title: Neurons isolated from primary motor cortex, control (biol rep 2)

description:
Library name: RM06
10X Genomics


title: DU145 cells,si-P53RRA

status: Public on May 30 2025

type: SRA

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

country: China

institute: Forevergen

library_source: transcriptomic

data_processing:
|log2 ratio | ≥ 1 and FDR ≤ 0.001 were regarded as significantly differentially expressed mRNAs.
Differentially expressed mRNAs were selected to conduct a heat map and hierarchical clustering analysis to show distinguishable mRNA expression profiles among the samples.
GO and pathway enrichment analyses were performed to identify potential biological processes of the differentially expressed mRNA based on the GO (http://geneontology.org/page/go-enrichment-analyses) and pathway (http://www.genome.jp/kegg/pathway.html) databases.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: prostate

growth_protocol: DU145 cells were cultured in RPMI-1640 (Gibco, A1049101, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco, 10091155), 1% penicillin (100 U/mL), and streptomycin (100 U/mL, Gibco, 15140122). Cells were maintained at 37°C in a humidified incubator with 5% CO2 and 95% air.

extract_protocol:
Total RNA was isolated from each group of DU145 cells using RNA-iSo PluS (Takara Bio Inc.)
Beads (Invitrogen, Carlsbad, CA) with oligo (dT) were used to isolate poly (A) mRNA after total RNA was collected. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer was used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QIAQuick PCR extraction kit (Qiagen, Hilden, Germany) and resolved with EB buffer for end reparation and adding poly (A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments as templates, with respect to the result of agarose gel electrophoresis.

treatment_protocol: First, DU145 cells were seeded in 6-well plates (2×105) and transfected with 200pmol P53RRA siRNA using Lipofectamine 3000 reagent (Invitrogen, L3000150, Shanghai, China). After 4 h, the medium was replaced with fresh RPMI-1640 medium containing 10% FBS. After another 48h of culture, the cells were harvested to extract proteins for the next analysis.

tag: tissue

value: prostate

tag: cell line

value: DU145 cells

tag: cell type

value: prostate cancer cell

tag: treatment

value: The si-P53RRA were transfected into DU145 cells


title: DU145 cells


title: Exp2_Prkar1a KD + Gcgr mAb_rep9

city: Tarrytown

first: Kehan

last: Bao

state: NY

address: 777 Old Saw Mill River Rd

country: USA

institute: Regeneron Pharmaceuticals

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17. Reads were decoded based on their barcodes, and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches. Reads mapped to the exons of a gene were summed at the gene level.
Assembly: GRCm38/mm10
Supplementary files format and content: csv files of raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was purified from liver tissue using MagMAX-96 for the Microarrays Total RNA Isolation kit (Ambion by Life Technologies), according to manufacturer specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using the Dynabeads® mRNA Purification kit (Invitrogen).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using the KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries.

value: liver

value: Prkar1a KD + Gcgr mAb


title: TSC352_BJ_ATAC_shNFIC-101

city: La Jolla

first: Tom

last: Suter

state: CA

address: 9500 Gilman Dr

department: Department of Medicine

institute: UCSD

library_source: genomic

data_processing:
Data was aligned to hg18 using STAR-aligner with parameters adjusted avoid spliced alignments.
Aligned reads were processed for downstream analysis using the HOMER (Heinz et al., 2010) “makeTagDirectory” program, filtering for tags that were uniquely mapped and only selecting at most one sequencing read per position per length of read.
bigWig files were generated using the makeBigWig.pl function in HOMER
Genome_build: hg18
Supplementary_files_format_and_content: .bigWig : display of ATAC-seq data on genome browser as a graph

molecule: genomic DNA

source_name: Foreskin dermal fibroblast

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.

extract_protocol:
~50,000 BJ fibroblasts (senescent or quiescent via contact inhibition) were collected via trypsinization, washed in PBS on ice, resuspended in 200uL ice cold ATAC-seq lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) by being gently pipetted up and down 10 times, and immediately centrifuged for at 1000g for 10 minutes at 4°C.  The tagmentation reaction was performed using the Nextera DNA Library Prep Kit (Illumina-FC-121-1030), with the pellet being resuspended in 50uL 1x TD buffer and with 2.5uL Tn5 Transposase.  This reaction was incubated at 37°C for 30 minutes, after which DNA was purified using MinElute Reaction Cleanup Kit (Qiagen-28204).
Tagmented DNA was prepared for Illumina sequencing using the KAPA Real-Time Library amplification kit (KAPA/Roche-KK2701), as per manufacturer’s instructions, using Illumina Nextera primers.  Individual samples’ reactions were removed upon their qPCR intensity reaching that of Standard 2, which was typically after around 10 cycles of amplification.  Once all samples were sufficiently amplified and removed, the samples were size selected for 150-800bp fragments using AmPureXP beads (Beckman-A63880).  Samples were then sequenced using Illumina’s Nextera sequencing primer on the HiSeq 2500 using 100 cycle single read runs.

treatment_protocol: Lentivirus was produced through transfection of packaging plasmids into 293T (ATCC® CRL-3216) cells grown to ~80% confluency.  All transfections were done using Lipofectamine 2000 (Thermo Fisher 12566014), following the manufacturer’s protocol, with the ratios of plasmids and Lipofectamine 2000 reagent listed below.  Lentivirus for use in shRNA knockdown experiments was generated by transfecting a 0.625 : 1.875 : 2.5 ug ratio of MDC envelope plasmid: psPAX2 packaging plasmid: pLKO.1 shRNA expressing transfer plasmid with 17ul Lipofectamine 2000 in a 6-well plate well.  Media was changed 6 hours post transfection, and the viral containing media was collected and replaced at 48 and 72 hours post transfection.  Viral containing media was centrifuged at 600g for 5 min and the viral supernatant was collected and stored at 4°C prior to transduction.  Lentiviral transduction was performed on senescent BJ fibroblasts at ~50% confluency.   pLKO.1 stable knockdown lines were generated using a 48 ul : 1952 ul ratio of pLKO.1 viral supernatant with fresh culture media.  All transduction mixtures were given to cells and allowed to incubate overnight with polybrene added at a final concentration of 8ug/ml.  Knockdown cells were then maintained in 0.6ug/ml puromycin starting 4 days after transduction, and cells were harvested 14 days after transduction.

value: BJ Fibroblast

tag: shRNA target

value: shRNA - NFIC

tag: Stage

value: Senescent


title: TSC350_BJ_ATAC_shNFIB-69

value: shRNA - NFIB


title: Exp2_Control AAV + Gcgr mAb_rep9

value: Control AAV + Gcgr mAb


title: Exp2_Control AAV + Control mAb_rep9

value: Control AAV + Control mAb


title: Exp2_Control AAV + Gcgr mAb_rep8


title: Neurons isolated from primary motor cortex, late learning (biol rep 2)

city: New York

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

description:
Library name: RM03
10X Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment and quantification using Cellranger version 3.1.0
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw h5 counts tables for each sample

source_name: brain; primary motor cortex

extract_protocol:
After CaMPARI labeling, mice were returned to their home cage for 15 minutes and then euthanatized by transcardial perfusion. Subsequent steps were adapted from previous studies describing a protocol optimized for preserving transcriptional state57. Perfusions were performed with with ice-cold choline solution: 2.1 g/l NaHCO3, 2.16 g/l glucose, 0.172 g/l, NaH2PO4 * H2O, 7.5mM MgCl2•6H2O, 2.5mM KCl, 10mM HEPES, 15.36 g/l choline chloride, 2.3 g/l ascorbic acid, and 0.34 g/l pyruvic acid. Thick sections were cut using a matrix, and M1 was quickly dissected. The dissected M1 tissue was further triturated with spring scissors. The tissue was then digested with the Papain dissociation system (Worthington) according to the manufacturer’s instructions. However, the EBSS solution was replaced with the following: HBSS (Life Technologies), 10mM HEPES (Sigma), 172mg/l kynurenic acid (Sigma), 0.86 g/l MgCl2•6H2O (Sigma), 6.3 g/l D-glucose (Sigma). Incubation with papain was conducted using a dialysis membrane (Fisher Scientific, Slide-a-Lyzer MINI Dialysis Device,10k molecular weight cut-off) suspended in a beaker of dissociation solution allowing for constant oxygenation (95% O2 and 5% CO2) of the solution without disrupting enzyme integrity within the dialysis membrane. After enzymatic dissociation, the tissue was broken into a single-cell suspension by gently pipetting using wide-bore pipette tips. The sample was cleaned using the Debris Removal Solution (Miltenyi Biotec) as described by the manufacturer. Cells were suspended in dissociation solution containing 0.04% BSA, Vybrant DyeCycle Ruby for exclusion debris, and RNAase inhibitors. Cell sorting was performed using a FACSAria Cell Sorter (Becton Dickinson) with a 130 um nozzle at 12 PSI using the following laser lines and filters: CaMPARI Green, 488 nm, 530/30 bandpass; CaMPARI Red, 561 nm, 610/20 bandpass; DyeCycle Ruby, 637 nm, 670/30 bandpass. Gates were set using a sample not expressing CaMPARI and a sample not exposed to photoconversion light. Any cells with detectable red fluorescence were collected.
10x Genomics Chromium 3' end v3

value: brain; primary motor cortex

value: neurons

tag: genotype

value: WT

tag: Sex

value: male

tag: age

value: 12-16 weeks


title: TSC348_BJ_ATAC_shp65-1

value: shRNA - p65


title: Neurons isolated from primary motor cortex, control (biol rep 1)

description:
Library name: RM05
10X Genomics


title: Neurons isolated from primary motor cortex, late learning (biol rep 3)

description:
Library name: RM04
10X Genomics


title: TSC346_BJ_ATAC_shSMAD3-72

value: shRNA - SMAD3


title: Exp2_Prkar1a KD + Control mAb_rep9

value: Prkar1a KD + Control mAb


title: Neurons isolated from primary motor cortex, early learning (biol rep 1)

description:
Library name: RM02
10X Genomics


title: Neurons isolated from primary motor cortex, late learning (biol rep 1)

description:
Library name: RM01
10X Genomics


title: TSC341_BJ_ATAC_shGFPN

value: shRNA - GFP - Control


title: TSB214_BJ_GRO_HPGA_RW_Rep2

description: Nascent RNA

data_processing:
Data was aligned to hg18 using STAR-aligner, with parameters adjusted to avoid spliced alignment.
Aligned reads were processed for downstream analysis using the HOMER (Heinz et al., 2010) “makeTagDirectory” program, filtering for tags that were uniquely mapped and only selecting at most one sequencing read per position per length of read.
bigWig files were generated using the makeBigWig.pl function in HOMER, using the -rnaseq style parameter.
Genome_build: hg18
Supplementary_files_format_and_content: .bigWig : display ofGRO-seq data on genome browser as a graph

