seq protocol.

treatment_protocol: Cells were changed the medium to fresh medium containing 500 µM biotin-aniline and incubate at 37℃ under 5% CO2 for 30 min. Then, H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min.

value: Human embryonic kidney


title: DSS1, scRNAseq

description: 10X Genomics


title: HEK293T_RNAseq_LINC00662_ASO_rep3

description:
HEK293T_LINC00662_ASO_rep3
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HC3, scRNAseq

description: 10X Genomics

source_name: traumatic ligament

value: traumatic ligament


title: HC2, scRNAseq

description: 10X Genomics


title: HC1, scRNAseq

description: 10X Genomics


title: DSS6, scRNAseq

description: 10X Genomics


title: DSS2, scRNAseq

description: 10X Genomics


title: DSS4, scRNAseq

description: 10X Genomics


title: HEK293T_RNAseq_LINC00662_ASO_rep1

description:
HEK293T_LINC00662_ASO_rep1
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_SETD5-AS1_ASO_rep3

description:
HEK293T_SETD5_AS1_ASO_rep3
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_SETD5-AS1_ASO_rep2

description:
HEK293T_SETD5_AS1_ASO_rep2
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_SETD5-AS1_ASO_rep1

description:
HEK293T_SETD5_AS1_ASO_rep1
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_LINC00641_ASO_rep3

description:
HEK293T_LINC00641_ASO_rep3
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_LINC00641_ASO_rep2

description:
HEK293T_LINC00641_ASO_rep2
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_NC_ASO_rep2

description:
HEK293T_NC_ASO_rep2
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_NC_ASO_rep1

description:
HEK293T_NC_ASO_rep1
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HEK293T_RNAseq_NC_ASO_rep3

description:
HEK293T_NC_ASO_rep3
HEK293T_ASO_RNAseq_samples_raw_counts.txt


title: HCT116_Chromseq_TAF3_rep2

description:
HCT116_TAF3_APEX2_rep2
HCT116_Chromseq_samples_raw_counts.txt

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19/mm10 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19/mm10
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HCT116 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in NIH3T3 cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in Neuro-2a cells
Supplementary files format and content: tab-delimited text file include Chrom-seq three biological replicates raw counts for each sample in HEK293T cells
Supplementary files format and content: tab-delimited text file include ASO_RNA-seq three biological replicates raw counts for each sample in HEK293T cells
Library strategy: Chrom-seq

value: Human colorectal cancer


title: HCT116_Chromseq_Control_rep3

description:
HCT116_Control_APEX2_rep3
HCT116_Chromseq_samples_raw_counts.txt


title: DSS3, scRNAseq

description: 10X Genomics


title: HEK293T_Chromseq_CBX1_W42A_rep3

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file include Chromseq three biological replicates raw counts for each sample

growth_protocol: Plate HEK293T cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.


title: p53 wild-type THP-1 cells

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

description: wild type p53

data_processing:
Raw sequence reads were initially processed using fqC (Babraham Institute, Cambridge, UK) for quality control, then adapter sequences and poor-quality reads were removed using Cutadapt. Quality-filtered reads were then mapped to the human genome using the Salmon (version 1.10.0) (Patro et al., 2017) software, and only uniquely mapped reads were kept.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

growth_protocol: TH-1 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
Total RNA was isolated using total RNA Purification Kit (B518651, Sangon Biotech). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells expressing p53-R282W were treated with indicated compound for 24 h.

value: Myeloid malignant cell line

value: wt


title: HCT116_Chromseq_TAF3_rep3

description:
HCT116_TAF3_APEX2_rep3
HCT116_Chromseq_samples_raw_counts.txt


title: HCT116_Chromseq_Control_rep2

description:
HCT116_Control_APEX2_rep2
HCT116_Chromseq_samples_raw_counts.txt


title: p53 R282W THP-1 cells treated with ATO (1 μg/ml )+DAC (5 μM) for 24 h

institute: Shanghai Jiao Tong University School of Medicine

description: D+A

value: ATO (1 ug/ml )+DAC (5 uM) for 24 h


title: p53 R282W THP-1 cells treated with DMSO for 24 h

description: Ctr

value: DMSO for 24 h


title: p53 R282W THP-1 cells treated with 1 μg/ml ATO for 24 h

description: ATO

value: 1 ug/ml ATO for 24 h


title: cta-seq_ultra-deep

first: Martin

last: Fahrenberger

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Structural and Computational Biology

