title: Sen-IR Tg treat rep 3, expt 3

description:
ITg_3
20240718_all_genome_counts.txt


title: Control_MV, rep3

status: Public on Sep 18 2024

type: SRA

city: Shanghai

first: Fuping

last: Wen

address: Yanchang Middle Road

country: China

institute: Shanghai Tenth People's Hospital

library_source: transcriptomic

data_processing:
After quantified, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: HGC-27 cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using Trizol following the standard protocol
Libraries were prepared according to Illumina's instructions

treatment_protocol: Cultured cells were treated with control MV or OLFM4 over expression MV for 24h

tag: cell line

tag: cell type

value: Gastric cancer cells

tag: genotype

value: Wild type

tag: treatment

value: Control MV


title: Sen-IR Tg treat rep 2, expt 3

city: Baltimore

first: Emmanouil

last: Maragkakis

state: MD

address: 251 Bayview Blvd, 10B133 Baltimore

department: Laboratory of Genetics and Genomics (LGG)

country: USA

institute: National Institute on aging

description:
ITg_2
20240718_all_genome_counts.txt

data_processing:
FAST5 files were basecalled into FASTQ files and demulitplexxed (pcb111-24) using Guppy and then aligned to the human transcriptome using minimap.
Assembly: hg38
Supplementary files format and content: processed data exists as a merged table of read counts for each gene where the columns are samples and the rows are genes. Counts are obtained as a sum of all transcriptomic counts for a particular gene.

growth_protocol: Cells were grown in 10% FBS DMEM high glucose media supplemented with non-essential amino acids

extract_protocol:
RNA was extracted from cells using Trizol and then subjected to  DNase treatment.
RNA was used in the Nanopore PCR-cDNA library kit (PCB
Long-read sequencing

treatment_protocol: Cells were treated with acute proteotoxic stress (thapsigargin, tg) and then allowed to recover after its removal. Senescence was explored using etoposide induction (Etop) or ionizing radiaiton induction (IR) and compared to healthy cycling cells (Cyc). The effects of stress were examined 24h post-stress unless otherwise indicated. The stress-induced changes in senescent cells were also rescued through addition of in vitro transcribed ATF4 lacking regulatory uORFS (ATF4-Δ)  transfected post-stress during the recovery period.

value: fibroblast


title: Kidney_6mo_2

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

country: Japan

institute: Osaka Metropolitan University

description: Kidney.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC.
Trimmed sequence reads were mapped to GRCm39 using STAR.
Read count extraction was performed using RSEM.
Count data were normalized using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Mice were euthanized and tissues were collected and immediately frozen pulverized in liquid nitrogen. Pulverized tissues were homogenized in RNAiso Plus (Takara) reagent using pestle and then RNA was isolated following the manufacturer's instructions.
The sequencing libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina) following the manufacturer's instructions.

tag: Sex

value: male

tag: strain

tag: tissue

value: Kidney

tag: age

value: Wild-type


title: Heart_30mo_1

description: Heart.txt

source_name: Heart

value: Heart


title: Control_MV, rep2


title: Trim-Away 2 cell stage _rep1 a-Smarca5_F02

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
Data was aligned to GRCm38 and processed using Bismark (version v0.23.1) in single-end mode.
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

molecule: genomic DNA

source_name: 2 cell stage embryos

extract_protocol:
DNA extracted and processed as described in the scNMT-sq protocol
bisulphite libraries were generated as described in scNMT-seq protocol; At the sample collection stage,  the individual embryos were incubated with GpC methyltransferase

value: 2 cell stage embryos


title: Heart_24mo_4

description: Heart.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_B02


title: EBV, rep3

treatment_protocol: Cultured cells were treated with control medium or EBV for 24h

value: EBV


title: Trim-Away 2 cell stage _rep1 a-Smarca5_G02


title: Sen-IR mock treat rep 2, expt 3

description:
I_2
20240718_all_genome_counts.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_H02


title: Sen-IR Tg treat rep 1, expt 3

description:
ITg_1
20240718_all_genome_counts.txt


title: Heart_24mo_2

description: Heart.txt


title: Heart_24mo_3

description: Heart.txt


title: Heart_24mo_1

description: Heart.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_C02


title: Sen-Etop Tg treat, ATF4-Δ transfected, rep 2, expt 2

description:
ETgdelta__2
20240419_all_genome_counts.txt


title: EBV, rep2


title: Sen-Etop Tg treat, ATF4-Δ transfected, rep 1, expt 2

description:
ETgdelta_1
20240419_all_genome_counts.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_F01


title: Sen-Etop mock treat, ATF4-Δ transfected, rep 3, expt 2

description:
Edelta_3
20240419_all_genome_counts.txt


title: Heart_15mo_3

description: Heart.txt


title: Control, rep3

value: Control


title: Trim-Away 2 cell stage _rep1 a-Smarca5_A02


title: Sen-Etop mock treat, ATF4-Δ transfected, rep 2, expt 2

description:
Edelta_2
20240419_all_genome_counts.txt


title: Control, rep2


title: Control, rep1


title: Sen-Etop mock treat, ATF4-Δ transfected, rep 1, expt 2

description:
Edelta_1
20240419_all_genome_counts.txt


title: Control_MV, rep1


title: Sen-IR mock treat rep 1, expt 3

description:
I_1
20240718_all_genome_counts.txt


title: PBMCs, CF, p15

city: Milan

first: Federico

last: Di Marco

state: Outside U.S./Canada

address: Via Olgettina 60

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced scRNAseq library was processed using STAR (version 2.5.3) for alignment on GRCh38 human reference genome. Reads were then assigned to genes and counts were extracted using featureCount (version 1.6.4). Cells with features number lower than 200 and genes expressed in less than 5 cells were filtered out for the analysis
Assembly: GRCh38
Supplementary files format and content: Tab separated values files

source_name: PBMC

extract_protocol:
Human PBMC were isolated from 7 mL of blood by density gradient centrifugation and immediately processed.
Single cells were encapsulated and barcoded using the 10x Chromium Controller platform (10X Genomics) and  Chromium Single Cell 3' Reagent Kit (v3.1 Chemistry) (10X Genomics). Sequencing libraries were prepared according to the manufacturer’s protocol. Size distribution and concentration of resulting libraries were assessed using HS DNA assay on TapeStation platform (Agilent). Libraries were sequenced on a Novaseq 6000 (Illumina) platform aiming at 50’000 reads per single cell.

value: PBMC

tag: disease state

value: CF


title: Sen-Etop Tg treat 24h recovery rep 3, expt 2

description:
ETg_3
20240419_all_genome_counts.txt


title: Heart_15mo_2

description: Heart.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_G01


title: Trim-Away 2 cell stage _rep1 a-Smarca5_B01


title: Heart_6mo_4

description: Heart.txt


title: Sen-Etop Tg treat 24h recovery rep 2, expt 2

description:
ETg_2
20240419_all_genome_counts.txt


title: Heart_15mo_4

description: Heart.txt


title: PBMCs, CF, p6

description: 10x Genomics


title: Trim-Away 2 cell stage _rep1 a-Smarca5_H01


title: Sen-Etop Tg treat 24h recovery rep 1, expt 2

description:
ETg_1
20240419_all_genome_counts.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_A01


title: Heart_6mo_1

description: Heart.txt


title: PBMCs, CF, p5

description: 10x Genomics


title: Sen-Etop mock treat rep 3, expt 2

description:
E_3
20240419_all_genome_counts.txt


title: Heart_15mo_1

description: Heart.txt


title: PBMCs, MABSC, p11

description: 10x Genomics

value: MABSC


title: Brain_30mo_4

description: Brain.txt

source_name: Brain

value: Brain


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_C05

value: Smarca5 +/- (mat KO)


title: Trim-Away 2 cell stage _rep1 a-Smarca5_E01


title: Sen-Etop mock treat rep 2, expt 2

description:
E_2
20240419_all_genome_counts.txt


title: Trim-Away 2 cell stage _rep1 a-Smarca5_D02


title: PBMCs, MABSC, p9

description: 10x Genomics


title: Brain_30mo_3

description: Brain.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_D03


title: Sen-Etop mock treat rep 1, expt 2

description:
E_1
20240419_all_genome_counts.txt


title: PBMCs, CF, p14

description: 10x Genomics


title: PBMCs, MABSC, p4

description: 10x Genomics


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_B03


title: Brain_30mo_2

description: Brain.txt


title: PBMCs, MABSC, p3

description: 10x Genomics


title: Heart_6mo_2

description: Heart.txt


title: Cyc Tg treat, ATF4-Δ transfected, rep 2, expt 2

description:
CTgdelta__2
20240419_all_genome_counts.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_B04


title: Heart_6mo_3

description: Heart.txt


title: Cyc Tg treat, ATF4-Δ transfected, rep 1, expt 2

description:
CTgdelta_1
20240419_all_genome_counts.txt


title: PBMCs, MABSC-PD, p13

description: 10x Genomics

value: MABSC-PD


title: Cyc mock treat, ATF4-Δ transfected, rep 3, expt 2

description:
Cdelta_3
20240419_all_genome_counts.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_H04


title: Brain_24mo_4

description: Brain.txt


title: Cyc mock treat, ATF4-Δ transfected, rep 2, expt 2

description:
Cdelta_2
20240419_all_genome_counts.txt


title: Brain_24mo_2

description: Brain.txt


title: Cyc mock treat, ATF4-Δ transfected, rep 1, expt 2

description:
Cdelta_1
20240419_all_genome_counts.txt


title: RNA-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND589

city: Philadelphia

first: Andrew

last: Wells

state: PA

address: 3615 Civic Center Blvd

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

data_processing:
The pair-end fastq files were mapped to the genome assembly hg19 by STAR (v2.6.0c) independently for each replicate. The GencodeV19 annotation was used for gene feature annotation and the raw read count for gene feature was calculated by htseq-count (v0.6.1)96 598 with parameter settings -f bam -r pos -s yes -t exon -m union. The gene features localized on chrM or annotated as rRNAs, small coding RNA, or pseudo genes were removed from the final sample-by-gene read count matrix.
Testing for differential expression was conducted with the glmQLFit approach implemented in edgeR . Genes with FDR<0.05 and abs(log2FC>1) between stages were considered differentially expressed.
TPM values were calculated for each sample.
Assembly: hg19
Supplementary files format and content: TPM values

source_name: University of Pennsylvania Human Immunology Core (donor collection) /Center for Spatial and Functional Genomics (cell isolation, library construction, and sequencing)

growth_protocol: Human primary CD4+ T cells were purified from the apheresis products obtained from healthy, screened human donors through University of Pennsylvania Human Immunology Core (HIC). Naïve CD4+ T cells were purified using EasySepTM Human naïve CD4+ T cell isolation kit II (STEM cells Technologies, cat#17555) by immunomagnetic negative selection as per manufacturer’s protocol.