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.  Cells grown in rapamycin were introduced to and maintained in 10nM rapamycin after recovery from thawing.  For rapamycin withdrawal experiments, rapamycin maintained cells were grown to arrest, which typically occurred between PD75-85.  These cells are termed High Passage Growth Arrested.  At this point, the cells were divided into two plates that were either maintained or withdrawn from rapamycin for 2 weeks until they were collected.

extract_protocol:
GRO-seq was performed as described in Li et al., 2013(Li et al., 2013).  In brief, approximately 10 million BJ fibroblasts (either senescent or quiescent) were used per experimental condition.  Cells were incubated for 5 minutes on ice in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2), then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), and finally re-suspended in 100ul freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).  The run-on reaction was then performed by mixing the re-suspended nuclei with an equal volume of run-on reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase-In, 1% sarkosyl, 500?M ATP, GTP, and Br-UTP, 2?M CTP) and incubating 5 min at 30°C.  TRIzol LS reagent (Invitrogen) was then used, as per manufacturer’s instructions, to extract nuclear run-on RNA (NRO-RNA).
NRO-RNA was then hydrolyzed to ~300bp fragments via 35 minute incubation on ice in 0.2M NaOH, after which it was treated with DNase I and Antarctic phosphatase.  Following this, Br-UTP labeled NRO-RNA was purified using anti-BrdU agarose beads (Santa Cruz Biotech) incubated rotating at 4°C for 3h in binding buffer (0.5×SSPE, 1mM EDTA, 0.05% tween).  NRO-RNA then underwent end-repair using T4 PNK (NEB), after which cDNA synthesis was performed.      RNA fragments underwent a poly-A tairing reaction via incubation with poly-A polymerase (NEB) for 30 min at 37°C, after which reverse transcription was performed using superscript III (Invitrogen) with oNTI223 primer (Table 3).  cDNA products were then run on a 10% polyacrylamide TBE-urea gel, after which products between 100-500bp were cut and recovered by gel extraction.  Afterwards, first strand cDNA was circularized via CircLigase (Epicentre), and then re-linearized by treatment with Ape1 (NEB).  The re-linearized cDNA was then size selected on a TBE gel and fragments between ~120-320 bp were recovered via gel extraction.  This cDNA was then amplified via PCR using Phusion High-Fidelity enzyme (NEB) with oNTI200 ID1-6 (each sample is amplified with a different ID# primer to impart a distinct barcode) and oNTI201 (Table 3) for deep sequencing using the HiSeq 2500 system with single read runs of 50 cycles.
GRO-seq

treatment_protocol: High Passage Growth Arrested BJ fibroblasts maintained in 10nM rapamycin were split into 2 separate wells and either maintained in or withdrawn from 10nM rapamycin treatment for 14 days until they were harvested.

value: High Passage Growth Arrested

value: Rapamycin Withdrawal


title: Neurons isolated from primary motor cortex, early learning (biol rep 3)

description:
Library name: RM09
10X Genomics


title: Exp2_Prkar1a KD + Gcgr mAb_rep7

value: liver

value: Prkar1a KD + Gcgr mAb


title: MZ WT 3

city: ST LOUIS

first: Iris

last: Lee

state: MO

institute: Washington University in St. Louis School of Medicine

description: Library name: wt_3

data_processing:
RNA sequencing (RNA-Seq) reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust samples for differences in library size
The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma
Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: Genomic features read count matrix (tab delimited)

source_name: MZ B cell

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen)
RNA libraries for RNA-seq were prepared according to the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol

value: MZ B cell


title: Exp2_Control AAV + Control mAb_rep8


title: MZ WT 2

description: Library name: wt_2


title: Exp2_Prkar1a KD + Gcgr mAb_rep6


title: TSB213_BJ_GRO_HPGA_RM_Rep2

description: Nascent RNA

value: BJ Fibroblast

value: Rapamycin Maintained


title: TSC349_BJ_ATAC_shNFIA-21

value: shRNA - NFIA

value: Senescent


title: TSB212_BJ_GRO_HPGA_RW_Rep1

description: Nascent RNA


title: Exp2_Control AAV + Control mAb_rep7

value: Control AAV + Control mAb


title: MZ CD55KO 3

description: Library name: cd55ko_3


title: MZ CD55KO 2

description: Library name: cd55ko_2


title: MZ WT 1

description: Library name: wt_1

value: WT


title: MZ CD55KO 1

description: Library name: cd55ko_1


title: TSB211_BJ_GRO_HPGA_RM_Rep1

description: Nascent RNA


title: TSB182_BJ_GRO_Intermediate

description: Nascent RNA

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:4 8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.

extract_protocol:
GRO-seq was performed as described in Li et al., 2013(Li et al., 2013).  In brief, approximately 10 million BJ fibroblasts (either senescent or quiescent) were used per experimental condition.  Cells were incubated for 5 minutes on ice in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2), then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), and finally re-suspended in 100ul freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).  The run-on reaction was then performed by mixing the re-suspended nuclei with an equal volume of run-on reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase-In, 1% sarkosyl, 500?M ATP, GTP, and Br-UTP, 2?M CTP) and incubating 5 min at 30°C.  TRIzol LS reagent (Invitrogen) was then used, as per manufacturer’s instructions, to extract nuclear run-on RNA (NRO-RNA).
NRO-RNA was then hydrolyzed to ~300bp fragments via 35 minute incubation on ice in 0.2M NaOH, after which it was treated with DNase I and Antarctic phosphatase.  Following this, Br-UTP labeled NRO-RNA was purified using anti-BrdU agarose beads (Santa Cruz Biotech) incubated rotating at 4°C for 3h in binding buffer (0.5×SSPE, 1mM EDTA, 0.05% tween).  NRO-RNA then underwent end-repair using T4 PNK (NEB), after which cDNA synthesis was performed.      RNA fragments underwent a poly-A tairing reaction via incubation with poly-A polymerase (NEB) for 30 min at 37°C, after which reverse transcription was performed using superscript III (Invitrogen) with oNTI223 primer (Table 3).  cDNA products were then run on a 10% polyacrylamide TBE-urea gel, after which products between 100-500bp were cut and recovered by gel extraction.  Afterwards, first strand cDNA was circularized via CircLigase (Epicentre), and then re-linearized by treatment with Ape1 (NEB).  The re-linearized cDNA was then size selected on a TBE gel and fragments between ~120-320 bp were recovered via gel extraction.  This cDNA was then amplified via PCR using Phusion High-Fidelity enzyme (NEB) with oNTI200 ID1-6 (each sample is amplified with a different ID# primer to impart a distinct barcode) and oNTI201 (Table 3) for deep sequencing using the HiSeq 2500 system with single read runs of 50 cycles.

value: Intermediate - Quiescent


title: Exp2_Control AAV + Control mAb_rep6


title: Exp2_Control AAV + Gcgr mAb_rep6

value: Control AAV + Gcgr mAb


title: TSB183_BJ_GRO_Senescent

description: Nascent RNA


title: Exp2_Prkar1a KD + Gcgr mAb_rep8


title: CM272, anti-BclXL and anti-PD-1, sample 2

city: Pamplona

first: Ruben

last: Pio

state: Navarra

address: Pio XII Avenue, 55

department: Solid Tumors

country: Spain

institute: Cima Universidad de Navarra

description:
Library name: Triple_2
10x Genomics

data_processing:
Cell Ranger (v7.0.0, 10x Genomics Inc) was used to align reads to the mouse genome (GRCm39) and generate gene-by-cell UMI count matrices. scRNA-seq computational guidelines were followed using R packages. Empty droplets were removed using DropleUtils 1.18.1 (FDR < 0.001). For quality control analysis, genes were filtered using SingleCellExperiment 1.20.1 based on the distribution of UMI reads, distribution of unique genes or >5% of UMIs mapped to mitochondrial genes. scDblFinder was used to identify and remove potential doublets. Genes with zero UMIs in all the cells were excluded from the analysis.
Assembly: GRCm39
Supplementary files format and content: Output files of 10x Cell Ranger software: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: LLC tumor

growth_protocol: LLC cells (2 million) were injected subcutaneously into the flanks of 8-12 week old female C57BL/6J mice.