institute: Max Perutz Labs

description: 10x Genomics Chromium Single Cell 3' v3

data_processing:
Dempultiplexed read-data was processed using CellRanger 7.1.0 to gain scRNA-seq count-matrices.
For the ultra-deep data CellRanger's UMI correction was not sufficient, UMIs were therefore corrected using a custom R-Scrip and counted again  (see publication).
Assembly: GRCh38
Supplementary files format and content: .csv files: raw count-matrices
Supplementary files format and content: .zip files: CellRanger output folders
Supplementary files format and content: .txt file: ultra-deep read summary table for custom UMI correction
Supplementary files format and content: .RDS file: corrected count matrix for ultra-deep cta-seq data

source_name: cerebral-organoid

growth_protocol: We sequenced a leftover cDNA library from a previously published study, for a detailed discription of this study refer to DOI: 10.1126/science.abf5546

extract_protocol:
refer to DOI: 10.1126/science.abf5546
cDNA from previous experiment was prepared for sequencing using 10X Dual Index Kit TT

treatment_protocol: refer to DOI: 10.1126/science.abf5546

value: cerebral-organoid

value: patient pbmcs


title: pt#3, pre

description: 10x Genomics

data_processing:
The CellRanger (10x Genomics, default settings, Version 6.0.2) pipelines were used to process Chromium single-cell data to align reads, generate feature-barcode matrices.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: PBMCs

extract_protocol:
Cellular suspensions were copartitioned with barcoded gel beads to generate single-cell gel bead-in-emulsion (GEM) and poly-adenylated transcripts were reverse-transcribed using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1
RNA libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the standard manufacturer’s protocol (PN-1000121, 10x Genomics)

treatment_protocol: Patients received co-treatment with one cycles of DAC (20 mg/m²/day) and ATO (0.16 mg/kg/day), administered for 5 consecutive days.

value: PBMCs

tag: Sex

value: Female

tag: age

value: 59 years old


title: pt#3, post

description: 10x Genomics

value: ATO+DAC


title: pt#1, post

description: 10x Genomics

value: 57 years old


title: pt#1, pre

description: 10x Genomics


title: HCT116_Chromseq_TAF3_rep1

description:
HCT116_TAF3_APEX2_rep1
HCT116_Chromseq_samples_raw_counts.txt


title: AssayD_Batch 1_Tat+_IP2,SupT1 cells,anti-FLAG,HIV

city: Gent

first: Wim

last: Trypsteen

state: East-Flanders

address: Corneel Heymanslaan 10

department: Internal Medicine

country: Belgium

institute: UGent

data_processing:
high performance computing RNAseq analysis pipeline
QC via FASTQC 0..11.8, bad read removal (min quality phred score >20) and adapter trimming (cutadap 3.4)
read mapping via STAR 2.6.0
count tables generated via HTSeq 0.11.0
count table normalization via deseq2
Assembly: hg38/enbsembl v91
Supplementary files format and content: tab-delimited text files including raw count tables

source_name: SupT1 cells

growth_protocol: Trex cell lines were cultured in RPMI (Gibco) , supplemented with 10% FCS (HyClone), Pen/Strep, sodium-pyruvate (1 mM; Gibco), HEPES (15 mM; Gibco), Blasticidine (10 µg/mL; InvivoGen), Zeocin (300 µg/mL; InvivoGen), at 5% CO2 and 37°C

extract_protocol:
miRNEasy micro kit (Qiagen) with on-column RNAse free DNAse set (Qiagen)
Total RNA library preparation was performed using the SMARTer Stranded Total RNA-Seq Mamalian Pico v2 Kit (Takara) using the manufacturer’s instructions with 8 µL RNA input, 4 min fragmentation and 16 PCR2 cycles.