extract_protocol:
RNA was isolated from ~ 1 million of each cell stage using Trizol Re- agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN>7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
Samples were then processed for the preparation of libraries using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio USA) according to the manufacturer’s instructions. Briefly, the purified first-strand cDNA is amplified into RNA-seq libraries using SeqAmp DNA Polymerase and the Forward and the Reverse PCR Primers from the Illumina Indexing Primer Set HT for Illumina. Quality and quantity of the libraries was assessed using the Agilent 2100 Bioanalyzer system and Qubit fluorometer (Life Technologies). Sequencing was performed on the NovaSeq 6000 platform atthe CHOP Center for Spatial and Functional Genomics

treatment_protocol: Isolated untouched, highly purified (93-98%) naïve human CD4 T cells were activated using anti-CD3+ anti-CD28 Dynabeads (1:1) (Thermofisher scientific, cat #11161D) for 8-24 hours. Cells were then used to prepare sequencing libraries.

tag: characteristic

value: cell_state:stimulated 24hr


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_F04


title: PBMCs, MABSC-PD, p12

description: 10x Genomics


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_A03


title: Brain_24mo_1

description: Brain.txt


title: RNA-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND581


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_A04


title: Cyc Tg treat 24h recovery rep 3, expt 2

description:
CTg_3
20240419_all_genome_counts.txt


title: Brain_15mo_4

description: Brain.txt


title: Brain_30mo_1

description: Brain.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_F03


title: RNA-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND543


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_D05


title: Brain_15mo_3

description: Brain.txt


title: RNA-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND589

value: cell_state:stimulated 8hr


title: PBMCs, MABSC-PD, p1

description: 10x Genomics


title: Cyc mock treat rep 3, expt 2

description:
C_3
20240419_all_genome_counts.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_C03


title: Brain_15mo_2

description: Brain.txt


title: Cyc Tg treat 24h recovery rep 1, expt 2

description:
CTg_1
20240419_all_genome_counts.txt


title: Brain_15mo_1

description: Brain.txt


title: Brain_24mo_3

description: Brain.txt


title: Cyc mock treat rep 2, expt 2

description:
C_2
20240419_all_genome_counts.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_E03


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_A05


title: Brain_6mo_4

description: Brain.txt


title: Cyc mock treat rep 1, expt 2

description:
C_1
20240419_all_genome_counts.txt


title: Brain_6mo_3

description: Brain.txt


title: Cyc Tg treat 24h recovery rep 2, expt 2

description:
CTg_2
20240419_all_genome_counts.txt


title: RNA-Seq Naïve CD4+ Tcell Unstimulated Donor ND589


title: Sen-Etop Tg treat 72h recovery rep 3, expt 1

description:
Etop_72h_Tg_3
20231222_all_genome_counts.txt


title: RNA-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND543


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_C04


title: RNA-Seq Naïve CD4+ Tcell Unstimulated Donor ND581


title: Brain_6mo_2

description: Brain.txt


title: EBV, rep1

value: Gastric cancer cells

value: Wild type


title: RNA-Seq Naïve CD4+ Tcell Unstimulated Donor ND543


title: Brain_6mo_1

description: Brain.txt

value: male


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_G04


title: Sen-Etop Tg treat 72h recovery rep 2, expt 1

description:
Etop_72h_Tg_2
20231222_all_genome_counts.txt

value: fibroblast


title: ATAC-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor TMP442

data_processing:
ATAC-seq peaks were called using the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). Briefly, pair-end reads from three biological replicates for each cell type were aligned to hg19 genome using bowtie2 , and duplicate reads were removed from the alignment. Narrow peaks were called independently for each replicate using macs2 (-p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits) and ENCODE blacklist regions (ENCSR636HFF) were removed from peaks in individual replicates. Reproducible peaks, peaks called in at least two replicates, were used to generate a consensus peakset. Signal peaks were normalized using csaw in 10kb bins background regions and low abundance peaks (CPM>1) were excluded from the analysis. Tests for differential accessibility was conducted with the glmQLFit approach implemented in edgeR88 563 using the normalization factors calculated by csaw. OCRs with FDR < 0.05 and abs(log2FC > 1) between stages were considered differentially accessible.
For bigwig files, individual replicate bam files were merged and indexed with samtools 1.11 and then converted to bigwig deeptools bamCoverage v3.5.1 with parameters --RPGC, --effectiveGenomeSize 2864785220 --binsize 10 --extend reads
Assembly: hg19
Supplementary files format and content: bigwig, fpkm

extract_protocol:
A total of 50,000 to 100,000 cells were centrifuged at 550g for 5min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50μL cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM  NaCl, 3mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550g for 10min at 4°C. Nuclei were resuspended in the Nextera transposition reaction mix (25μL 2x TD Buffer, 2.5μL Nextera Tn5 transposase (Illumina Cat #FC-121-1030), and 22.5μL nuclease free H2O) on ice, then incubated for 45min at 37°C.
The tagmented DNA was then purified using the Qiagen MinElute kit eluted with 10.5μL Elution Buffer (EB). Ten microliters of purified tagmented DNA was PCR amplified using Nextera primers for 12cycles to generate each library. PCR reaction was subsequently cleaned up using 1.5x AMPureXP beads (Agencourt) and concentrations were measured by Qubit. Libraries were paired-end sequenced on the Illumina Libraries were paired-end sequenced on the Illumina Novaseq 6000 platform (100bp read length).


title: RNA-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND581


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_E05


title: 6M_KO_GP_FULL_4

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
The bulk RNA-seq reads were trimmed to remove the adapter and segments of bad quality. The trimmed reads were then mapped to the mouse reference genome mm10 using HISAT236.
HTSeq-count were then used to quantify the raw gene expression count matrices for all samples. The raw gene expression count matrices were then normalized using the DESeq226, which also identify the differential genes between samples of different conditions.
Assembly: mm10
Supplementary files format and content: tab-delimited tsv files include RPKM values for each Sample

growth_protocol: Mice were handled at the age of 1 month (1M), 6 month (6M) and 20 month (20M, only for WT mice).

extract_protocol:
Nucleospin RNA II kits was used for total RNA extraction.Subsequent denaturation by magnetic oligo (dT) beads was performed before the RNA sample purification. After the first-strand cDNA being obtained by reverse transcription of purified mRNA, and a second cDNA being synthesized, fragmented DNA samples were blunt ended and adenylated at the 3’ ends. Adaptors were ligated to construct a library.
Following purification, mRNA library was constructed, fragmented, amplified and loaded into the nanoarray and sequencing was performed on Illumina Novaseq 6000 platform following the vendor’s recommender protocol.

treatment_protocol: The osteoclasts (OCs)  were differentiated on bone slices from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) for 2 days or untill the big multinucleated cell presenting. Cells were maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

value: Osteoclast (OC)

value: Terc-/-

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) untill the big multinucleated cell presenting


title: Sen-Etop Tg treat 48h recovery rep 3, expt 1

description:
Etop_48h_Tg_3
20231222_all_genome_counts.txt


title: ATAC-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND578


title: 6M_KO_GP_FULL_2


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_D04

value: 2 cell stage embryos


title: ATAC-Seq Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND517


title: Sen-Etop Tg treat 48h recovery rep 2, expt 1

description:
Etop_48h_Tg_2
20231222_all_genome_counts.txt


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_B05


title: SMARCA5+/- 2 cell stage embryos (matKO females)_rep2_E04


title: ATAC-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor TMP442


title: Sen-Etop Tg treat 24h recovery rep 3, expt 1

description:
Etop_24h_Tg_3
20231222_all_genome_counts.txt


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_C01

value: Smarca5 +/+


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_B02


title: ATAC-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND578


title: 6M_GP_FULL_2

value: Wild typt (WT)