extract_protocol:
On day 15, tumors were harvested and processed under sterile conditions. Single-cell suspensions of tumors were obtained by mechanical and enzymatic dissociation using 1 mg/mL collagenase D and 50 µg/mL DNase I at 37°C for 30 minutes. EDTA (6 µM) was then used to block collagenase and DNase I activities. Erythrocytes were lysed, and cells were resuspended in 35% Percoll solution and centrifuged at 2,000 rpm for 15 minutes without brake. The supernatant was discarded and cells were preincubated with Fc block for 15 minutes at 4ºC, and then labeled with fluorochrome-conjugated antibodies against CD45, CD11b and Ly6G. Dead cells were labeled with SYTOX Blue. CD45+ and double CD11b-/Ly6G- cells were sorted.
The transcriptome of the cells was sequenced using Single Cell 3' Reagent Kits v3.1 (10X Genomics). Briefly, 20,000 cells (except for sample Triple_2, where only 5,840 cells could be obtained) were loaded at a concentration of 1,000 cells/µL on a Chromium X instrument (10X Genomics) to capture single cells in gel bead-in-emulsions (GEMs). In this step, each cell was encapsulated with primers containing a fixed Illumina Read 1 sequence, a cell-identifying 16 nt 10X barcode, a 12 nt unique molecular identifier (UMI), and a poly-dT sequence. After cell lysis, reverse transcription yielded full-length barcoded cDNA. This cDNA was then released from the GEMs, amplified by PCR and purified using magnetic beads (SPRIselect, Beckman Coulter). Enzymatic fragmentation and size selection were used to optimize cDNA size prior to library construction. Fragmented cDNA was end-repaired, A-tailed and ligated to Illumina adaptors. A final PCR amplification with barcoded primers allowed for sample indexing. Library quality control and quantification were performed using the Qubit 3.0 Fluorometer (Life Technologies) and the 4200 TapeStation System (Agilent), respectively. Sequencing was performed on NextSeq2000 and NovaSeq6000 instruments (Illumina) aiming for at least 20,000 reads/cell.

treatment_protocol: Tumor-bearing mice were treated with vehicle, 5 mg/kg CM272 (i.p.; 5 days per week, starting on day 6), 100 μg anti-PD-1 (i.p.; days 7, 10 and 14) and/or 5 mg/kg A1331852 (i.p.; 3 days per week starting on day 7).

value: LLC tumor

value: Immune cells

value: CM272, anti-BclXL and anti-PD-1

tag: batch


title: Exp2_Control AAV + Control mAb_rep5


title: TSC345_BJ_ATAC_shSMAD2-71

value: shRNA - SMAD2


title: TSB181_BJ_GRO_Young

description: Nascent RNA

value: Young - Quiescent


title: TSF134_BJ_Senescent_anti-NFI_TGFB2

data_processing:
Data was aligned to hg18 using STAR-aligner with parameters adjusted avoid spliced alignments.
Aligned reads were processed for downstream analysis using the HOMER (Heinz et al., 2010) “makeTagDirectory” program, filtering for tags that were uniquely mapped and only selecting at most one sequencing read per position per length of read.
bigWig files were generated using the makeBigWig.pl function in HOMER, using the -chipseq style parameter
Genome_build: hg18
Supplementary_files_format_and_content: .bigWig : display of ChIP-seq data on genome browser as a graph

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Samples prepared for ChIP of histone modifications were fixed in 1% formaldehyde for 10 minutes at room temperature, while samples prepared for ChIP of transcription factors were double cross-linked in either 2mM DSG alone for 45 minutes at room temperature followed by 10 minute fixation with 1% formaldehyde.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used for each histone or transcription factor ChIP assay, respectively, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of histone modifications were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 0.1% SDS, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 500mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (10mM Tris/HCl pH7.4, 250mM LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  ChIPs of transcription factors were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 300mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (20mM Tris/HCl pH7.4, 400mM NaCl, 1% Triton-X-100, 2mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using either the KAPA LTP Library Preparation Kit (KK8232) or KAPA Hyper Prep Kit (KK8500) for histone or transcription factor ChIPs, respectively, following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 75 cycles.

treatment_protocol: Senescent BJ fibroblasts were treated with SMAD2/3 regulating ligands Activin A (100ng/ml), TGFB2 (1ng/ml), Inhibin A (100ng/ml)+TGFB2 (1ng/ml), or Inhibin A (100ng/ml) for 14 days prior to being harvested for ChIP-seq.

tag: antibody

value: NFI:Santa Cruz sc-5567 (H-300)


title: Exp2_Prkar1a KD + Control mAb_rep8

value: liver

value: Prkar1a KD + Control mAb


title: U87MG-Luc cells, tumor4, after radiotherapy

city: SHANGHAI

first: Ruimin

last: Wang

state: SHANHAI

address: 1954 hUASHAN ROAD

institute: Shanghai Jiao Tong University

description: Sample17 was named "RT762" in raw file

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads  for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimated text file includes raw counts for each Sample

source_name: orthotopic tumor model using SPF-grade female BALB/c nude mice, aged 5-6 weeksnude mice

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit.
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 44.01-50.97 M raw reads for each sample were generated. Raw reads of FASTQ format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads. Then, about 41.39-48.48 M clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.

tag: host

value: nude mice

value: tumor tissue

tag: injected cell_line

value: human glioblastoma cell line


title: CM272, anti-BclXL and anti-PD-1, sample 1

description:
Library name: Triple_1
10x Genomics


title: CM272 and anti-BclXL, sample 3

description:
Library name: CM_BclX_3
10x Genomics

value: CM272 and anti-Bcl-XL


title: U87MG-Luc cells, tumor3, after radiotherapy

description: Sample16 was named "RT758" in raw file


title: TSF133_BJ_Senescent_anti-NFI_Control

value: BJ Fibroblast

value: Senescent


title: Exp2_Prkar1a KD + Control mAb_rep7


title: CM272 and anti-BclXL, sample 2

description:
Library name: CM_BclX_2
10x Genomics


title: Exp2_Control AAV + Gcgr mAb_rep7


title: U87MG-Luc cells, tumor2, after radiotherapy

description: Sample15 was named "RT756" in raw file

value: WT


title: Exp2_Prkar1a KD + Gcgr mAb_rep5

value: Prkar1a KD + Gcgr mAb


title: TSF124_BJ_Senescent_anti-SMAD23_TGFB2

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined


title: Exp2_Prkar1a KD + Control mAb_rep6


title: CM272 and anti-PD-1, sample 3

description:
Library name: CM_aPDI_3
10x Genomics

value: LLC tumor

value: CM272 and anti-PD-1


title: U87MG-Luc cells, tumor1, after radiotherapy

description: Sample14 was named "RT753" in raw file


title: anti-BclXL and anti-PD-1, sample 1

description:
Library name: BclX_aPDI_1
10x Genomics

value: Immune cells

value: anti-Bcl-XL and anti-PD-1


title: TSF122_BJ_Senescent_anti-SMAD23_Activin


title: U87MG-Luc cells, tumor2, befor radiotherapy

description: Sample11 was named "T-752-2" in raw file


title: U87MG-Luc cells, tumor3, befor radiotherapy

description: Sample12 was named "T-759" in raw file


title: U87MG-Luc cells, tumor4, befor radiotherapy

description: Sample13 was named "T-763-1" in raw file


title: Exp2_Prkar1a KD + Control mAb_rep5


title: TSF67_BJ_HPGA_anti-H3K27ac_RW_Inhibin+TGFB2

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:4 8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.  Cells grown in rapamycin were introduced to and maintained in 10nM rapamycin after recovery from thawing.  Rapamycin maintained cells were collected for RNA-seq and ChIP-seq at PD31 and PD66 to correspond with similar PD young and senescent non-rapamycin treated cells.  For rapamycin withdrawal experiments, rapamycin maintained cells were grown to arrest, which typically occurred between PD75-85.  These cells are termed High Passage Growth Arrested.  At this point, the cells were divided into two plates that were either maintained or withdrawn from rapamycin for 2 weeks until they were collected.

treatment_protocol: High Passage Growth Arrested BJ fibroblasts maintained in 10nM rapamycin were then either maintained or withdrawn from rapamycin for 14 additional days, and treated with either control or SMAD2/3 regulating ligands Activin A (100ng/ml), TGFB2 (1ng/ml), Inhibin (100ng/ml)+TGFB2 (1ng/ml), or Inhibin (100ng/ml) treatments during this 14 day period.

value: H3K27ac:abcam ab4729

value: High Passage Growth Arrested

value: Rapamycin Withdrawn + Inhibin + Tgfb2


title: vehicle, sample 1

description:
Library name: Ctrl_1
10x Genomics

value: Vehicle


title: U87MG-Luc cells, tumor1, befor radiotherapy

description: Sample10 was named "T-751" in raw file

value: nude mice


title: vehicle, sample 2

description:
Library name: Ctrl_2
10x Genomics


title: Exp2_Control AAV + Gcgr mAb_rep4

value: liver

value: Control AAV + Gcgr mAb


title: N6A-SKO-4

city: Xi'an

first: Luo

last: Yuru

state: Shannxi

address: 28 Xianning West Road

department: Health Science Center

institute: Xi'an Jiaotong University

description: Library name: N6A-SKO-4

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through fastp software.
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).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: txt files of readcount value for each sample

source_name: testis

extract_protocol:
Total RNA was extracted from heart ventricles using TRIzol reagent (Sigma)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,Catalog #: E7530L)