treatment_protocol: Doxycyline induction was performed either constitutively or with 1 µg/mL for 16h

value: SupT1 cells

value: T cell line

value: Doxycycline constitutive

tag: treatment doxycyline

value: no

tag: treatment rip_antibody

value: anti-FLAG

tag: treatment infection

value: VSV-G pseudotyped NL4.3 HSA-IRES-Nef dEnv

tag: treatment infection_time


title: AssayD_Batch 1_GFP+_IP1,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_GFP+_IP2,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_Tat+_IgG2,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_Tat+_IP3,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_Tat+_IgG1,SupT1 cells,anti-FLAG,HIV


title: HCT116_Chromseq_Control_rep1

description:
HCT116_Control_APEX2_rep1
HCT116_Chromseq_samples_raw_counts.txt

value: Human colorectal cancer


title: AssayD_Batch 1_Tat+_IP1,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_NC+_IgG2,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_NC+_IgG3,SupT1 cells,anti-FLAG,HIV


title: HEK293T_Chromseq_CBX1_W42A_rep1

value: Human embryonic kidney


title: HEK293T_Chromseq_CBX1_W42A_rep2


title: AssayD_Batch 1_NC+_IgG1,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_NC+_IP3,SupT1 cells,anti-FLAG,HIV


title: p53 R282W THP-1 cells treated with 5 μM DAC for 24 h

description: DAC

value: Myeloid malignant cell line

value: 5 uM DAC for 24 h


title: AssayD_Batch 1_NC+_IP2,SupT1 cells,anti-FLAG,HIV


title: cta-seq_typical

city: Vienna

description: 10x Genomics Chromium Single Cell 3' v3

tag: tissue

value: cerebral-organoid


title: AssayD_Batch 1_NC+_IP1,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_MA+_IgG3,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_MA+_IgG2,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_MA+_IP3,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_MA+_IP1,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_GFP+_IP3,SupT1 cells,anti-FLAG,HIV


title: AssayC_Batch 1_GFP_IP3,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_GFP_IP1,SupT1 cells,anti-FLAG


title: AssayD_Batch 1_MA+_IP2,SupT1 cells,anti-FLAG,HIV


title: AssayD_Batch 1_Tat+_IgG3,SupT1 cells,anti-FLAG,HIV


title: AssayC_Batch 1_GFP_IP2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_Tat_IgG3,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_NC_IgG3,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_MA_IgG2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_NC_IP1,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_NC_IP2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_NC_IgG2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_NC_IP3,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_MA_IgG3,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_MA_IgG1,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_MA_IP3,SupT1 cells,anti-FLAG


title: AssayD_Batch 1_MA+_IgG1,SupT1 cells,anti-FLAG,HIV


title: AssayC_Batch 1_MA_IP2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_MA_IP1,SupT1 cells,anti-FLAG


title: AssayB_Batch 2_GFP2_STRIP3,Jurkat Trex cells,anti-STREP

source_name: Jurkat Trex cells

value: Jurkat Trex cells

value: Doxycyline inducible

value: yes

tag: treatment doxycyline_time

value: anti-STREP


title: AssayB_Batch 2_GFP2_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_GFP2_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Gag_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Gag_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Gag_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayC_Batch 1_Tat_IP3,SupT1 cells,anti-FLAG


title: AssayB_Batch 1_NC_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Gag_UC2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Gag_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayC_Batch 1_Tat_IgG2,SupT1 cells,anti-FLAG


title: AssayB_Batch 2_Gag_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_NC_UC2,Jurkat Trex cells,anti-STREP


title: AssayC_Batch 1_Tat_IP1,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_Tat_IP2,SupT1 cells,anti-FLAG


title: AssayC_Batch 1_Tat_IgG1,SupT1 cells,anti-FLAG


title: AssayB_Batch 1_NC_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayC_Batch 1_NC_IgG1,SupT1 cells,anti-FLAG


title: AssayB_Batch 2_Pol_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Pol_UC2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_NC_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_NC_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Pol_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_NC_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Pol_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Pol_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_GFP1_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_GFP1_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Pol_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_GFP1_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_Rev_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_Rev_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_Rev_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_Rev_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_UC2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 1_MA_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_UC1,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_UC2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_UC3,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_STRIP2,Jurkat Trex cells,anti-STREP


title: AssayB_Batch 2_Tat_STRIP1,Jurkat Trex cells,anti-STREP


title: AssayA_Batch 6_GFP6_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayB_Batch 1_Rev_UC2,Jurkat Trex cells,anti-STREP