title: Sen-Etop Tg treat 72h recovery rep 1, expt 1

description:
Etop_72h_Tg_1
20231222_all_genome_counts.txt


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_E02


title: 6M_GP_FULL_1


title: 6M_GP_FULL_4


title: Sen-Etop Tg treat 24h recovery rep 1, expt 1

description:
Etop_24h_Tg_1
20231222_all_genome_counts.txt


title: ATAC-Seq Naïve CD4+ Tcell Unstimulated Donor TMP442


title: Sen-Etop Tg treat 24h recovery rep 2, expt 1

description:
Etop_24h_Tg_2
20231222_all_genome_counts.txt


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_D01


title: Sen-Etop mock treat rep 3, expt 1

description:
Etop_0h_A_3
20231222_all_genome_counts.txt


title: 6M_KO_GP_FULL_1


title: Sen-Etop mock treat rep 2, expt 1

description:
Etop_0h_A_2
20231222_all_genome_counts.txt


title: ATAC-Seq Naïve CD4+ Tcell Unstimulated Donor ND578


title: 6M_GP_3

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) for 2 days


title: ATAC-Seq Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND517


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_H02


title: HiC Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor TMP442

data_processing:
Paired-end reads from two replicates were pre-processed using the HICUP pipeline v0.7.489 568 , with bowtie as aligner and hg19 as the reference genome. The alignment .bam file were parsed to .pairs format using pairtools v0.3.0 and converted to pre-binned Hi-C matrix in .cool format by cooler v0.8.10 with multiple resolutions (500bp, 1kbp, 2kbp, 2.5kbp, 4kbp, 5kbp, 10kbp, 25kbp, 40kbp, 50kbp, 100kbp, 250kbp, 500kbp, 1Mbp and 2.5Mbp) and normalized with ICE method
For each cell stage, significant intra-chromosomal interaction loops were determined under multiple resolutions (1kb, 2kb and 4kb) using the Hi-C loop caller Fit-HiC2 v2.0.794 (FDR<1e-6) on merged replicates matrix.
Assembly: hg19
Supplementary files format and content: cool: sparse binary matrix file; tsv: tab seperated differential contact data for promoter loops

extract_protocol:
Hi-C library preparation was performed using the Arima-HiC kit (Arima Genomics Inc), according to the manufacturer’s protocols. Briefly, cells were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using AmpureXP  beads (Beckman Coulter).
The size-selected fragments were then enriched using Enrichment Beads (provided in the Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with the Swift Accel-NGS 2SPlus DNA Library Kit (Swift, 21024) and Swift 2S Indexing Kit (Swift, 26148). The purified, PCR-amplified DNA underwent standard QC (qPCR, Bioanalyzer, and KAPA Library Quantification [Roche, KK4824]) and was sequenced with unique single indexes on the Illumina NovaSeq 6000 Sequencing System using 200 bp reads


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_F02


title: 6M_GP_1


title: Sen-Etop Tg treat 48h recovery rep 1, expt 1

description:
Etop_48h_Tg_1
20231222_all_genome_counts.txt


title: ATAC-Seq Naïve CD4+ Tcell Unstimulated Donor ND517


title: 6M_GP_2


title: 519_6M_KO_GP_FULL_3


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_H05


title: HiC Naïve CD4+ Tcell 24hr Stimulated (TCR and CD28) Donor ND517


title: Mn_US3

first: Wanbo

last: Zhu

state: None Selected

address: No600, Yishan road, Shanghai, China

institute: Shanghai Sixth Peoples Hospital Affiliated to Shanghai Jiao Tong University

data_processing:
1 Data preprocessing and genomic alignment Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads need to be filtered by quality. Trimmomatic [1] software was first used for quality control and linker removal, and then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using Rockhooper2 [2] to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment
2 Genetic assembly and structural 2.1 UTR and novel gene prediction Identify the sequence of genes in an annotated gene or an unannotated area. Seeds gene sequence is a sequence area at genome that contains 10 bases at least and each one in this area are covered at least T sequence (T means a function of the2.2 Operator prediction Prokaryotes function on several related genes in are arranged in series with the often constitute manipulation substructure expression as a unit, is regulated by the common upstream area and the downstream transcription termination signal control. When transcribed, multiple structural genes are transcribed onto one mRNA strand and then translated into proteins. Rockhopper2 was used to develop the operon prediction algorithm from pure sequence features to combine experimental data of RNA-seq (ie, the gene expression quantity), that is to use bayesian classifier model to predict operons by combine the inter-genic distance and gene expression quantity, the sensitivity and specificity of the prediction algorithm are as high as 95%. Calculate and visualize 5 the predicted length distribution of operons, the number of structural genes involved, and the operon chain distribution count of genome-wide base average coverage sequence ). Through the bayesian model to judge whether the seed, seed each gene sequences repeatedly extended again after merging adjacent sequence of seeds or overlapping genes ultimately get the genetic map is obtained based on sequence alignment data reference gene annotation to the map and comparison, identification of boundary and the new genes.
3 Gene expression analysis The direct expression of a gene expression level is its abundance. The higher the degree of gene abundance, the higher the gene expression level. In transcriptome sequencing analysis, the expression level of genes was estimated by locating the count of sequencing sequence (reads) in the genome area or the exon region of the gene. The Reads count is positively correlated with the length of the gene and the depth of the sequencing, in addition to the true expression level of the gene. We used the known reference gene sequences as the database, and the expression abundance of each gene in each sample was identified by sequence similarity comparison.Rockhooper2 was used to obtain the number of reads aligned to the gene in each sample and then to calculate RPKM[3].The calculated transcript expression levels can be directly used to compare transcript expression differences between different samples, and this method can eliminate the effect of differences in transcriptional length and sequencing amount on the expression of transcripts. Visualize quantitative data to obtain box plots, density plots, expression plots, etc. to determine differences in expression across all sample
4 Difference analysis and functional analysisUsing the estimateSizeFactors function of the R package of DESeq [4] (2012) to standardize counts, and use the nbinomTest function to calculate the pvalue and foldchange of difference comparison. Pick out the difference transcripts that p-value less than 0.05 and Difference of multiples more than two, and the GO and KEGG enrichment analysis of the differential genes was performed by hypergeometric distribution tests to determine the biological functions or pathways that are mainly affected by differential genes
Assembly: GCF_003052445.1_ASM305244v1
Supplementary files format and content: counts.txt

organism: Staphylococcus aureus

growth_protocol: The frozen Staphylococcus aureus (ATCC 43300) strain was defrosted at room temperature and cultured in trypsin soybean broth medium (TSBG) containing 0.25% glucose through inoculation ring dipped in bacterial solution. After overnight in a shaking bed at 37℃, a logarithmic growth phase bacterial solution was formed. The gradient dilution contained 109 CFU/mL bacterial suspension, and the dilution was 100 times to produce 107 CFU/mL working bacterial solution. The sterilized aseptic titanium sheet was placed into the 24-well plate, 800μL of working bacterial solution was taken and added into the 24-well plate, and then placed in a 37℃ temperature box. Carefully remove the orifice plate and carefully update the TSBG medium every 24 hours. After 48 hours of culture, the supernatant medium was sucked out, and the titanium sheet attached to the biofilm was found in the 24-well plate.

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times.  Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate  the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the  lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass  the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into  the same Collection Tube.  F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into  the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the  center of the filter. Leave it at the room temperature for 2 min. Spin for 20–30 sec at maximum speed  to recover the RNA. Collect the eluate (which contains the RNA) and store it at -70°C.
a. Add 5 μL rRNA Binding Buffer and 5 μL rRNA Removal Mix-Gold to each well with 10 μL total RNA (1 μg). Gently pipette the entire volume up anddown 6 times to mix thoroughly.  b. Incubate the PCR plate at 68°C for 5 min, and then place at room temperature for 1 min. c. Add 35 μL of rRNA Removal Beads to each well of the new PCR plate. Adjust the pipette to 45 μL, then with the tip of the pipette at the bottom of the well, pipette quickly up and down 20 times to mix thoroughly. Incubate at room temperature for 1 min. Place the PCR plate on the magnetic stand at room temperature for 1 min. Transfer all of the supernatant from each well to the corresponding well of the new PCR plate. d. Add 99 μL of RNAClean XP beads (If starting with degraded total RNA, add 193 μL of RNAClean XP beads to each well) to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min. e. Place the PCR plate on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well of the PCR plate. f. Add 200 μL freshly prepared 70% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. Let the PCR plate stand at room temperature for 15 min to dry. g. Add 11 μL Elution Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min. Transfer 8.5 μL supernatant from the PCR plate to the new 0.2 ml tube. h. Add 8.5 μL Elute, Prime, Fragment High Mix to each well of the plate. Gently pipette the entire volume up and down 6 times to mix thoroughly. i. Incubate at 94°C for 8 min, hold at 4°C, and then centrifuge shortlya. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well of the PCR plate. Gently pipette the entire volume up and down 6 times to mix thoroughly.  b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C.
2.3 Synthesize Second Strand cDNA  a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well of the PCR plate. b. Add 20 μL Second Strand Marking Master Mix. Gently pipette the entire volume up and down 6 times to mix thoroughly. c. Incubate at 16°C for 60 min. Remove the plate from the thermal cycler2.3.1 Purification  a. Add 90 μL mixed AMPure XP beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard 135 μL supernatant from each well of the plate. d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time. f. Let the plate stand at room temperature for 15 min to dry, and then remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. h. Incubate the plate at room temperature for 2 min. Then place the plate on the magnetic stand at room temperature for 5 min. i. Transfer 15 μL supernatant from the plate to the new PCR plate. 2.4 Adenylate 3’ Ends a. Add 2.5 μL of diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL 9  Resuspension Buffer) to each well of the plate.  b. Add 12.5 μL of A-Tailing Mix to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 2.5 Ligate Adapters  a. Add 2.5 μL of diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) to each well of the plate. b. Add 2.5 μL of Ligation Mix to each well of the plate. c. Add 2.5 μL of RNA Adapter Index to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. d. Incubate at 30°C for 10 min. e. Add 5 μL of Stop Ligation Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. 2.5.1 Purification  a. Add 42 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. c. Remove and discard 79.5 μL supernatant from each well of the plate. d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time for a total of two 80% EtOH washes. f. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. 10 h. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 minutes or until the liquid is clear. i. Transfer 50 μL supernatant from each well of the plate to the corresponding well of the new PCR plate. j. Add 50 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. k. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. l. Remove and discard 95 μL supernatant from each well of the plate. m. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. n. Repeat step m one time for a total of two 80% EtOH washes. o. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. q. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 min or until the liquid is clear. r. Transfer 20 μL supernatant from each well of the plate to the corresponding well of the new PCR plate. 2.6 Enrich DNA Fragments  a. Add 5 μL of PCR Primer Cocktail to each well of the PCR plate. b. Add 25 μL of PCR Master Mix to each well of the PCR plate. Gently pipette the entire volume up and down to mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 s; 15 cycles 98°C for 10 s, 60°C for 30 s, 72°C for 30 s; 1 cycle 72°C for 5 min; hold at 10°C. 11 2.7.1 Purification  a. Add 50 μL of the mixed AMPure XP Beads to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min. b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. c. Remove and discard 95 μL supernatant from each well of the PCR plate. d. With the PCR plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time for a total of two 80% EtOH washes. f. With the PCR plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. h. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min or until the liquid is clear. i. Transfer 30 μL supernatant from each well of the PCR plate to the corresponding well of the new PCR plate. 2.8 Validate library  a. Load 1 μL sample on an Agilent Technologies 2100 Bioanalyze. b. Check the size and purity of the sample