value: testis


title: TSF66_BJ_HPGA_anti-H3K27ac_RW_Inhibin

value: BJ Fibroblast

value: Rapamycin Withdrawn + Inhibin


title: Exp2_Control AAV + Control mAb_rep4

value: Control AAV + Control mAb


title: N6A-SKO-3

description: Library name: N6A-SKO-3


title: U87MG-Luc cells, control4

description: Sample9 was named "Cs-590" in raw file

value: adjacent non-cancerous tissue

value: human glioblastoma cell line

value: WT


title: Exp2_Prkar1a KD + Gcgr mAb_rep4

value: Prkar1a KD + Gcgr mAb


title: U87MG-Luc cells, control3

description: Sample8 was named "Cs-587" in raw file


title: TSF125_BJ_Senescent_anti-SMAD23_Inhibin+TGFB2

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: Senescent


title: Exp2_Control AAV + Control mAb_rep3


title: N6A-SKO-2

description: Library name: N6A-SKO-2


title: CM272 and anti-PD-1, sample 1

description:
Library name: CM_aPDI_1
10x Genomics

value: LLC tumor

value: Immune cells

value: CM272 and anti-PD-1


title: Exp2_Control AAV + Gcgr mAb_rep5


title: TSF123_BJ_Senescent_anti-SMAD23_Inhibin


title: TSF64_BJ_HPGA_anti-H3K27ac_RW_TGFB2

value: H3K27ac:abcam ab4729

value: High Passage Growth Arrested

value: Rapamycin Withdrawn + Tgfb2


title: U87MG-Luc cells, control2

description: Sample7 was named "Cs-584" in raw file

value: nude mice


title: Exp2_Control AAV + Gcgr mAb_rep3

value: liver

value: Control AAV + Gcgr mAb


title: TSF121_BJ_Senescent_anti-SMAD23_Control

value: BJ Fibroblast


title: N6A-SKO-1

description: Library name: N6A-SKO-1

value: testis


title: TSF63_BJ_HPGA_anti-H3K27ac_RW_Activin

value: Rapamycin Withdrawn + Activin A


title: Exp2_Prkar1a KD + Gcgr mAb_rep3


title: TSF61_BJ_HPGA_anti-H3K27ac_RM_Inhibin+TGFB2

value: Rapamycin Maintained + Inhibin + Tgfb2


title: CTL-3

description: Library name: CTL-3

value: CTL


title: Exp2_Prkar1a KD + Control mAb_rep4

value: Prkar1a KD + Control mAb


title: Exp2_Control AAV + Gcgr mAb_rep2


title: U87MG-Luc cells, tumor3

description: Sample3 was named "T-587" in raw file

value: tumor tissue

value: human glioblastoma cell line

value: WT


title: TSF60_BJ_HPGA_anti-H3K27ac_RM_Inhibin

value: Rapamycin Maintained + Inhibin


title: TSF65_BJ_HPGA_anti-H3K27ac_RW_Control

value: Rapamycin Withdrawn


title: CTL-1

description: Library name: CTL-1


title: CTL-4

description: Library name: CTL-4


title: U87MG-Luc cells, tumor4

description: Sample4 was named "T-588" in raw file


title: U87MG-Luc cells, control1

description: Sample6 was named "Cs-586" in raw file

value: adjacent non-cancerous tissue


title: Exp2_Control AAV + Gcgr mAb_rep1


title: Ndufs4 KO LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 4

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

data_processing:
Lung tissue samples were homogenized using a TissueRuptor (Qiagen) handheld rotor-stator homogenizer in PBS. Total RNA was extracted from clarified lung tissue and LET1 cell homogenates using an RNeasy Mini Kit (Qiagen). RNAseq was performed by an outside commercial laboratory (Novogene, Sacramento, CA). Messenger RNA was purified using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized with random hexamer primers, followed by second strand cDNA synthesis using dTTP. Libraries then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Sequencing was performed on the Illumina NovaSeq 6000 with 150bp paired-end reads. Reads were aligned to reference genome mm10 with Hisat2 v2.0.5, and raw read counts were determined using FeatureCounts v1.5.0-p3. Raw count normalization and differential expression analysis was performed using DESeq2 1.42.0 76. Volcano plots were prepared using EnhancedVolcano 1.20 with apeglm fold change shrinkage 77. For subsequent analysis, genes were considered significant if padj < 0.05 and log2 fold change > |0.263| where applicable. For viral read analysis, X31 sequences were downloaded through NCBI Virus using taxid:132504, 2006 sequences. fastq files were then aligned to the mouse genome using salmon 78, and unmapped sequences were collected and mapped to the X31 viral genome with Magic-BLAST 79. Reads mapping to each viral gene were then counted with salmon.GSEA. Gene sets were ranked by t-stat determined by DESeq2 prior to enrichment analysis. GSEA and visualization was performed with clusterProfiler 4.11.0 80.
Assembly: mm10
Supplementary files format and content: Mouse lung gene counts are mouse_lung_gene_count.xls
Supplementary files format and content: LET1 cell salmon outout are in individual  sample.sf output files.

growth_protocol:
WT and Ndufs4 KO mice were housed in a pathogen-free facility and had access to Purina Lab Diet rodent chow, product no. 5LL2, and autoclaved reverse osmosis water. Mice were kept in a temperature (22 ± 2 °C) and humidity (30-70%) controlled environment with a 12 h light-dark cycle. Cages housing Ndufs4 KO mice were provided food on the floor everyday following weaning.
WT and Ndufs4 KO LET1 cells were cultured in complete cell culture media (high glucose DMEM containing 10% (v/v) fetal bovine serum (FBS) and 100 U/mL penicillin-streptomycin) and maintained at 37 °C and 5% CO2

extract_protocol:
RNA was harvested using Rneasy Mini Kit (Qiagen).
For mouse lung and LET1 cell RNA samples: RNA libraries for RNAseq were prepared by Novogene using their established protocols. In brief, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library [Parkhomchuk D et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic acids research, 2009]. For non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked for Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol:
Mouse adapted human influenza virus A/X/31 (X31) subtype H3N2 was used for all IAV infections. WT and Ndufs4 KO mice were exposed to aerosolized 8.55 x 1010 foci forming units in 7 mL water. After 4 days post-infection, mouse lungs were harvested for RNA extraction.
IAV infection of WT and Ndufs4 KO LET1 cells was conducted using 1% (v/v) X31 IAV strain (8.55 x 109 FFU/mL) in complete cell culture media without FBS for 2 h in the absence of exogenous trypsin at 37 °C and 5% CO2. After incubation with virus, media was aspirated and cell monolayers were washed once with PBS followed by refreshment with complete cell culture media and incubation for an additional 22 h at 37 °C and 5% CO2 prior to RNA extracton.

value: LET1 cells

value: Ndufs4 KO

value: IAV (H3N2) infected

tag: time

value: 24 hours post-infection


title: Exp2_Prkar1a KD + Control mAb_rep3

value: liver


title: TSF56_BJ_HPGA_anti-H3K27ac_RM_Control

value: BJ Fibroblast

value: H3K27ac:abcam ab4729

value: High Passage Growth Arrested

value: Rapamycin Maintained


title: Ndufs4 KO LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 5


title: PANC-1_DMSO_4

first: Xiaoyan

last: Xu

address: No. 21, Yinquan South Road

institute: Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cell line

value: Human pancreatic cancer cell

value: DMSO


title: U87MG-Luc cells, tumor2

description: Sample2 was named "T-586" in raw file

value: nude mice

value: tumor tissue

value: human glioblastoma cell line


title: TSF59_BJ_HPGA_anti-H3K27ac_RM_Control


title: Exp2_Prkar1a KD + Gcgr mAb_rep2

value: Prkar1a KD + Gcgr mAb


title: WT LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 4

value: WT


title: TSF62_BJ_HPGA_anti-H3K27ac_RW_Control

value: Rapamycin Withdrawn


title: TSF146_BJ_HPGA_anti-p65_R10_Withdrawal_Inhibin

value: p65:Santa Cruz sc-372 (C-20)

value: Rapamycin Withdrawn + Inhibin


title: TSF58_BJ_HPGA_anti-H3K27ac_RM_TGFB2

value: Rapamycin Maintained + Tgfb2


title: TSF57_BJ_HPGA_anti-H3K27ac_RM_Activin

value: Rapamycin Maintained + Activin A


title: U87MG-Luc cells, tumor1

description: Sample1 was named "T-584" in raw file


title: U87MG-Luc cells, tumor5

description: Sample5 was named "T-590" in raw file


title: TSF145_BJ_HPGA_anti-p65_R10_Withdrawal_Control

value: BJ Fibroblast


title: CTL-2

description: Library name: CTL-2

value: testis

value: CTL


title: WT LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 5

value: LET1 cells

value: IAV (H3N2) infected

value: 24 hours post-infection


title: Exp2_Control AAV + Control mAb_rep2

value: liver

value: Control AAV + Control mAb


title: Ndufs4 KO LET1 cells, uninfected, 24 hours post-mock infection, replicate 5

value: Ndufs4 KO

value: uninfected

value: 24 hours post-mock infection


title: PANC-1_DMSO_2

value: cell line

value: Human pancreatic cancer cell

value: DMSO


title: PANC-1_DMSO_5


title: Exp2_Prkar1a KD + Control mAb_rep1

value: Prkar1a KD + Control mAb


title: Exp2_Prkar1a KD + Control mAb_rep2


title: Ndufs4 KO LET1 cells, uninfected, 24 hours post-mock infection, replicate 4


title: PANC-1_LY_5

value: 20μM LY


title: Exp2_Control AAV + Control mAb_rep1


title: TSF144_BJ_HPGA_anti-p65_R10_Withdrawal_TGFB2

value: p65:Santa Cruz sc-372 (C-20)