title: AssayA_Batch 6_GFP6_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_GFP6_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_NC_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_Vif_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_Vif_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayB_Batch 1_Rev_STRIP3,Jurkat Trex cells,anti-STREP


title: AssayA_Batch 6_Vif_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_Vif_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_Vif_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_GFP5_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_GFP5_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 6_Vif_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_GFP5_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_RT_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_GFP4_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_IN_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_GFP4_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_MA_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_Gag_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_Pol_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_MA_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_MA_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_GFP3_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_MA_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_GFP3_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 5_PR_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_GFP4_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_GFP3_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 4_MA_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GFP2_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_p6_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GFP2_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GFP2_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Nef_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 3_Vpr_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_GP120_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GFP1_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_CA_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GFP1_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_Rev_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP41_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GFP1_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP41_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 2_Vpu_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP41_IP1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP41_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IgG3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IgG2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IgG1,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IP3,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IP2,Jurkat Trex cells,anti-FLAG


title: AssayA_Batch 1_GP160_IP1,Jurkat Trex cells,anti-FLAG


title: MOLM13, 5uM DB2115, 1hr PRO-seq rep1

city: Bronx

first: Samuel

middle: John

last: Taylor

address: 1300 Morris Park Ave, Chanin building 601

institute: Albert Einstein College of Medicine

description: MOLM13 1hr DB

data_processing:
library strategy: PRO-seq
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner
Nascent RNA Sequencing Analysis Pipeline was used to determine gene body changes of transcription
Assembly: hg38
Supplementary files format and content: bedgraph of positive and negative sense RNA nascent transcripts

source_name: hematopoietic

growth_protocol: Cells were maintained in 10% FBS, 1% Pen Strep, RPMI media

extract_protocol:
PRO-seq was performed in two biological replicates as previously described using approximately 20 million nuclei per run on with GTP, ATP, UTP, and biotin-11-CTP (PerkinElmer) using 0.5% Sarkosyl (Fisher Scientific) to prevent transcription initiation.
RNA was reversed transcribed and amplified to make the cDNA library for sequencing by the Vanderbilt University Medical Center (VUMC) VANTAGE Genome Sciences Shared Resource on an Illumina NovaSeq 6000 (PE-150, 50 million reads).

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB2115, or Vehicle (0.001% DMSO) for 1-12hrs

value: hematopoietic

value: Acute myeloid leukemia

tag: molecule type

value: Nascent RNA


title: MOLM13, 5uM DB2115, 4hr PRO-seq rep2

description: MOLM13 4hr DB

tag: cell type


title: MOLM13, 5uM DB2115, 4hr PRO-seq rep1

description: MOLM13 4hr DB


title: MOLM13, 5uM DB2115, 12hr PRO-seq rep2

description: MOLM13 12hr DB


title: MOLM13, 5uM DB2115, 12hr PRO-seq rep1

description: MOLM13 12hr DB


title: MOLM13, 5uM DB2115, 1hr PRO-seq rep2

description: MOLM13 1hr DB


title: MOLM13, VEH, 12hr PRO-seq rep2

description: MOLM13 0hr

value: VEH


title: PDLSCs_Control_3

city: Jinan

first: Qiaohui

last: Ying

state: Shandong

address: No.44-1 Wenhua Road West, 250012, Jinan, Shandong, China

department: Department of Orthodontics

institute: Shandong University

data_processing:
To ensure the quality and reliability of data analysis, it is necessary to filter the raw data. This includes removing reads with adapters, removing reads containing 'N' (where 'N' indicates bases that cannot be determined), and removing low-quality reads (reads where bases with a Qphred score of ＜=5 account for more than 50% of the read length). Additionally, the clean data will be assessed for Q20, Q30, and GC content.
Download the reference genome and gene model annotation files directly from the genome website. Use HISAT2 v2.0.5 to build indices for the reference genome, and align the paired-end clean reads to the reference genome using HISAT2 v2.0.5.
FeatureCounts (version 1.5.0-p3) is used to count the reads mapped to each gene. Subsequently, the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene is calculated based on the gene's length, along with the count of reads mapped to that gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

source_name: Periodontal ligament

extract_protocol:
RNA was purified from total RNA using poly-T oligo-attached magnetic beads. 1 μg of total RNA was used for the construction of sequencing libraries.
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeg PE Cluster Kit v3-cBot-HS (llumia),according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an lllumina Novaseg platform and 150 bp paired-end reads were generated.