treatment_protocol: After adding 100 μg/mL nanomaterials into the bacterial suspension of each group, the bacteria were incubated for 12 hours. Bacterial precipitation was obtained by centrifugation.

value: WT

value: Treated by MnPM+US


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_G05


title: Mn_US2


title: HiC Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor TMP442


title: HiC Naïve CD4+ Tcell 8hr Stimulated (TCR and CD28) Donor ND517


title: 519_6M_KO_GP_FULL_1


title: C3

value: Non treatment


title: Mn_US1


title: HiC Naïve CD4+ Tcell Unstimulated Donor TMP442


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_G02


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_C02


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_F01


title: C2


title: 519_1M_KO_GP_FULL_2


title: HiC Naïve CD4+ Tcell Unstimulated Donor ND517


title: Etoposide-induced senecent cells Ribo-seq, 3

first: Manolis

address: 251 Bayview Boulevard

institute: National Institute on Aging

data_processing:
FASTQ files were demultiplexed using bcl2fastq conversion software (Illumina) and then aligned to the human genome or transcriptome using STAR v2.7.10b.
Differential gene expression and other analysis was performed using DESeq2 v1.36.0.
Assembly: hg38
Library strategy: Ribo-Seq

growth_protocol: Cells were grown in 10% FBS DMEM high glucose media supplemented with non-essential amino acids and antibiotic/antimycotics.

extract_protocol:
RNA was extracted using  by drop-wise addition of polysome lysis buffer (20 mM Tris pH 7.4, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, 50 mM KCl, 1% Triton x-100, 0.1 mg/mL cyclohexamide, 1X HALT protease-phosphatase inhibitors).
50 ug of bulk RNA from lysate (measured by nanodrop) was used for Trizol purification of RNA-seq and 50 ug of lysate was prepared for Ribo-seq.
Ribo-seq lysates were treated with 1 uL of RNAse I (thermofisher) and incubated at 4C with rotation for 40 min; reaction was then stopped with 100 U of SUPERasein (thermofisher).
Lysates were then centrifuged through a sucrose cusion to precipitate ribosome pellets. Pellets weree then suspended in Trizol for RNA preparation.
Prepared RNA was DNAse I treated and then gel purified for riboseq footprints (25-40 nts) followed by extraction.
Extracted RNA was then depleted of rRNA (thermofisher).
RNA-seq RNA was prepared using Tru-Seq Stranded RNA library kit (Illumina) while Ribo-seq RNA was prepared using NEBNext Multiplex Small RNA Library prep (New England Biolabs)

treatment_protocol:
Etop senescent cells were induced through 3 treatments with 50 uM etoposide over 10 days with harvest or further treatment on the 10th day.
IR senescent cells were induced through 15gy of ionizing radiation and then harvested after 10 days of incubation
Cycling cells were harvested at 40-60% confluency before harvest or futher treatment.

value: Fibroblasts

value: Etoposide 50 uM, 10d


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_D02


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_A02


title: 519_1M_KO_GP_FULL_1


title: 519_1M_KO_GP_FULL_3


title: post 10wAIR_F3_oxRRBS

city: Minneapolis

first: Natalia

last: Tretyakova

state: Minnesota

address: 2231 6th St SE Room 2-147

department: Medicinal Chemistry

institute: University of Minnesota

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc3_oxBS_S9

data_processing:
Trimmomatic to remove low quality bases and adapter contamination
HISAT2 to map read pairs to the mm10 genome
Samtools to sort mapped reads by query name and filter by mapping quality
featureCounts to quantify gene expression
edgeR to analyze gene expression data
Assembly: mm10
Supplementary files format and content: CSV with the test results for differential gene expression. Contains Ensembl ID, base mean expression, log2(fold change), nominal P-values, and FDR values

source_name: Lung

extract_protocol:
Genomic DNA isolated from Type II alveolar epithelial cells of control and treated A/J mice was prepared for RRBS and oxo-RRBS using the Ovation RRBS Methyl-Seq System with TrueMethyl oxBS module (NuGEN, Redwood City, CA) according to the manufacturer’s protocol. Library amplification was optimized as directed using qPCR, and the libraries were amplified accordingly followed by Agencourt bead clean-up.
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples from 9 mice were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS) by the University Flow Cytometry Resource at the University of Minnesota using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was saved for downstream analyses. A portion of the cell pellet (1.25 x 105 – 5 x 105 cells) was set aside to isolate protein. The remaining sample was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.

value: Lung

value: female

value: Alveolar type II epithelial cells

value: 14 weeks filtered air


title: C1


title: 519_6M_KO_GP_FULL_2


title: post 10wAIR_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc1_oxBS_S7


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_B01


title: 20M_GP_FULL_3


title: Sen-Etop mock treat rep 1, expt 1

description:
Etop_0h_A_1
20231222_all_genome_counts.txt

value: fibroblast


title: Etoposide-induced senecent cells Ribo-seq, 1


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_A01


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_G01


title: Ionizing Radiation induced senescent cells Ribo-seq, 2

value: Ionizing radiation (15 gy) induced senescence


title: post 10wCS_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs2_oxBS_S11

value: 10 weeks cigarette smoke folowed by 4 weeks filtered air


title: 20M_GP_FULL_1

value: Osteoclast (OC)

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) untill the big multinucleated cell presenting


title: 20M_GP_4


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_H01

value: 2 cell stage embryos

value: Smarca5 +/+


title: post 10wCS_F3_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs3_oxBS_S12


title: SMARCA5+/+ 2 cell stage embryos (matKO females)_rep2_E01


title: 20M_GP_FULL_4

value: Wild typt (WT)


title: 20M_GP_3

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) for 2 days


title: Etoposide-induced senecent cells Ribo-seq, 2

value: WT


title: T6C

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
RNA-Seq reads were aligned using STAR (STAR_2.6.1c) to a concatenated reference comprised of the Homo sapiens (GRCh38.p12 assembly) and Mus musculus (GRCm38.p6 assembly) genomes.
The resulting alignments were separated into species-specific bam files, converted back to fastq files and processed through individual human and mouse pipelines
Assembly: GRCh38.p12 assembly and GRCm38.p6 assembly

organism:
Homo sapiens
Mus musculus

source_name: tumor

growth_protocol: All animal studies were performed in accordance with protocols approved by the New York Medical College Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted from tumors using RNeasy mini kit (Qiagen) after homogenization of tumors by Tumor Dissociation Kit (Miltenyi Biotec) combined with the gentleMACS Dissociator.
Library was constructed using RNA as input using Illumina TruSeq Stranded Total RNA library preparation kit

treatment_protocol: NK cells were injected at dose of 1x107 cells/animal via i.v. injection

value: tumor

tag: tumor section

value: C

value: NK treated


title: post 10wCS_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs1_oxBS_S10

value: Lung


title: 20M_GP_2


title: 1M_WT_GP_FULL_gaiwei3


title: post 10wAIR_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc2_oxBS_S8

value: female


title: post 10wAIR_F3_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc3_BS_S3

value: Alveolar type II epithelial cells


title: Contact-inhibited quiescent cells Ribo-seq, 3

value: Fibroblasts

value: Contact-inhibited quiescent cells


title: Contact-inhibited quiescent cells Ribo-seq, 1


title: T6P

value: P


title: Contact-inhibited quiescent cells Ribo-seq, 2


title: post 10wAIR_F2_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc2_BS_S2

value: 14 weeks filtered air


title: 1M_WT_GP_FULL_gaiwei2

value: Osteoclast (OC)


title: post 10wAIR_F1_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fc1_BS_S1


title: 1M_WT_GP_FULL_gaiwei1

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) untill the big multinucleated cell presenting


title: Cycling cells Ribo-seq, 3


title: Ionizing Radiation induced senescent cells Ribo-seq, 1

value: Ionizing radiation (15 gy) induced senescence


title: post 10wCS_F3_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs3_BS_S6

value: 10 weeks cigarette smoke folowed by 4 weeks filtered air


title: Cycling cells Ribo-seq, 2


title: T4C


title: 1M_WT_GP_FULL_4

value: Wild typt (WT)