value: High Passage Growth Arrested

value: Rapamycin Withdrawn + Tgfb2


title: PANC-1_DMSO_3


title: PANC-1_DMSO_1


title: WT LET1 cells, uninfected, 24 hours post-mock infection, replicate 5

value: WT


title: Exp2_Prkar1a KD + Gcgr mAb_rep1

value: Prkar1a KD + Gcgr mAb


title: Ndufs4 KO LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 3

value: LET1 cells

value: IAV (H3N2) infected


title: Exp1_Control_rep10

value: liver


title: TSF147_BJ_HPGA_anti-p65_R10_Withdrawal_Inhibin+TGFB2

value: BJ Fibroblast

value: Rapamycin Withdrawn + Inhibin + Tgfb2


title: PANC-1_LY_3


title: Exp1_Gcgr KD_rep10

value: Gcgr KD0


title: Exp1_Gnas KD_rep10

value: Gnas KD0


title: Ndufs4 KO LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 2

value: Ndufs4 KO

value: 24 hours post-infection


title: WT LET1 cells, uninfected, 24 hours post-mock infection, replicate 4

value: uninfected

value: 24 hours post-mock infection


title: PANC-1_LY_4

value: cell line

value: Human pancreatic cancer cell

value: 20μM LY


title: TSF143_BJ_HPGA_anti-p65_R10_Withdrawal_Activin

value: p65:Santa Cruz sc-372 (C-20)

value: High Passage Growth Arrested

value: Rapamycin Withdrawn + Activin A


title: PANC-1_LY_2


title: Exp1_Gnas KD_rep9

value: Gnas KD


title: TSF132_BJ_HPGA_anti-NFI_RW_Control

value: NFI:Santa Cruz sc-5567 (H-300)

value: Rapamycin Withdrawn


title: TSF142_BJ_HPGA_anti-p65_R10_Withdrawal_Control

value: BJ Fibroblast


title: TSF141_BJ_HPGA_anti-p65_R10_Maintained_Control

value: Rapamycin Maintained


title: Ndufs4 KO LET1 cells, uninfected, 24 hours post-mock infection, replicate 3

value: LET1 cells


title: Exp1_PKA KD_rep8

value: liver

value: PKA KD


title: Ndufs4 KO LET1 cells, uninfected, 24 hours post-mock infection, replicate 2

value: Ndufs4 KO

value: 24 hours post-infection


title: WT LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 2

value: WT

value: IAV (H3N2) infected


title: TSF131_BJ_HPGA_anti-NFI_RM_Control


title: WT LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 3


title: TSF110_BJ_HPGA_anti-SMAD23_RW_Control

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined


title: 8679-e-nrc-6wk

city: St. LOuis

first: Vladimir

last: Lamm

address: 660 S. Euclid Avenue

department: Gastroenterology

institute: Washington University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Colon

extract_protocol:
RNA was isolated by RNAeasy kit (Qiagen).
RNA libraries for RNA-Seq were prepared using manufacturer's protocols.

value: Colon

tag: condition

value: Normal Ascending

tag: patient id#

value: Post (Week 6)


title: 9120-e-nrc

value: Baseline


title: Ndufs4 KO LET1 cells, uninfected, 24 hours post-mock infection, replicate 1

value: uninfected


title: Exp1_PKA KD_rep10

value: PKA KD0


title: Exp1_Gcgr KD_rep9

value: Gcgr KD


title: Exp1_Control_rep9

value: Control


title: 9120-e-ri

value: Rectum Inflamed


title: TSF112_BJ_HPGA_anti-SMAD23_RW_Inhibin+TGFB2

value: BJ Fibroblast

value: High Passage Growth Arrested

value: Rapamycin Withdrawn + Inhibin + Tgfb2


title: TSF108_BJ_HPGA_anti-SMAD23_RW_Activin

value: Rapamycin Withdrawn + Activin A


title: Exp1_Epac2 KD_rep9

value: liver

value: Epac2 KD


title: 8549-e-lci-6wk

value: Left Colon Inflamed


title: TSF107_BJ_HPGA_anti-SMAD23_RW_Control

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: Rapamycin Withdrawn


title: Exp1_PKA KD_rep9

value: PKA KD


title: TSF111_BJ_HPGA_anti-SMAD23_RW_Inhibin

value: Rapamycin Withdrawn + Inhibin


title: Exp1_Epac2 KD_rep10

value: Epac2 KD0


title: 8679-e-ri-6wk

value: Colon

value: Rectosigmoid Inflamed

value: Post (Week 6)


title: WT LET1 cells, IAV (H3N2) infected, 24 hours post-mock infection, replicate 1

value: LET1 cells

value: WT

value: IAV (H3N2) infected

value: 24 hours post-infection


title: WT LET1 cells, uninfected, 24 hours post-mock infection, replicate 1

value: uninfected

value: 24 hours post-mock infection


title: 8533-e-ri

value: Rectum Inflamed

value: Baseline


title: TSF106_BJ_HPGA_anti-SMAD23_RM_Inhibin+TGFB2

value: BJ Fibroblast

value: High Passage Growth Arrested

value: Rapamycin Maintained + Inhibin + Tgfb2


title: Ndufs4 KO mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 5

source_name: Mouse lung

value: Mouse lung

value: Ndufs4 KO

value: 4 days post-infection


title: Exp1_Control_rep8

value: liver

value: Control


title: TSF109_BJ_HPGA_anti-SMAD23_RW_TGFB2

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: Rapamycin Withdrawn + Tgfb2


title: 8657-e-ri-6wk

value: Colon

value: Post (Week 6)


title: WT LET1 cells, uninfected, 24 hours post-mock infection, replicate 3

value: LET1 cells

value: WT


title: 8657-e-nlc-6wk

value: Normal Descending


title: WT LET1 cells, uninfected, 24 hours post-mock infection, replicate 2

value: uninfected

value: 24 hours post-mock infection


title: TSF103_BJ_HPGA_anti-SMAD23_RM_TGFB2

value: BJ Fibroblast

value: Rapamycin Maintained + Tgfb2


title: Exp1_Gnas KD_rep8

value: Gnas KD


title: 8494-e-ri-6wk

value: Rectum Inflamed


title: Exp1_Epac2 KD_rep6

value: Epac2 KD


title: TSF101_BJ_HPGA_anti-SMAD23_RM_Control

value: High Passage Growth Arrested

value: Rapamycin Maintained


title: PANC-1_LY_1

value: cell line

value: Human pancreatic cancer cell

value: 20μM LY


title: Exp1_Epac2 KD_rep8

value: liver


title: Exp1_Gcgr KD_rep8

value: Gcgr KD


title: TSD325_IMR90_Senescent_anti-NFI

source_name: Lung fibroblast

growth_protocol: IMR90s (ATCC CCL-186) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:8 split.  IMR90s were considered to be young when collected below PD34 after thawing and showed a doubling time of less than 2 days, while IMR90s were considered to reach replicative senescence when collected above PD52 and failed to double after 1 week.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing IMR90s were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Samples prepared for ChIP of histone modifications were fixed in 1% formaldehyde for 10 minutes at room temperature, while samples prepared for ChIP of transcription factors were double cross-linked in either 2mM DSG alone for 45 minutes at room temperature followed by 10 minute fixation with 1% formaldehyde.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used for each histone or transcription factor ChIP assay, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of histone modifications were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 0.1% SDS, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 500mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (10mM Tris/HCl pH7.4, 250mM LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  ChIPs of transcription factors were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 300mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (20mM Tris/HCl pH7.4, 400mM NaCl, 1% Triton-X-100, 2mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using either the KAPA LTP Library Preparation Kit (KK8232) or KAPA Hyper Prep Kit (KK8500) for histone or transcription factor ChIPs, respectively, following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 75 cycles.

value: NFI:Santa Cruz sc-5567 (H-300)

value: Senescent


title: Ndufs4 KO mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 4

value: Mouse lung

value: Ndufs4 KO

value: IAV (H3N2) infected

value: 4 days post-infection


title: 8445-e-nsc-6wk

value: Colon

value: Normal Sigmoid

value: Post (Week 6)


title: 8533-e-ntc

value: Normal Transvere

value: Baseline


title: TSF105_BJ_HPGA_anti-SMAD23_RM_Inhibin

value: BJ Fibroblast

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: High Passage Growth Arrested

value: Rapamycin Maintained + Inhibin


title: TSF104_BJ_HPGA_anti-SMAD23_RM_Control

value: Rapamycin Maintained


title: Exp1_Epac2 KD_rep7

value: liver

value: Epac2 KD


title: WT mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 4

value: WT


title: 8445-e-nr-6wk

value: Normal Rectum


title: WT mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 3

value: Mouse lung


title: Ndufs4 KO mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 3

value: Ndufs4 KO

value: IAV (H3N2) infected


title: Exp1_Gnas KD_rep6

value: Gnas KD


title: Ndufs4 KO mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 2

value: 4 days post-infection


title: Ndufs4 KO mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 1


title: Exp1_Gcgr KD_rep7

value: Gcgr KD


title: WT mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 2


title: WT mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 5


title: TSF102_BJ_HPGA_anti-SMAD23_RM_Activin

value: Rapamycin Maintained + Activin A


title: 8482-e-ri

value: Colon

value: Rectum Inflamed

value: Baseline


title: 8522-e-ri


title: 8482-e-nlc

value: Normal Left


title: Exp1_Gnas KD_rep7


title: 8381-e-nlc-bs


title: TSD331_IMR90_Young_anti-p65

value: p65:Santa Cruz sc-372 (C-20)

value: Young - Quiescent


title: 8381-e-ri-bs


title: Exp1_PKA KD_rep6

value: liver

value: PKA KD


title: Exp1_PKA KD_rep7


title: TSD321_IMR9_Young_anti-NFI

value: NFI:Santa Cruz sc-5567 (H-300)


title: Exp1_PKA KD_rep5


title: 8378-e-ri-6wk

value: Post (Week 6)


title: TSD318_IMR90_Senescent_anti-H3K4me2_Rep2

value: H3K4me2:abcam ab7766

value: Senescent


title: TSD341_IMR90_Young_anti-SMAD23

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined


title: 8414-e-ri-6wk

value: Rectosigmoid Inflamed


title: TSD345_IMR90_Senescent_anti-SMAD23


title: TSD335_IMR90_Senescent_anti-p65


title: WT mouse lung, IAV (H3N2) infected, 4 days post-infection, replicate 1

value: Mouse lung

value: WT

value: IAV (H3N2) infected

value: 4 days post-infection


title: 8378-e-nr-6wk

value: Colon

value: Normal Rectum (sigmoid)


title: P8-Rack7-cKO-bio rep2

city: Shanghai

first: jiao

last: fangfang

address: DongAn Road 131

institute: fudan university

data_processing:
Sequencing reads were mapped to mouse reference genome (mm10) using the software Hisat2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes row counts for each sample.