value: Periodontal ligament

value: PDLSCs

value: Mesenchymal stem cells

value: WT


title: AssayA_Batch 1_GP41_IgG1,Jurkat Trex cells,anti-FLAG

value: T cell line

value: anti-FLAG

value: no


title: MCF7 cells, Control

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
The purity, concentration and integrity of RNA samples are tested using advanced molecular biology equipment to ensure the use of qualified samples for transcriptome sequencing.
Briefly, First of all, ligated the 3′ SR and 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 18 nt or longer than 30 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase. Randfold tools soft was used for novel miRNA secondary structure prediction.
Prior to differential gene expression analysis, for each sequenced library, differential expression analysis of two samples was performed using the edgeR. Pvalue was adjusted using q value. |log2(FC)|≥0.58;Pvalue≤0.05 was set as the threshold for significantly differential expression.
Assembly: Homo_sapiens.GRCh38_release95
Supplementary files format and content: read counts

growth_protocol: MCF-7 cell line was cultured in DMEM (Gibco) supplemented with 10% FBS and streptomycin/penicillin (100 U/mL) at 37˚C in an atmosphere of 5% CO2.After transient transfection of MCF7 cells with siNC (control) or si-LSD1 (KD) or pcDNA3.1-LSD1 (RE) using Lipofectamine 3000 for 24 h, the cell supernatants were collected after 36 h of culture with a change of serum-free medium.

extract_protocol:
The QIAGEN miRNeasy Mini Kit  was used to extract the total RNA from the exosomes
Per the manufacturer's instructions, the VAHTS Small RNA Library Prep Kit for Illumina directives. The Illumina Nova seq platform was used for the sequencing.

value: Breast cancer cells


title: PDLSCs_oeKDM6B_1

value: KDM6B Overexpression


title: PDLSCs_oeKDM6B_2


title: Dn8 CD14+ Monocytes of healthy donors

city: Tomsk

first: Irina

last: Larionova

state: Tomsk oblast

address: Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia

country: Russia

institute: Tomsk State University

description: Healthy Control

data_processing:
RRBS sequencing data processing included quality control and trimming of technical sequences, mapping of reads to the reference genome, counting the level of cytosine methylation in the CpG context, and differential methylation analysis. Quality control and trimming of adapter sequences were performed in FastQC programs and Trim_Galore. Mapping of RRBS reads to the human reference genome GRCh38 was performed using the Bismark program. Cytosine methylation levels in CpG context were also counted in Bismark.
Assembly: hg38
Supplementary files format and content: Bismark Coverage tab-separated file with methylation calling counts per each CpG site

source_name: CD14+ Monocytes

extract_protocol:
The peripheral blood mononuclear cells (PBMCs) were separated from whole blood by density gradient centrifugation using Lymphosep, Lymphocyte Separation Media (#L0560-500, Biowest, France), 1.077 g/ml density, at 600g for 30 minutes. The isolation of monocytes from PBMCs was performed using positive magnetic selection with CD14+ MACS beads (#130-050-201, Miltenyi Biotech, Germany), resulting in 90–98% monocyte purity as confirmed by flow cytometry. After monocyte isolation, the samples were washed twice with DPBS without calcium and magnesium at 300 g for 10 minutes. Subsequently, the cell precipitate was lysed using lysis buffer RLT (#79216, Qiagen, USA) and stored at -80°C until further experiments. Lysed monocytes were used for DNA isolation and reduced representation bisulfite sequencing (RRBS-Seq). DNA were extracted from lysed monocyte samples using AllPrep DNA/RNA/miRNA Universal Kit (#80224, Qiagen, USA). The quality of DNA was assessed by TapeStation 4150 automated electrophoresis system (#RRID: SCR_019393, Agilent Technology, USA). The quantity of DNA was assessed by Qubit 4 fluorometer (#RRID: SCR_018095, ThermoFisher Scientific, USA). Samples were purified using magnetic beads AMPure XP (Beckman Coulter) and concentration was controlled using Fluoroskan.
Libraries were prepared using Zymo-Seq RRBS Library Kit (#D5461) and Zymo-Seq UDI Primer Plate (#D3096) (Zymo Research, USA), according to the manufacturer’s instructions. Sequencing was performed by the Illumina NovaSeq 6000 platform (Illumina, USA).