title: T5P


title: 1M_WT_GP_FULL_3


title: Cycling cells Ribo-seq, 1


title: Etoposide-induced senecent cells RNA-seq, 3

value: Etoposide 50 uM, 10d


title: T4P


title: post 10wCS_F1_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs1_BS_S4


title: T3P


title: 10wAIR_F3_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc3_OXO_S9

value: 10 weeks filtered air


title: T3C

value: tumor


title: T5C

value: C


title: 1M_KO_GP_FULL_4

value: Terc-/-


title: Etoposide-induced senecent cells RNA-seq, 1

value: WT


title: 1M_KO_GP_FULL_3


title: Ionizing Radiation induced senescent cells RNA-seq, 3


title: Etoposide-induced senecent cells RNA-seq, 2


title: T1P

value: NK treated


title: T1C


title: 10wAIR_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc1_OXO_S7

value: Lung

value: female

value: Alveolar type II epithelial cells


title: post 10wCS_F2_RRBS

description:
Project_019_MeC_hmC_Counts.txt.gz
Project_019_MeC_DMR.bed.gz
Project_019_hmC_DMR.bed.gz
14cs_fs2_BS_S5


title: 10wCS_F3_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs3_OXO_S12

value: 10 weeks cigarette smoke


title: 1M_KO_GP_FULL_1


title: Ionizing Radiation induced senescent cells RNA-seq, 2

value: Fibroblasts


title: 10wCS_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs1_OXO_S10


title: 10wAIR_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc2_OXO_S8


title: wt-sap-rep1

city: wenzhou

first: Tan

last: Zhang

address: Nanbaixiang street

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Total pancreatic RNA from experimental mice were extracted followed protocol mentioned above and then made to cDNA librares for sequencing with NEBNext Ultra II Directional RNA Library Prep Kit (#E7760S, NEB, USA).
Then the libraries were sequenced on NovaSeq 6000 platform (Illumina).
The pair-end sequencing data was treated by fastp software to filter reads with bad quality, and then mapped to Ensembl GRCm38.p6 reference genome by CLC genomic worbench 12.0 (Qiagen).

source_name: pancreas

extract_protocol:
Trizol was used to extract RNA from pancreatic tissue after lapping with liquid nitrogen
NEBNext Ultra II Directional RNA Library Prep Kit

value: pancreas

value: male

value: wt

value: faee-sap(POA and ethanol)


title: U6C

value: untreated


title: wt-ns-rep2

value: control(narmal saline)


title: U6P

value: P


title: wt-ns-rep1


title: 1M_WT_GP_FULL_1

value: Osteoclast (OC)

value: Wild typt (WT)

value: Differentiated on bone slice from bone marrow-derived macrophage (BMMs) by cytokine MCSF (25ng/ml) and RANKL (100ng/ml) untill the big multinucleated cell presenting


title: U5C

value: tumor

value: C


title: 10wAIR_F3_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc3_BS_S3

value: Lung

value: 10 weeks filtered air


title: Contact-inhibited quiescent cells RNA-seq, 3

value: WT

value: Contact-inhibited quiescent cells


title: Contact-inhibited quiescent cells RNA-seq, 2

value: Fibroblasts


title: Ionizing Radiation induced senescent cells Ribo-seq, 3

value: Ionizing radiation (15 gy) induced senescence


title: cko-sap-rep2

value: pancreas

value: male

value: PFKFB3 cko


title: U5P

value: untreated


title: Contact-inhibited quiescent cells RNA-seq, 1


title: cko-sap-rep1

value: faee-sap(POA and ethanol)


title: Cycling cells RNA-seq, 2


title: 10wAIR_F1_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc1_BS_S1

value: female

value: Alveolar type II epithelial cells


title: U4P

value: P


title: 10wCS_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs2_OXO_S11

value: 10 weeks cigarette smoke


title: wt-sap-rep2

value: wt


title: U4C

value: tumor

value: C


title: 10wAIR_F2_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fc2_BS_S2

value: Lung

value: 10 weeks filtered air


title: cko-ns-rep2

value: control(narmal saline)


title: 10wCS_F3_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs3_BS_S6


title: Cycling cells RNA-seq, 1

value: Fibroblasts

value: WT


title: U2C


title: cko-ns-rep1

value: pancreas


title: 10wCS_F2_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs2_BS_S5


title: MIA PaCa-2, hypoxia, CEBPD, 3

city: Amsterdam

first: C.

middle: Arnold

last: Spek

address: Meibergdreef 9

department: CEMM

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were aligned using STAR v. 2.7.1
Genes were annotated using Gencode v38
Assembly: NCBI37/hg19
Supplementary files format and content: counts

source_name: pancreatic ductal adenocarcinoma

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine and antibiotics in humidified atmosphere with 1% oxygen at 37C.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA extraction kit (Macherey-Nagel). RNA quality was assessed by bioanalysis (Agilent) and samples with RNA integrity number > 7 were included for RNA sequencing using > 200 ng of total RNA.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche) following manufacturer's protocols.

treatment_protocol: Cells were treated with 2 ug/ml doxycycline hyclate (Sigma) in complete medium for 48 hours.

value: pancreatic ductal adenocarcinoma

value: MIA PaCa-2

value: tet-on CEBPD

value: doxycycline 2 ug/ml


title: U2P

value: untreated


title: 10wCS_F1_RRBS

description:
Project_016_MeC_hmC_Counts.txt.gz
Project_016_MeC_DMR.bed.gz
Project_016_hmC_DMR.bed.gz
10cs_fs1_BS_S4

value: female

value: Alveolar type II epithelial cells


title: MIA PaCa-2, hypoxia, CEBPD, 2


title: U1C


title: V_A

first: Yu

last: Xiao

address: No. 160 Pujian Road, Pudong New Area, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: GRCm39 (http://asia.ensembl.org/Mus_musculus/Info/Index)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous tumor in mice

extract_protocol:
Subcutaneous tumor tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1× Red Blood Cell Lysis buffer (Thermo Fisher Scientific, cat. no. 00-4333-57) . Dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments)
Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 5’ end of the transcripts linked with the cell barcode and UMI. Single-cell RNA libraries were prepared using the Chromium Single Cell 5’v2 Reagent (10x Genomics), and TCR/BCR transcripts were enriched with the Chromium Single Cell V(D)J Reagent kits (10x Genomics). Each sequencing library was generated with a unique sample index.

value: male

value: Subcutaneous tumor cells


title: A

description: 10x Genomics

value: A


title: 3wAIR_F3_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc3_OXO_S9

value: 3 weeks filtered air


title: 3wAIR_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc2_OXO_S8

value: Lung


title: U1P

value: tumor

value: P


title: MIA PaCa-2, hypoxia, CEBPD, 1


title: V

description: 10x Genomics

value: V


title: Ionizing Radiation induced senescent cells RNA-seq, 1

value: Fibroblasts

value: WT

value: Ionizing radiation (15 gy) induced senescence


title: MIA PaCa-2, hypoxia, CTRL, 2

value: pancreatic ductal adenocarcinoma

value: MIA PaCa-2

value: tet-on CTRL


title: 3wAIR_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc1_OXO_S7


title: MIA PaCa-2, hypoxia, CTRL, 1

value: doxycycline 2 ug/ml


title: 81-195-2017-4-26-2017_S81

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 36 bases, and leading and trailing basepairs below a quality score of 3
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 14 --dta -x GCF_002263795.1_ARS-UCD1.2
Read assembly and quantification was performed with StringTie v2.1.7 with parameters -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE.py with parameters python prepDE.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.32.1.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: comma-delimited text file of gene counts for each sample

molecule: polyA RNA

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: brd severity

value: Healthy

tag: year

tag: sample day

value: Male

tag: animal id

tag: developmental stage

value: Bull


title: 3wCS_F3_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs3_OXO_S12

value: female

value: Alveolar type II epithelial cells

value: 3 weeks cigarette smoke


title: 3wCS_F2_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs2_OXO_S11

value: Lung


title: HLOs, Input

city: Cincinnati

first: Hasan Al

last: Reza

address: 3333 Burnet Ave

department: Developmental Biology

institute: CCHMC

description: 10x Genomics

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using trim_galore v0.6.6, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 reference genome using bwa-mem v0.7.17. Only uniquely mapping reads with at most two mismatches were retained. Samtools was used to sort and index bam files and picard was used to remove duplicates.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.01
Assembly: GRCh38.p13/hg38
Supplementary files format and content: bed files (except for Input sample)

source_name: Human Liver Organoids

extract_protocol:
Organoids were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonication device (Diagenode). ChIP DNA was obtained by following the manufacturer’s protocol for High-Sensitivity ChIP Kit, Abcam using ChIP Grade Anti-EP300/KAT3B antibody, Abcam.
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library Kit by Medgenome, Inc. 50 ng of DNA was provided as starting material for input and ip samples for sequencing. 40M (PE100) total reads per sample were generated for each sample.

value: Human Liver Organoids

value: Hepatocytes

tag: time

value: Day 32

tag: chip antibody


title: 79-185-2017-4-26-2017_S79


title: Sample-10 tumor DC-1

type: RNA

city: Boston

first: Pankaj

last: Sharma

state: MA

address: 220 Longwood Ave.

institute: Boston Childrens Hospital

description: Tumor DCs

data_processing: Amplification of the gene encoding for beta-actin served as internal control, and relative gene expression levels were calculated using the 2-ΔΔCT method.