source_name: Brain

growth_protocol: Primary astrocyte was extracted from mice brain at different postnatal days, and cultured with primary astrocyte medium (iCell Bioscience Inc).

extract_protocol: The mRNA capture and sequencing were performed by Azenta life science.

value: Brain

value: Postnatal day 8

value: Primary astrocyte

value: Rack7 conditional knockout


title: Exp1_Control_rep7

value: liver

value: Control


title: P8-WT-bio rep2


title: Exp1_Gcgr KD_rep6

value: Gcgr KD


title: TSD317_IMR90_Senescent_anti-H3K4me2_Rep1

value: H3K4me2:abcam ab7766


title: Exp1_Control_rep6


title: P8-WT-bio rep1


title: 8362-e-ri-6wk

value: Rectum Inflamed

value: Post (Week 6)


title: 8377-e-nr-6wk


title: Exp1_Epac2 KD_rep5

value: Epac2 KD


title: P6-Rack7-cKO-bio rep2

value: Postnatal day 6


title: TSD315_IMR90_Young_anti-H3K4me2_Rep1

value: Young - Quiescent


title: 8318-e-nri

value: Rectosigmoid Inflamed

value: Baseline


title: TSD316_IMR90_Young_anti-H3K4me2_Rep2


title: TSD314_IMR90_Senescent_anti-H3K27ac_Rep2

value: H3K27ac:abcam ab4729

value: Senescent


title: P6-WT-bio rep2

value: Brain

value: WT


title: Exp1_Gcgr KD_rep5


title: Exp1_Gnas KD_rep5

value: Gnas KD


title: P6-Rack7-cKO-bio rep1

value: Primary astrocyte

value: Rack7 conditional knockout


title: 8257-e-sci

value: Colon

value: Sigmoid Inflamed

value: Baesline


title: P8-Rack7-cKO-bio rep1

value: Postnatal day 8


title: TSD313_IMR90_Senescent_anti-H3K27ac_Rep1


title: 8250-e-sci-bs


title: P1-Rack7-cKO-bio rep2

value: Postnatal day 1


title: TSD311_IMR90_Young_anti-H3K27ac_Rep1


title: Exp1_Gcgr KD_rep4

value: liver

value: Gcgr KD


title: P6-WT-bio rep1

value: Postnatal day 6


title: 8255-e-ri-bs

value: Rectosigmoid Inflamed


title: TSD312_IMR90_Young_anti-H3K27ac_Rep2

value: Young - Quiescent


title: Exp1_Control_rep5

value: Control


title: 8250-e-nsc-bs

value: Normal Sigmoid

value: Baseline


title: Exp1_PKA KD_rep4

value: PKA KD


title: P1-Rack7-cKO-bio rep1

value: Brain


title: TSB916_BJ_PD66_anti-H3K27ac_Rapa

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Samples prepared for ChIP of histone modifications were fixed in 1% formaldehyde for 10 minutes at room temperature.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used for each ChIP assay, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of histone modifications were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 0.1% SDS, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 500mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (10mM Tris/HCl pH7.4, 250mM LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA). After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using either the KAPA LTP Library Preparation Kit (KK8232), following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 50 cycles.

treatment_protocol: Cells grown in rapamycin were introduced to and maintained in 10nM rapamycin after recovery from thawing.  Rapamycin maintained cells were collected for ChIP-seq at PD31, PD49, and PD66 to correspond with similar PD young, intermediate, and senescent non-rapamycin treated cells.

value: BJ Fibroblast

value: H3K27ac:abcam ab4729

value: Senescent

value: Rapamycin


title: 8249-e-sci-6wk

value: Colon

value: Sigmoid Inflamed

value: Post (Week 6)


title: Exp1_Epac2 KD_rep4

value: liver

value: Epac2 KD


title: P1-WT-bio rep2

value: Postnatal day 1

value: Primary astrocyte

value: WT


title: Exp1_Epac2 KD_rep3


title: 8249-e-ntc-6wk

value: Normal Transverse Colon


title: TSB915_BJ_Intermediate_PD49_anti-H3K27ac_Rapa

value: Intermediate - Quiescent


title: P1-WT-bio rep1


title: TSB914_BJ_Young_PD31_anti-H3K27ac_Rapa

value: Young - Quiescent


title: 8178-e-nc-8wk

value: Rectum Normal

value: Post (Week 8)


title: RKO,SUZ12,ChIP

data_processing:
ChIP-seq reads were aligned to a concatenated genome sequence of mouse (mm10) using bowtie2. In which, H3K27me3 spike-in ChIP-seq reads were aligned to a concatenated genome sequence of mouse (mm10) and Drosophila (dm6) using bowtie2(3).
Peaks were called using MACS2.
Assembly: mm10
Supplementary files format and content: narrowPeak/broadPeak (except for input sample)

extract_protocol:
Primary astrocytes were cross-linked with 1% formaldehyde (Sigma) for 10 min and stopped with 125 mM glycine. Cells were then lysed with ChIP lysis buffer (50 mM Hepes (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Na-deoxycholate, 0.05% SDS,1 mM PMSF, and 1 mM DTT) and sonicated with a Qsonica sonicator.
The sequencing libraries for ChIP-seq were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607-02, Vazyme) according to the manufacturer’s instructions.

value: Brain

tag: chip antibody

value: SUZ12( #3737, Cell signaling technology)

value: Rack7 conditional knockout


title: Exp1_Control_rep4

extract_protocol:
Total RNA was purified from liver tissue using MagMAX-96 for the Microarrays Total RNA Isolation kit (Ambion by Life Technologies), according to manufacturer specifications. Genomic DNA was removed using MagMAX Turbo DNase buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using the Dynabeads® mRNA Purification kit (Invitrogen).
Strand-specific RNA sequencing (RNA-seq) libraries were prepared using the KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries.

tag: tissue

value: Control


title: 8161-e-sci

value: Colon

value: Sigmoid Colon Inflamed

value: Baseline


title: TSB912_BJ_Intermediate_PD49_anti-H3K27ac_Control

tag: cell line

value: BJ Fibroblast

value: H3K27ac:abcam ab4729

value: DMSO


title: RKO,EED,ChIP

tag: cell type

value: Primary astrocyte

value: EED(16818-1-AP, Proteintech)


title: 8161-e-ntc

value: Normal Transverse


title: Exp1_Gnas KD_rep4

value: liver

tag: treatment

value: Gnas KD


title: 8138-e-ri-6wk

value: Rectosigmoid Inflamed

value: Post (Week 6)


title: WT,SUZ12,ChIP

value: Brain

value: WT


title: Exp1_PKA KD_rep2

value: PKA KD


title: TSB911_BJ_Young_PD31_anti-H3K27ac_Control

value: Young - Quiescent


title: 8027-e-ri

value: Colon


title: Exp1_Gnas KD_rep3


title: 8027-e-nrc

value: Normal Right


title: TSB905_BJ_Intermediate_PD49_anti_H3K4me2_Rapa

value: H3K4me2:abcam ab7766

value: Intermediate - Quiescent

value: Rapamycin


title: WT,EZH2,ChIP

value: EZH2(#5246, Cell signaling technology)


title: WT,EED,ChIP

value: Primary astrocyte

value: Rack7 conditional knockout


title: TSB904_BJ_Young_PD31_anti_H3K4me2_Rapa

value: BJ Fibroblast


title: Exp1_Control_rep3

value: liver

value: Control


title: TSB903_BJ_Senescent_PD66_anti_H3K4me2_Control

value: Senescent

value: DMSO


title: Exp1_Epac2 KD_rep2

value: Epac2 KD


title: Exp1_Gnas KD_rep2

value: Gnas KD


title: 7933-e-ri

value: Rectosigmoid Inflamed

value: Baseline


title: Exp1_PKA KD_rep3

value: PKA KD


title: WT, PRC2, input

value: Brain

value: WT


title: TSB913_BJ_Senescent_PD66_anti-H3K27ac_Control

value: H3K27ac:abcam ab4729


title: 7933-e-nc

value: Colon

value: Normal Baseline


title: TSB902_BJ_Intermediate_PD49_anti_H3K4me2_Control

value: H3K4me2:abcam ab7766

value: Intermediate - Quiescent


title: RKO,EZH2,ChIP

value: Primary astrocyte

value: EZH2 (#5246, Cell signaling technology)

value: Rack7 conditional knockout


title: 7883-e-sci

value: Sigmoid Colon Inflamed


title: RKO,H3K27me3,ChIP

value: H3K27me3(#9733, Cell signaling technology); spike-in antibody (61686, Active motif)


title: TSB901_BJ_Young_PD31_anti_H3K4me2_Control

value: BJ Fibroblast

value: Young - Quiescent

value: DMSO


title: Exp1_Gnas KD_rep1

value: liver

value: Gnas KD


title: SCB_074

city: Edmonton

first: Nidheesh

last: Dadheech

state: Alberta

address: 5-126C LKS centre for research and innovation, Alberta diabetes institute, University of Alberta, 112 St, 87 AV, NW

department: Surgery

country: Canada

institute: University of Alberta

description: 10x Genomics

data_processing:
The resulting FASTQ files were aligned using Cell Ranger V.7.0.0 with Single Cell 3’ V3 chemistry on the 10X Cloud pipeline.
Assembly: human reference genomes (GRCh38)

source_name: Human iPSC

extract_protocol:
S6w1 SC-islets were dispersed by incubating with 2 ml of Accutase solution containing RockI (2 µL/mL) for 10 minutes at 37°C. Isolated single cells were strained with 40micron cell strainer and then counted for live dead staining to measure live cells. A cell suspension of 1 million cells per mL was resuspended for total RNA isolation and libraray preperation.
Samples of S6w1 SC-islet Cells were prepared following the protocol of the 10X Genomics Single Cell 3’ V3.1 Reagent Kit. They were processed using the 10X Genomic Chromium Controller for partitioning and barcoding, and the cDNA library was generated at the Advanced Cell Exploration Core- University of Alberta. The total cell concentration was assessed using the Countess, followed by sequencing on the NovaSeq 6000 System (Illumina) at the core facility at Centre for Health Genomics and Informatics, University of Calgary. The resulting FASTQ files were aligned using Cell Ranger V.7.0.0 with Single Cell 3’ V3 chemistry on the 10X Cloud pipeline.