value: CD14+ Monocytes

tag: disease

value: Healthy Control


title: PDLSCs_Control_2


title: Dn5 CD14+ Monocytes of healthy donors

description: Healthy Control


title: PDLSCs_oeKDM6B_3


title: Dn7 CD14+ Monocytes of healthy donors

description: Healthy Control


title: MOLM13, VEH, 12hr PRO-seq rep1

state: NY

description: MOLM13 0hr


title: MCF7 cells, KD


title: PDLSCs_Control_1


title: Dn1 CD14+ Monocytes of healthy donors

description: Healthy Control


title: Dn3 CD14+ Monocytes of healthy donors

description: Healthy Control


title: Oc9 CD14+ Monocytes of HGSOC patients

description: Patients received platinum-based neoadjuvant chemotherapy (NACT) [carboplatin plus paclitaxel] prior to surgery

value: High-grade serous ovarian cancer

value: NACT-treated


title: Oc10 CD14+ Monocytes of HGSOC patients


title: Oc4 CD14+ Monocytes of HGSOC patients

description: Patients had debulking surgery without upfront NACT

value: Treatment-naive


title: Cal27 cell, KD-2

city: Nanjing

first: Jiayi

last: Zhang

address: Hanzhong Road 140#

institute: Nanjing Medical University

data_processing:
The sequencing reads were mapped onto the reference gene set by using Bowtie1 software . A Perl script program was used to process the mapping results and the gene expression profile was generated.
Assembly: GRCh38.p13_104
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cal27 cells were cultured in high-glucose DMEM (Gibco) containing 10% FBS and 1% penicillin/streptomycin at 37 ℃ in the 5% CO2-humidifed incubator.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The lentivirus was transfected to knockdown DAZAP1, and the empty vector was co-transfected as a negative control.

value: oral cancer cell line

value: DAZAP1 knockdown


title: Oc7 CD14+ Monocytes of HGSOC patients


title: Oc8 CD14+ Monocytes of HGSOC patients


title: Oc5 CD14+ Monocytes of HGSOC patients


title: Cal27 cell, KD-3


title: MCF7 cells, RE


title: Oc2 CD14+ Monocytes of HGSOC patients


title: Oc3 CD14+ Monocytes of HGSOC patients


title: Cal27 cell, KD-1


title: Cal27 cell, NC-3

value: control


title: Cal27 cell, NC-1


title: Dn2 CD14+ Monocytes of healthy donors

description: Healthy Control


description:
HEK293T_ChIP_H3K9me3_Input_LINC00662_ASO_rep2
HEK293T_H3K9me3_Input_LINC00662ASOMIX.bigwig

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
The sequencing reads were subject to removal of adapter and quality filter using Cutadapt (v3.3).
The trimmed reads were aligned to hg19 genome using Bowtie2 (v2.4.2) with the parameters: bowtie2 --no-unal.
PCR duplicates were removed using GATK MarkDuplicates (v4.1.9.0) with the parameters: gatk MarkDuplicates --REMOVE_DUPLICATES true.
Peak calling was performed using MACS2 (v2.2.7.1) with the parameters: macs2 callpeak -f BAMPE -g hs.
Assembly: hg19
Supplementary files format and content: bigwig, all samples
Supplementary files format and content: narrowPeak, all samples

growth_protocol: Antisense oligonucleotides (ASOs) including ASOSETD5-AS1, ASOLINC00641 and ASO LINC00662 were transfected into HEK293T cells grown on the 6-well plates, and incubated for 48h.

extract_protocol:
1% Formaldehyde (Sigma, F8775) was added into each well to crosslink the cells for 10 min with a slight shaking at room temperature.chromtin was sonicated using Covaris M220 sonicator.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645).

value: Human embryonic kidney