label: SYBR Green

source_name: MCA101 mouse fibrosarcoma tumor DCs

growth_protocol: DC2.4 cells were purchased from Millipore Sigma and were cultured in complete RPMI medium containing 10% FBS, penicillin (100 U/ml) and streptomycin (100 ug/ml), sodium pyruvate (1 mM), L-glutamine (2 mM), beta-mercaptoethanol (50 µM), and HEPES (100 mM). All cells were cultured in an incubator at 37°C, 5% CO2, and 95% relative humidity.In seperate experiment, mice were subcutaneously injected with either 1 x 106 live MCA101 tumor cells in the shaved right flank. Thereafter, tumors were cut into small pieces and were digested in 20 ml of RPMI containing collagenase D (400 mg/ml), collagenase VIII (400 mg/ml), and 2% FCS for 1 hour at 37ºC. Subsequently, 70% and 30% percoll density gradients were used to remove debris and dead cells, and single cell suspensions were collected from the gradient interface. Spleens and tumor-draining lymph nodes (dLNs) were cut and dissociated with 10 U/ml collagenase I and 30 U/mL DNase I (Millipore Sigma) for 45 min at 37°C, and single cell suspensions were collected by passing cells through 70-micron cell strainers. Red blood cells from all samples were removed using erythrocyte lysis buffer. Single cells suspensions from spleen and tumor (MCA101) were stained with antibodies directed against CD11c, MHC-II, CD103, CD8, F4/80, CD11b and CD45, and CD103-pos/CD8-pos DC1 cells  purified using FACS sorting. DC2.4 cells were collected upon trypsinization after 4 days of 2.5 ng/ml TGF-beta stimulation. Expression of genes involved in glycosylation were quantified by quantitative real-time PCR (qRT-PCR) using the glycosylation RT2 Profiler PCR Array according to the manufacturer’s instructions (PAMM-046Z, Qiagen). Briefly, RNA was isolated using the RNeasy Kit (Qiagen), and 50-100 ng RNA was converted to cDNA using the RT2 First Strand Kit (Qiagen). The cDNAs were subjected to amplification using gene-specific primers and SYBR Green (RT2 SYBR Green Master Mix, Qiagen) in an Ab7100 Real-Time PCR System (Thermo Fisher Scientific).

treatment_protocol: DC2.4 cells were seeded in complete RPMI at 75% confluency in 24-well plates and DC2.4 cells were stimulated with 10 ng/ml recombinant TGF-beta.

tag: tag

value: CD103-positive Dendritic cells


title: 3wCS_F1_oxRRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs1_OXO_S10

tag: cell type


title: MIA PaCa-2, hypoxia, CTRL, 3

tag: cell line

value: tumor

tag: genotype

tag: treatment


title: HLOs, Control, EP300

description: 10x Genomics

tag: tissue


title: Sample-11 tumor DC-1

description: Tumor DCs

extract_protocol: RNA was isolated using the RNeasy Kit (Qiagen)


title: Sample-9 Splenic DC-1

description: Control

source_name: Mouse spleen

value: XCR-1-positive Dendritic cells


title: 82-199-2017-4-26-2017_S82

tag: Sex


title: 77-177-2017-4-26-2017_S77


title: 78-181-2017-4-26-2017_S78


title: 3wAIR_F2_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc2_BS_S2

value: 3 weeks filtered air


title: HCLOs, PCO, EP300

description: 10x Genomics

value: Bilirubin 1 mg/L


title: Sample-7 Splenic DC-1

description: Control


title: 3wAIR_F3_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc3_BS_S3


title: Sample-12 tumor DC-1

description: Tumor DCs


title: 80-187-2017-4-26-2017_S80


title: HCLOs, EP300

description: 10x Genomics

value: 72.3 GFP + mGULO

value: Bilirubin 1 mg/L + Doxycycline 100 ng/ml


title: 3wAIR_F1_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfc1_BS_S1


title: 76-169-2017-4-26-2017_S76

value: Healthy


title: 75-168-2017-4-26-2017_S75

value: Male

value: Steer


title: 3wCS_F3_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs3_BS_S6

value: female


title: 3wCS_F2_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs2_BS_S5

value: Alveolar type II epithelial cells


title: Sample-5 DC2.4 TGF-b stimulated

description: TGF-b treated

source_name: Immortalized murine dendritic cells

value: Dendritic cells


title: 74-167-2017-4-26-2017_S74

value: Bull


title: HCLOs, PCO, snRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using cellranger v7.0.1, alevin-fry v0.8.0, and starsolo v2.7.9a.
The fastq files were aligned to the hg38 human reference transcriptome and the UMI and nuclei barcodes were extracted.
SoupX v1.6.0 was used to remove ambient RNA and other technical artifacts from the count matrices.
The UMIs were quantified per-gene and per-cell for normalization.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
HCLOs were pulverized with liquid nitrogen and nuclei prepared, sorted and counted as described by Wu et. al. with addition of 0.04% BSA/PBS in the final buffer
Library was constructed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

value: Human Liver Organoids


title: Sample-6 DC2.4 TGF-b stimulated

description: TGF-b treated


title: Sample-8 Splenic DC-1

description: Control


title: Sample-4 DC2.4 TGF-b stimulated

description: TGF-b treated


title: 73-162-2017-4-26-2017_S73


title: 72-160-2017-4-26-2017_S72


title: HCLOs, snRNAseq

description: 10x Genomics

value: Hepatocytes


title: Sample-3 DC2.4 unstimulated

description: Control


title: HCLOs, PPO, snRNAseq

description: 10x Genomics

value: mGULO

value: Day 32

value: Doxycycline 100 ng/ml


title: HCLOs, PPO,EP300

description: 10x Genomics


title: 71-158-2017-4-26-2017_S71


title: 3wCS_F1_RRBS

description:
Project_012_MeC_hmC_Counts.txt.gz
Project_012_MeC_DMR.bed.gz
Project_012_hmC_DMR.bed.gz
3sfs1_BS_S4

value: Lung

value: 3 weeks cigarette smoke


title: PKM2-/- heart, 3d MI 3

city: Honolulu

first: Katie

middle: CY

last: Lee

state: HI

address: 651 Ilalo St., BSB 311

department: Center for Cardiovascular Research

institute: University of Hawaii at Manoa

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using PRINSEQ (parameter: Q<30).
Trimmed sequence reads were aligned to mm10 using HISAT2.
Sequence alignment map files were mapped to mouse gene models using featureCounts.
Read count extraction and normalization were perfomed using DESeq2.
Assembly: mm10
Supplementary files format and content: Comma separated values file includes DESeq2 normalized counts for each sample

source_name: heart

extract_protocol:
RNA was extracted from mouse left ventricle tissue using the Rneasy mini kit (Qiagen). 500ng of RNA was used for the construction of sequencing libraries.
rRNA was removed using the rRNA depletion kit v2 (New England Biolabs). cDNA libraries for sequencing was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with index primers NEBNext Multiplex Oligos for Illumina sets 1 and 2 (New England Biolabs).

treatment_protocol: The LAD was permanently ligated to induce MI. Sham surgeries were performed similarly, but without ligation of the LAD.

tag: strain

tag: gender

value: male

tag: age

value: 8-12 weeks

value: heart

value: 3d MI


title: HLOs, Healthy iPSC 3,Bilirubin 1 mg/L, day 27

data_processing:
Samples were sequenced with 150bp pair-end sequencing at a depth of 20M reads per sample by Novogene. Inc.
Clean data were generated from the raw data that was filtered by data-processing steps, including removal of adapter sequences, reads with more than 10% N, and low-quality sequences (the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read).
Trimmed sequence reads were mapped to Gencode Release 39 (GRCh38.p13) using Salmon 1.8.0 pipeline to obtain raw transcript counts.
Raw counts data was imported with Tximport and was converted to a DESeq2 dataset and normalized using DESeq2's variance stabilizing transformation to obtain normalized Log2 Counts-per-Million (CPM) values.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: comma-separated values files include log2 vst normalized CPM values for each Sample.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Over 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

value: wild type

value: Day 27

value: Bilirubin 1 mg/L


title: PKM2-/- heart, 3d MI 2


title: 70-156-2017-4-26-2017_S70

tag: brd severity

value: Male


title: PKM2-/- heart, 3d MI 1


title: HLOs, Healthy iPSC 1,Bilirubin 1 mg/L, day 27


title: Sample-2 DC2.4 unstimulated

description: Control

value: Dendritic cells


title: Orc2194E_nonreplicating [MUT4_0]

city: Hong Kong

first: Yuanliang

last: Zhai

address: Kadoorie Biological Sciences Building, The University of Hong Kong, Pok Fu Lam Rd

country: Hong Kong

institute: The University of HongKong

description: Yeast whole-genome sequencing.

data_processing:
Adapter/N/low quality data were removed from raw data using SOAnuke and clean reads were obtained.
Clean reads were mapped to sacCer3 using localMapper (https://github.com/DNAReplicationLab/localMapper). The required software versions are: bowtie2 2.5.3, picard 2.27.5, samtools 1.18, bedtools 2.31.0
Further analysis was carried out by Repliscope package 1.1.1 ( https://github.com/DNAReplicationLab/Repliscope) under R version 4.3.0.
Assembly: sacCer3
Supplementary files format and content: bed (peak calling) generated directly from localmapper.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells cultured in YPG medium were diluted into 200 ml YPG medium to an OD600nm of 0.2 and further incubated at 30℃ until the OD600nm reached 0.5. For G2/M-phase synchronization, the cells were first arrested in G1 phase with 10 µg/ml α-factor for 2 hrs. The cells were then pelleted, washed twice with pre-chilled MQ H2O, and resuspended with 200 ml of fresh YPD containing 15 µg/ml nocodazole (Cell Signaling), which led to efficient G2/M arrest and orc2-1 depletion. After incubation for 3 more hours at 30℃, the cells were harvested and washed twice with pre-cooled MQ H2O. The cells arrested by nocodazole could be released into YPD medium with 10 µg/ml α-factor for the second round of G1 synchronization. Replication was initiated by removing α-factor, and cell harvesting was performed at the time point determined by the FACS profile, which was 30 minutes.