treatment_protocol: Stem cell-derived islets were generated from human induced pluripotent stem cells reporgramed from patient-derived peripheral blood monocluear cells

value: Human iPSC

value: Islet cells

value: iPSC-derived Islets


title: TSB906_BJ_PD66_anti_H3K4me2_Rapa

value: Senescent

value: Rapamycin


title: TSB566_BJ_Senescent_anti-H4R3me2sym_shJMJD6-54

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:4 8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.  Long term shRNA experiments were done by transducing either pLKO.1 or GIPZ lentivirus into young (<PD30) BJ fibroblasts.  For both pLKO.1 and GIPZ constructs in young fibroblasts, cells were maintained under selection by 0.6ug/ml of puromyin and expanded for 2 weeks until they were frozen down.  Frozen stable lines were then thawed and grown continuously until reaching senescence, and the timing of their population doublings were recorded over time.

extract_protocol:
Native ChIP was performed as described in Wagschal et al., 2007 (Wagschal et al., 2007), summarized as follows, noting alterations to the original protocol.  5-10 million BJ fibroblasts, either senescent or quiescent via contact inhibition, were harvested via trypsinization, making sure that cells are in a single cell suspension.  Cells were then transferred to a 15ml conical tube and pelleted at 3000g, for 5 minutes, at 4C.  All subsequent steps and buffers, unless otherwise noted, were performed and maintained at 4C.  Cells were resuspended in 2ml nuclei preparation buffer I (0.3M sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15mM Tris-HCl ph 7.5, 0.5mM DTT, 1x dissolved cOmplete Protease Inhibitor Cocktail), and were then mixed gently with 2ml of nuclei preparation buffer 2 (0.3M sucrose, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 15mM Tris-HCl ph 7.5, 0.5mM DTT, 1x dissolved cOmplete Protease Inhibitor Cocktail, 0.4% NP-40), and the mixture was then incubated on ice for a maximum of 5 minutes.  8 ml of nuclei preparation buffer III was added to 2 new separate 14ml polypropylene tubes.  2ml of the 4ml cell suspension was layered on top of each 8ml sucrose cushion and centrifuged in a pre-chilled swing-out rotor at 10,000g, for 20 minutes at 4C.  The supernatant was removed from the top, with attention paid to ensure that none of the supernatant remained.  The nuclear pellet was resuspended in 1ml of MNase digestion buffer (0.32M sucrose, 4mM MgCl2, 1mM CaCl2, 50mM Tris-HCl ph 7.5, 0.1 mM PMSF), split into two aliquots of 500ul in two separate 1.5ml Eppendorf tubes, 1ul of MNase enzyme (NEB-M0247S) was added to each tube, and the tubes were incubated for 2 and 5 minutes at 37C.  The reaction was stopped by adding 5ul of 0.5M EDTA and 5ul of 0.5M EGTA to each reaction, which were then chilled on ice.  Each tube was centrifuged for 10,000 rpm for 10 minutes at 4C and the supernatant, which contains the first fraction of soluble chromatin, was collected.   Each remaining nuclear pellet was then resuspended in 500ul dialysis-lysis buffer (1mM Tris-HCl ph 7.5, 0.2 mM PMSF, 0.2mM EDTA), incubated for 1 hour at 4C, and samples were re-centrifuged at 10,000 rpm for 10 minutes at 4C and each samples’ supernatant, containing the second fraction of soluble chromatin, was collected.  Concentrations of each fraction were then measured via Qubit, and the fragment size distribute of each fraction was checked via agarose gel electrophoresis to confirm similar digestion between each biological sample.  Fractions were then diluted in their respective buffers to ensure a similar concentration of chromatin in each fraction, and then equal volumes of each fraction of each biological sample were pooled and diluted so that each ChIP reaction contained ~10ug chromatin in 500ul of buffer, and was equal parts MNase digestion buffer and dialysis-lysis buffer, and equally parts each fraction of chromatin.  1ml of ChIP incubation buffer (50mM Tris-HCl, ph 7.5, 5mM EDTA, 50mM NaCl, 1x dissolved cOmplete Protease Inhibitor Cocktail) was then added to each 500ul ChIP reaction.  5ug of antibody was then added to each reaction, which were then rotated overnight at 4C.  20 uL of Protein G Dynabeads (Thermo Fisher) per ChIP reaction were then washed and blocked overnight in 1% BSA/glycogen in ChIP incubation buffer, and resuspended in their original volume of ChIP incubation buffer.      After the reactions’ overnight incubation, 20ul of the beads were then added to each ChIP reaction and incubated under rotation for 4 hours at 4C.  Beads were then washed, using the same magnetic washing protocol as with the fixed ChIP reactions, 2 times with Washing Buffer A (50mM Tris-HCl, ph 7.5, 10mM EDTA, 75mM NaCl), 2 times with Washing Buffer B (50mM Tris-HCl, ph 7.5, 10mM EDTA, 125mM NaCl), and 2 times with Washing Buffer C (50mM Tris-HCl, ph 7.5, 10mM EDTA, 175mM NaCl).  Beads were then resuspended in 48 ul Proteinase K digestion buffer with 2 mg/ml Proteinase K, and incubated for 30 minutes at 50C, after which the supernatant was collected and purified via QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB.  Samples were then further sonicated for 10 minutes to ensure that immunoprecipitated chromatin from polynucleosomes would between 100-300bp for sequencing.
Libraries were then prepared for deep sequencing with the Illumina HiSeq 2500 system using the KAPA LTP Library Preparation Kit (KK8232), following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 50 cycles.

treatment_protocol: Lentivirus was produced through transfection of packaging plasmids into 293T (ATCC® CRL-3216) cells grown to ~80% confluency.  All transfections were done using Lipofectamine 2000 (Thermo Fisher 12566014), following the manufacturer’s protocol, with the ratios of plasmids and Lipofectamine 2000 reagent listed below.  GIPZ stable knockdown lines were generated using a 667ul : 1333ul ratio of GIPZ viral supernatant to fresh culture media.  pLKO.1 stable knockdown lines were generated using a 48 ul : 1952 ul ratio of pLKO.1 viral supernatant with fresh culture media.  All transduction mixtures were given to cells and allowed to incubate overnight with polybrene added at a final concentration of 8ug/ml.  Knockdown cells were then maintained in 0.6ug/ml puromycin starting 4 days after transduction, until they were harvested at the senescent or young-quiescent stage.

value: H4R3me2s:ChIP-seq:Millipore 17-10250

tag: shRNA target

value: shRNA - JMJD6-construct 53


title: SCB_073

description: 10x Genomics


title: WT,H3K27me3,ChIP

value: Brain

value: Primary astrocyte

value: WT


title: TSB565_BJ_Senescent_anti-H4R3me2sym_shJMJD6-51

tag: Stage

value: shRNA - JMJD6-construct 51


title: Exp1_Gcgr KD_rep3

value: Gcgr KD


title: RKO, PRC2, input

tag: genotype

value: Rack7 conditional knockout


title: Exp1_Control_rep1

value: Control


title: pLenti-hPGK-rtTA2-TREUPP1/CHTF18/BNC1-IRES-GFP

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

institute: CNAG

description: 5-prime 10x Genomics

data_processing:
10x Genomics Cell Ranger 7.0.0 count
Assembly: GRCh38
Supplementary files format and content: Tab separated files and matrices

source_name: Melanocytes

extract_protocol: single cell 5-prime RNAseq protocol, 10x Genomics

value: Melanocytes

value: MEL-F-NEO


title: TSB564_BJ_Senescent_anti-H4R3me2sym_shNS

value: BJ Fibroblast

value: shRNA - Non-silencing - Control


title: WT,H3K27me3, input


title: RKO,H3K27ac,ChIP

value: H3K27ac (ab4729, Abcam)


title: Exp1_Epac2 KD_rep1

value: liver

value: Epac2 KD


title: pLenti-hPGK-rtTA2-p2A-mCherry-TRE-BRAFV600E

description: 5-prime 10x Genomics


title: 3B_D+R_2_rep2

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads.
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse (mm39) reference genome.
featureCounts software (v2.0) was used to get the raw gene level mRNA expression counts.
Assembly: mm39
Supplementary files format and content: txt format raw counts of each gene
Supplementary files format and content: Expression.txt

growth_protocol: HepG2 and Hep3B cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum, glutamine, and penicillin/streptomycin (Gibco) at 37 °C 5% carbon dioxide (CO2).

extract_protocol:
mRNA high throughput sequencing was performed by Biotree (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample prepa_x0002_ration kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument.

treatment_protocol: HepG2 and Hep3B cells in logarithmic growth phase were seeded onto a 6-well plate. The following day, DAPT (10 μM) as Notch inhibitors, STAT3 inhibitors RUXO (10 μM), and their combination were administered for 72 hours. Samples were collected for transcriptome sequencing. HepLPC co-cultured HepG2 or Hep3B cells were used as positive controls.

value: liver cancer cells

value: Adding Notch inhibitor (10 μM DAPT) and STAT3 inhibitor (10 μM RUXO) to the culture medium to treat cells


title: TSB563_BJ_Young_anti-H4R3me2sym_shJMJD6-53

value: H4R3me2s:ChIP-seq:Millipore 17-10250

value: Young - Quiescent

value: shRNA - JMJD6-construct 53


title: Exp1_PKA KD_rep1

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina bcl2fastq v2.17. Reads were decoded based on their barcodes, and read quality was evaluated with FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (NCBI GRCm38) using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches. Reads mapped to the exons of a gene were summed at the gene level.
Assembly: GRCm38/mm10
Supplementary files format and content: csv files of raw counts for each sample

value: PKA KD


title: Exp1_Control_rep2


title: RKO,H3K4me3,ChIP

value: Brain

value: Primary astrocyte

value: H3K4me3(#9727, Cell signaling technology)


title: RKO,H3K27me3,input

value: Rack7 conditional knockout


title: 3B_D+R_1_rep1


title: TSB562_BJ_Young_anti-H4R3me2sym_shJMJD6-51

value: shRNA - JMJD6-construct 51


title: TSB561_BJ_Young_anti-H4R3me2sym_shNS


title: RKO,H3K4me1,ChIP

value: H3K4me1(39297, Active motif)


title: 3B_R_2_rep2

value: Adding STAT3 inhibitor (10 μM RUXO) to the culture medium to treat cells


title: WT,H3K27ac,ChIP

value: WT


title: Exp1_Gcgr KD_rep1

value: Gcgr KD


title: Exp1_Gcgr KD_rep2

value: liver


title: 3B_R_1_rep1


title: GRC355_CC7_S1

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

description: Library name: GRC355_CC7_S1

data_processing:
For Experiment 1, basecall files were converted to FASTQ by bcl2fastq2, demultiplexed, quality trimmed, and filter using ea-utils (https://expressionanalysis.github.io/ea-utils/ ; last accessed 01-21-2020). Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed.
For Experiment 2, Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed, respectively in Partek Flow (v.8.0.19.0428; St. Louis, MO).
Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR (v.2.5.3a) with default settings in Partek Flow and strand specificity detection enabled for the paired-end reads from Experiment 1 but not for Experiment 2.
Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation.
Assembly: GRCz11/93 gene annotation
Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples
Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples

organism: Danio rerio

source_name: pooled heads collected anterior to swim bladder of larval zebrafish

extract_protocol:
Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis, LLC (Morrisville, NC, USA). Samples from experiment 2 underwent RNA extraction at US EPA (Durham, NC, USA) using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit.
For Experiment 1, paired-end (50 base pair) total RNA-sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit for rRNA depletion (Illumina, San Diego, California, cat. No. RS-1222303) at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly, rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer (DNA 1000 kit #5067-1504) and qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA). Sample libraries were then normalized, randomly pooled, and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2, purified RNA from each sample (500 ng per sample) were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA (Durham, NC, USA). PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size (bp) was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library (μl x nM) was pooled from 16 randomized libraries to make the sequencing samples (total 2 pools of 16 libraries each) and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR (Single Read).

tag: strain

value: mixed wild type zebrafish line US EPA

tag: lifestage

value: larvae

value: 10 days post fertilization

value: Conventionally colonized with microbes (control)

tag: experiment


title: 3B_D_2_rep2

value: liver cancer cells

value: Adding Notch inhibitor (10 μM DAPT) to the culture medium to treat cells


title: GRC355_CC6_S13

description: Library name: GRC355_CC6_S13

value: pooled heads collected anterior to swim bladder of larval zebrafish

tag: age


title: WT,H3K4me1,ChIP

value: Brain


title: TSC826_Bj_Senescent_anti-SMAD2/3_Rep1

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Sampleswere double cross-linked in 2mM DSG alone for 45 minutes at room temperature followed by 10 minute fixation with 1% formaldehyde.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used for each transcription factor ChIP assay, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of transcription factors were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 300mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (20mM Tris/HCl pH7.4, 400mM NaCl, 1% Triton-X-100, 2mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using the KAPA Hyper Prep Kit (KK8500), following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 50 cycles.

value: BJ Fibroblast

tag: antibody

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: Senescent


title: WT,H3K4me3,ChIP

value: Primary astrocyte

value: H3K4me3(#9727, Cell signaling technology)


title: 3B_D_1_rep1


title: RKO, K4me1/3, K27ac, input

value: Rack7 conditional knockout


title: TSC825_BJ_Young_anti-SMAD2/3_Rep1

value: Young - Quiescent


title: GRC355_CC4_S6

description: Library name: GRC355_CC4_S6


title: C-3B_2_rep2

value: co-culture with HepLPCs in normal DMEM medium


title: WT, K4me1/3, K27ac, input

value: WT


title: GRC355_CC3_S10

description: Library name: GRC355_CC3_S10

value: mixed wild type zebrafish line US EPA


title: RKO, RACK7, ChIP

value: RACK7(A302-089A, Bethyl)


title: TSB923_BJ_Senescent_anti-NFI_Rep2

value: NFI:Santa Cruz sc-5567 (H-300)


title: C-3B_1_rep1


title: GRC355_CC2_S12

description: Library name: GRC355_CC2_S12

value: larvae

value: 10 days post fertilization

value: Conventionally colonized with microbes (control)


title: TSC806_BJ_Senescent_anti-SMAD2/3_Rep2


title: WT, RACK7, ChIP


title: 3B_NC_1_rep1

value: liver cancer cells

value: normal control


title: TSC803_BJ_Young_anti-NFI_Rep1

value: BJ Fibroblast


title: TSB922_BJ_Young_anti-NFI_Rep2


title: GRC355_AX7_S12

description: Library name: GRC355_AX7_S12

value: pooled heads collected anterior to swim bladder of larval zebrafish

value: Axenic


title: GRC355_CC1_S14

description: Library name: GRC355_CC1_S14


title: TSC804_BJ_Senescent_anti-NFI_Rep1

value: Senescent


title: WT, RACK7, input

value: Brain

value: Primary astrocyte


title: RKO, RACK7, input

value: Rack7 conditional knockout


title: G2_D+R_2_rep2

value: Adding Notch inhibitor (10 μM DAPT) and STAT3 inhibitor (10 μM RUXO) to the culture medium to treat cells


title: TSC802_IMR90_RAS_OIS_anti-H3K27ac

treatment_protocol: IMR90s prepared for oncogene induced senescence were transduced at PD30 with retrovirus produced by either pBABE-puro or pBABE-puro H-Ras V12.  4 days post transduction, cells were maintained under selection of 1ug/ml of puromycin until being harvested at 14 days post transduction.

value: H3K27ac:abcam ab4729

value: Oncogene Induced Senescence

value: pBABE-h-Ras Treated


title: G2_D+R_1_rep1


title: GRC355_AX4_S8

description: Library name: GRC355_AX4_S8

value: mixed wild type zebrafish line US EPA


title: GRC355_CC5_S9

description: Library name: GRC355_CC5_S9

value: larvae


title: TSC801_IMR90_GFP_Control_anti-H3K27ac

value: Quiescent

value: pBABE-GFP Control Treated


title: G2_R_2_rep2

value: liver cancer cells

value: Adding STAT3 inhibitor (10 μM RUXO) to the culture medium to treat cells


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 3

city: Pittsburgh

first: Aaron

last: Yang

state: PA

address: 4401 Penn Ave

institute: University of Pittsburgh

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Raw count values generated with Subread
Gene expression values were nromalized to transcripts per million
Differential peak analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains transcripts per million (TPM)

source_name: splenocytes

growth_protocol: To expand Pmel-1 mouse CD8+ T cells in vitro, bulk splenocytes were plated in the presence of the T cells’ cognate peptide (1uM gp100) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50ug/mL mouse rIL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol:
SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: 5mM DCA was added to DCA-conditioned cultures daily

value: splenocytes

value: CD8+ T cell

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: dichloroacetate (DCA)

value: Day 7


title: TSC805_BJ_Young_anti-SMAD2/3_Rep2

value: BJ Fibroblast

value: SMAD2/3:Santa Cruz sc-6032 (N19) and sc-133098 (C-8), equal micrograms of both combined

value: Young - Quiescent


title: GRC355_AX3_S5

description: Library name: GRC355_AX3_S5

value: pooled heads collected anterior to swim bladder of larval zebrafish

value: 10 days post fertilization

value: Axenic


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 2


title: GRC355_AX1_S2

description: Library name: GRC355_AX1_S2

value: mixed wild type zebrafish line US EPA


title: 3B_NC_2_rep2

value: normal control


title: G2_R_1_rep1


title: Pmel-1 T cells, DCA-treated, Day 7, mouse 1


title: G2_D_2_rep2

value: Adding Notch inhibitor (10 μM DAPT) to the culture medium to treat cells


title: GRC355_AC7_S7

description: Library name: GRC355_AC7_S7

value: larvae

value: Conventionally re-colonized with microbes on day 1