extract_protocol:
Resuspend cells in 500 μl of buffer containg 1.2 M Sorbitol, 200 mM Tris-HCl (pH 8.0), 20 M EDTA, and add 50 μl of 10 mg/ml zymolyase T20 and 0.5 μl β-mercaptoethanol. Incubate samples at 37 °C for 30 min in a water bath. Pellet cells by centrifugation at 16,000g for 2 min at RT, remove the supernatant and set up the following reactions for each sample: 50 mM Tris-HCl (pH 8.0), 100 mM EDTA, 100 mM NaCl, 0.5% SDS, 83.3 mM Sorbitol, 0.33 mg/mL Protease K, 83.3 μg/mL RNaseA. Incubate at 55 °C in a water bath for 2–6 h. Using ethanol precipitation method to pellet the genome DNA.  Resuspend the DNA pellet in TE buffer.
More than 1 µg of DNA with good integrity was required. Library preparation and sequencing were commercial services by BGI with a DNBseq platform following the procedure of: DNA fragmentation; fragment size selection; end repair and "A" tailing; adaptor ligation; product size selection; PCR; library QC.

treatment_protocol: To stop the progressing DNA elongation, 0.1% NaZ3 was added immediately after cell collection.


title: PKM2-/- heart, sham 3

value: sham


title: 68-139-2017-4-26-2017_S68

tag: year

value: Steer


title: 69-155-2017-4-26-2017_S69

value: Healthy

tag: sample day

value: Bull


title: HLOs, mGULO iPSC 3, Dox 100 ng/ml, day 27

value: Human Liver Organoids

value: mGULO

value: Hepatocytes

value: Dox 100ng/ml


title: Orc2DeltaN200_replicating [N200_30]

description: Yeast whole-genome sequencing.


title: PKM2-/- heart, sham 2

value: male


title: 66-130-2017-4-26-2017_S66

tag: animal id


title: PKM2-/- heart, sham 1

value: 8-12 weeks


title: 67-133-2017-4-26-2017_S67

tag: developmental stage


title: Orc2DeltaN200_nonreplicating [N200_0]

description: Yeast whole-genome sequencing.


title: HLOs, mGULO iPSC 1, Dox 100 ng/ml, day 27

tag: time


title: HLOs, mGULO iPSC 2, Dox 100 ng/ml, day 27


title: Sample-1 DC2.4 unstimulated

description: Control


title: PKM2-/- heart, baseline 2

value: heart


title: WT_nonreplicating [FL_0]

description: Yeast whole-genome sequencing.

value: WT


title: HLOs, Healthy iPSC 3,Control, day 27

value: wild type

value: Control


title: HLOs, Healthy iPSC 2,Bilirubin 1 mg/L, day 27

value: Day 27

value: Bilirubin 1 mg/L


title: PKM2-/- heart, baseline 1


title: 64-123-2017-4-26-2017_S64

value: Male


title: 65-125-2017-4-26-2017_S65


title: Ifnlr1-/- Day 5 post MA10 SARS-CoV-2 Mouse Lung 3-Replicate 1

first: Emily

last: Hemann

address: 460 W 12th Ave

institute: Ohio State University

data_processing:
Raw RNA-seq files (fastq) were de-multiplexed using Illumina bcl2fastq (v.2.17).
Reads were trimmed using cutadapt, and quality scores were assigned via FastQC.
Sequencing reads were aligned to the Mus musculus genome build mm10 using STAR, and gene counts were generated via HTseq using Rosalind (v.3.34.2.2; [https://rosalind.bio/]).
Gene counts were filtered, normalized, and subjected to statistical analysis to determine differential gene expression as previously described in Forero, et al, 2019, Immunity.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
RNA was extracted from lung homotenates in Trizol using a Ribopure extraction kit
RNA libraries for RNA-seq were prepared by Genewiz.

value: Lung

value: 10^5 TCID50 SARS-CoV-2 MA10


title: HLOs, Healthy iPSC 2,Control, day 27


title: 63-115-2017-4-26-2017_S63

value: Healthy

value: Steer


title: 62-109-2017-4-26-2017_S62

value: Bull


title: RPE-1_Nutlin-3a_3

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422.
We used Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v3.3. Potential sequencing errors were detected and corrected using Rcorrector v1.0.4. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1 for uniqueness.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.102 (46), using the mapping software segemehl (47, 48) v0.3.4 with adjusted accuracy (95%) and split-read option enabled. Mappings were filtered by Samtools v1.12 (49) for uniqueness.
Following pre-processing of the data, read quantification was performed on exon level using featureCounts v2.0.1, parametrized according to the strand specificity inferred through RSeQC v4.0.0. Differential gene expression and its statistical significance was identified using DESeq2 v1.32.0.
Assembly: hg38
Supplementary files format and content: DESeq2 results table

source_name: retina

growth_protocol: HCT116 cells were grown in high glucose DMEM with pyruvate. RPE-1 hTERT cells were cultured in DMEM:F12 media. Culture media were supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol.
Libraries were prepared from 200 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (New England Biolabs). Quantification and quality checked of libraries was done using a 4200 Tapestation instrument and a DNA 1000 kit (Agilent Technologies).
Libraries were pooled and sequenced on a NovaSeq 6000 SP 100 cycle v1.5 run. System runs in 101 cycle/single-end/standard loading workflow mode.

treatment_protocol: Cells were treated with Nutlin-3a 10 µM or DMSO control for 24 h

value: retina

value: RPE-1 hTERT

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 µM 24 h


title: PKM2fl/fl heart, 3d MI 2

value: male

value: 8-12 weeks

value: heart

value: 3d MI


title: PKM2fl/fl heart, 3d MI 3


title: 61-105-2017-4-26-2017_S61


title: RPE-1_Nutlin-3a_2


title: B6 WT Day 5 post MA10 SARS-CoV-2 Mouse Lung 3-Replicate 1

value: WT


title: Ifnlr1-/- Day 5 post MA10 SARS-CoV-2 Mouse Lung 2-Replicate 1


title: Orc2194E_replicating [MUT4_30]

description: Yeast whole-genome sequencing.


title: WT_replicating [FL_30]

description: Yeast whole-genome sequencing.


title: PKM2fl/fl heart, sham 3

value: sham


title: PKM2fl/fl heart, 3d MI 1


title: PKM2fl/fl heart, sham 2


title: B6 WT Day 5 post MA10 SARS-CoV-2 Mouse Lung 2-Replicate 1


title: 59-199-2017-3-29-2017_S59

value: Male


title: 60-104-2017-4-26-2017_S60


title: B6 WT Day 5 post MA10 SARS-CoV-2 Mouse Lung 1-Replicate 1

value: Lung


title: RPE-1_Nutlin-3a_1


title: PKM2fl/fl heart, sham 1


title: 58-187-2017-3-29-2017_S58


title: HLOs, Healthy iPSC 1,Control, day 27

value: Human Liver Organoids

value: Hepatocytes

value: wild type

value: Day 27

value: Control


title: RPE-1_DMSO_1

value: retina

value: RPE-1 hTERT

value: DMSO 24 h


title: Ifnlr1-/- Day 5 post MA10 SARS-CoV-2 Mouse Lung 1-Replicate 1

value: 10^5 TCID50 SARS-CoV-2 MA10


title: RPE-1_DMSO_2

value: epithelial cells

value: wild-type


title: 57-195-2017-3-29-2017_S57

value: Healthy

value: Bull


title: Ifnlr1-/- Day 2 post MA10 SARS-CoV-2 Mouse Lung 1-Replicate 1


title: Ifnlr1-/- Day 2 post MA10 SARS-CoV-2 Mouse Lung 3-Replicate 1


title: PKM2fl/fl heart, baseline 2

value: male

value: 8-12 weeks

value: heart


title: 56-192-2017-3-29-2017_S56

value: Male


title: Ifnlr1-/- Day 2 post MA10 SARS-CoV-2 Mouse Lung 2-Replicate 1

value: Lung


title: PKM2fl/fl heart, baseline 1


title: HCT116_Nutlin-3a_2

source_name: colon

value: colon

value: Nutlin-3a 10 µM 24 h


title: 55-185-2017-3-29-2017_S55


title: Ifnlr1-/- Naïve Mouse Lung 4-Replicate 1

value: Naive


title: HCT116_Nutlin-3a_1


title: RPE-1_DMSO_3


title: 54-181-2017-3-29-2017_S54


title: 120CHp

city: Stellenbosch

first: Evelyn

last: Maluleke

state: Western cape

address: Victoria street

department: Viticulture and Oenology

country: South Africa

institute: Stellenbosch University

data_processing:
STAR 2.6.1
Sequencing reads underwent quality and adaptor contamination checks both before and after trimming using FastQC 0.11.9. Trim Galore 0.6.5 was then employed to eliminate low-quality reads (Q <20), polyA reads, ambiguous reads containing N, and those shorter than 20 nt, while Cutadapt 1.7.1 was used to trim adapters from the remaining reads.
Trimmed sequence reads were mapped to a concatenated genome (Hypbu1+B05. 10). Parameters (Mismatch= (--outFilterMismatchNmax 10)
The GeneCounts function from STAR was used to obtain read counts
Assembly: Hypbu1 and B05. 10
Supplementary files format and content: tab-delimited txt file for each timepoint

organism: Hyphopichia pseudoburtonii

source_name: monoculture, control, 120h

growth_protocol: H. pseudoburtonii Y963 and B .cinerea were maintained on WL agar and Malt extract agar respectively. Bothe cultures were grown at 25°C

extract_protocol:
total RNA was extracted using a modified version of the hot acidic phenol method originally described by Collart and Oliviero
RNA libraries for RNAISeq were prepared using the Ion Total Transcriptome Sequencing Kit v2

treatment_protocol: H. pseudoburtonii was co-cultured with B. cinerea (coculture/treated), and controlas were prepared by growing H. pseudonurtonii in the absence of B. cinerea (monoculture/control)

value: eukaryotic

tag: hp strain

tag: bc strain

value: monoculture, control, 120h


title: 120BHp


title: HCT116_DMSO_3

tag: cell type


title: 120AHp


title: 53-177-2017-29-2017_S53


title: Ifnlr1-/- Naïve Mouse Lung 1-Replicate 1


title: HCT116_Nutlin-3a_3

tag: cell line


title: HCT116_DMSO_2

tag: genotype


title: B6 WT Day 2 post MA10 SARS-CoV-2 Mouse Lung 3-Replicate 1

value: WT

tag: treatment


title: 48CHp

source_name: monoculture, control, 48h

tag: tissue

value: monoculture, control, 48h


title: 51-168-2017-3-29-2017_S51

tag: Sex

value: Steer


title: HCT116_DMSO_1

value: epithelial cells

value: DMSO 24 h


title: B6 WT Day 2 post MA10 SARS-CoV-2 Mouse Lung 2-Replicate 1

value: 10^5 TCID50 SARS-CoV-2 MA10


title: 48BHp


title: 48AHp


title: B6 WT Day 2 post MA10 SARS-CoV-2 Mouse Lung 1-Replicate 1


title: 24CHp

source_name: monoculture, control, 24h

value: monoculture, control, 24h


title: 50-167-2017-3-29-2017_S50

value: Bull


title: SKOV3/DDP_Pae_1

city: Wuhan

first: Jingchun

last: Liu

state: HUBEI

address: Zhangzhidong road

institute: Renmin Hospital of Wuhan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel  network flow algorithm as well as an optional de novo assembly step to assemble and  quantitate fulllength transcripts representing multiple splice variants for each gene  locus.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 4 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Genome_build: Homo_sapiens_AR109
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cisplatin‑resistant human epithelial  ovarian cancer cell line

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
A total amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under elevated  temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H-  ). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5  min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

tag: agent

value: Paeonol


title: 49-166-2017-3-29-2017_S49


title: 24AHp


title: Ifnlr1-/- Naïve Mouse Lung 2-Replicate 1

source_name: Lung


title: 24BHp


title: 47-160-2017-3-29-2017_S47

value: Healthy


title: SKOV3/DDP_Pae_3


title: B6 WT Naïve Mouse Lung 1-Replicate 1


title: B6 WT Naïve Mouse Lung 2-Replicate 1


title: SKOV3/DDP_2


title: 46-158-2017-3-29-2017_S46

value: Male


title: 52-169-2017-3-29-2017_S52


title: agshNC#3

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

data_processing:
Fo small RNAs, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming process were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were aligned to the human genome (GRCh38) by using Bowtie2 (v2.3.5.1). Reads that cannot be aligned to the human genome were then aligned to agshRNA. The sequences and lengths of reads aligned to agshRNA were then determined using an in-house script. Reads mapped to genome were further categorized as miRNA, tRNA, snoRNA etc. by using htseq-count (v0.11.2).
For total RNAs, libraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. All reads were mapped to the human genome (GRCh38) using Hisat2(v2.1.0) and then annotated using htseq-count(v0.11.2)
Assembly: Human genome (GRCh38)
Supplementary files format and content: small RNA sequencing: bed format
Supplementary files format and content: Transcriptome sequencing: expression matrix counted by htseq-count

source_name: Human  HEK293T cells

extract_protocol:
For small RNA sequencing, Total RNA was extrated using Trizol regent accounding to the manufacturer's instructions. For transcriptome sequencing, RNA was extracted using Total RNA kit according to the manufacturer's instuctions
TruSeq Small RNA Library Preparation Kits (Illumina) (for small RNAs); MGIEasy RNA Library Preparation Kits (BGI) (for total RNAs)
Illumina HiSeq 2000 (for small RNAs); MGISEQ2000 (BGI) (for total RNAs)

value: Human  HEK293T cells

value: agshNC


title: B6 WT Naïve Mouse Lung 4-Replicate 1

value: Lung


title: SKOV3/DDP_Pae_2


title: SKOV3/DDP_3


title: HUVEC_Ang Ⅱ-1 [SAMPLE 4]

city: Shanghai

first: Hao

last: Lin

state: Shanghai

address: No. 389, Xincun Road

department: Department of Cardiology

institute: Tongji Hospital, School of Medicine, Tongji University,

data_processing:
Raw reads form the sequencing data, after removal the adaptors and filtering out low quality reads, were labeled Cleandata. Then, rRNA residues were removed by comparing known rRNA to get statistical data.
It needs to align twice, due to the particularity of splice site reads. Firstly, one normal alignment of reads using Tophat2 software and exclude fusion gene alignments, thereby gain the reads which cannot align to the reference genome. For unmapped reads of gene fusion align, we used Tophat-fusion of Tophat2 software. And to acquire potential looping reads.This two-step alignment procedure was the 2 basic steps for circRNAs prediction.
The circRNA were identified and performed by RiboBio (Guangzhou, China). Then, to compare the positions of the two ends of the identified circRNA splicing site on the genome using the ANNOVAR software, and to annotate circRNAs by aligning against multiple databases. At last, the origin of circRNA in the genome was predicted according to the origin of the sequences at both ends of the circular RNA splicing site.
The circRNA expression level was based on the predicted circRNA sequence, and was obtained by counting the number of circRNA reads and calculating its RPM (Reads Per Million mapped reads). RiboBio uses HTseq software to calculate the count value for each circRNA, and then further calculate its RPM value. The formula for calculating the RPM value is as follows, RPM = (circRNA readCount*1,000,000)/total mapped reads.
Assembly: Hg19
Supplementary files format and content: We used HTseq software to calculate the count value for each circRNA, and then further calculate its RPM value. The formula for calculating the RPM value is as follows, RPM = (circRNA readCount*1,000,000)/total mapped reads.

source_name: HUVEC

growth_protocol: HUVEC cultured in Dulbecco’s Modified Eagle Medium (DMEM, low glucose, Hyclone) supplemented with 5% FBS (Gibco), 3% penicillin/streptomycin (Gibco)

extract_protocol:
Then total RNA of above HUVECs were extracted using mirVanaTM RNA Isolation Kit. Total RNA concentration was determined using NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined with Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA libraries for RNA-seq were constructed by RiboBio (Guangzhou, China) following illumina protocols.

value: HUVEC

value: ea.hy 926

value: human umbilical vein endothelial cells

value: Ang Ⅱ treatment


title: 44-155-2017-3-29-2017_S44


title: HUVEC_HG-2 [SAMPLE 3]

value: WT

value: high glucose treatment


title: agshNC#1


title: SKOV3/DDP_1


title: 48-162-2017-3-29-2017_S48

value: Steer


title: 43-147-2017-3-29-2017_S43


title: HUVEC_HG-1 [SAMPLE 2]


title: agshEV71-h1#2


title: HUVEC_NC [SAMPLE 1]


title: SKOV3_Pae_1

source_name: cisplatin‑sensitive human epithelial  ovarian cancer cell line


title: agshEV71-h1#1


title: SKOV3_Pae_3


title: 42-139-2017-3-29-2017_S42


title: SKOV3_3


title: E15.5Heart, HighFatDiet, Rep3

city: Houston

first: Yun

last: Huang

address: 2121 W HOLCOMBE blvd, Room 429

department: Health Science Center

data_processing:
Adaptor trimming of raw reads was performed by TrimGalore v0.5.0 with default parameters.
High-quality reads (Q ≥ 20) were uniquely aligned to the mm10 reference genome using Bowtie2 with the ‘--very-sensitive’ option
The resulting alignment of each sample (with two biological replicates) was analyzed by Genrich v.0.5 (https://github.com/jsh58/Genrich) with ATAC-seq mode (option: -j, -q 0.05, -d 150)
Bedtools merge was used to count the reads that fell into non-overlapped peak regions
Differential chromatin accessible regions were detected using DESeq2 with normalized peak signals (fold change ≥ 2; FDR < 0.05)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: E15.5 embryonic heart

growth_protocol: Timed mating was applied and the day when a vaginal plug was found was defined as E0.5. At E15.5, embryonic hearts were dissected out to perform the ATAC-seq analysis.

extract_protocol:
To isolate the nuclei for ATAC-seq, embryonic heart tissues were first rinsed with ice-old PBS. Nuclei were then extracted using a dounce homogenizer in ATAC lysis buffer.
ATAC-seq libray preparation was performed using the ATAC-seq kit (Active motif, 53150) in accordance with the manufacturer’s instructions.

treatment_protocol: For the maternal high-fat diet experiments, female mice at 8–10 weeks old were fed with high-fat diet (60 kcal% fat, D12492i, Research Diets, USA) for 9 weeks before timed mating. The age-matched mice were fed normal diet (10 kcal% fat, D12450Ji, Research Diets) for 9 weeks before timed mating and used as control.

value: E15.5 embryonic heart

value: embryonic heart cell

value: high-fat diet


title: agshNC#2


title: agshEV71-h1#3


title: 41-133-2017-3-29-2017_S41

source_name: Whole blood

value: Bull