title: irradiation-induced senescent, RG7388, rep 6

data_processing:
The first 14 nt of both R1 and R2 reads were trimmed using CutAdapt
Trimmed reads were aligned to reference genome using bwa
Aligned reads were sorted and filtered by samtools
Copy number variation were called by ginkgo
Assembly: hg38
Supplementary files format and content: deletions detected in each sample in a bed format.
Library strategy: single nucleus WGS

extract_protocol:
Cells were trypsinized, washed in PBS, and resuspended at 20x cell pellet volume in cold nuclear isolation buffer A with digitonin (50 nM HEPES pH 7.3, 150 mM NaCl, 1x dual protease and phosphatase inhibitor, 25 g/mL digitonin) by pipetting. The suspensions were rotated at 4°C for 30 minutes, then centrifuged at 500g for 5 minutes at 4°C. Nuclear pellets were washed twice with cold NIB-250 buffer (250 mM sucrose, 15mM Tris-Cl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2) and resuspended in sorting buffer (DPBS with 2% FBS, 0.5 mM spermidine, 500 ng/mL DAPI). Nuclei were sorted by FACSAriaII with a 100um nozzle (see also Fig.S7) into individual strip tubes containing LIANTI lysis buffer.
PicoPLEX Gold

treatment_protocol: Cells were split after returning to confluence in 3 days, then treated with MDM2 inhibitors, RG7388 (Selleckchem), 5 minutes after IR. Drugs were replaced by media change every 3 days after irradiation and collected 11 days after IR


title: Endosperm 42, MuActive plant ND67-42

status: Public on May 09 2025

type: SRA

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

country: USA

institute: University of Georgia

description:
MuSeq2 Endosperm chip from MuActive plant ND67-42
Library name: E42

library_source: genomic

data_processing:
Processed file "MuSeq2 data for maize tissues.csv.gz" was generated by mapping the Mu sequencing reads to the W22 V2 genome using Bowtie2 and bam files were converted to txt files which were then imported into R. Sample txt files were filtered and combined into a large matrix, containing unique molecules detected per sample per genome location across all MuSeq2 samples in the dataset.
Processed file "'MuSeq2 data for maize tissues _ separated Left and Right transposon borders.tar'" was generated from "MuSeq2 data for maize tissues.csv.gz" by separating the molecules based on transposon border. Each row represents the chromosome, position, and direction for each molecule detected.
Assembly: W22 Version 2
Supplementary files format and content: To generate processed file "MuSeq2 data for maize tissues.csv.gz", Sequencing reads were mapped to the W22 V2 genome with Bowtie2. Reads were then converted to molecule counts using both the adapter ligation position and a unique molecular identifier (UMI) incorporated during adapter ligation. Molecule counts mapping to both sides of the transposon border were combined. The rownames in this file are listed as chromosome:position1,position2 where positions 1 and 2 are the first genomic coordinate immediately adjacent to the the left and right side of the transposon insertion (respectively).
Supplementary files format and content: Processed file "MuSeq2 data for maize tissues separated Left and Right transposon borders.tar” data was generated as an intermediate in calculating "MuSeq2 data for maize tissues.csv.gz". This contains two csv files with the molecule counts separated for left and right side of the transposon. The rownames are given as chromosome:position where the position is the genomic coordinate immediately adjacent to the transposon border.

molecule: genomic DNA

organism: Zea mays

source_name: Endosperm

growth_protocol: All Mu-Active plants were first grown in vermiculite and transplanted 10-13 days after sowing to soil, where they were grown in maturity in a greenhouse. Mu-Inactive samples were grown in soil and grown for 10-13 days until the V2 stage before being harvested.

extract_protocol:
Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution.
Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details
A universal adapter was ligated onto the sheared DNA, then DNA fragments spanning the genome-transposon junction were amplified by PCR and sequenced using the MuSeq2 protocol.

tag: tissue

value: Endosperm

tag: genotype

value: W22 MuActive


title: HDM201, 24 months, male, rep 2

status: Public on Feb 11 2025

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: transcriptomic

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: mm10
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: This study was approved by the Institutional Animal Care and Use Committee at Sanford Burnham Prebys MDI. C57BL6 mice were purchased from Jackson Labs and Charles River and group housed under specific pathogen free conditions with ad libitum access to water and food (Teklad 2018).

extract_protocol:
Fresh liver was lysed in Trizol (Ambion 15596026), and RNA was isolated with chloroform according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with 10 mg/kg HDM201 (Novartis) suspended in phosphate-buffered methylcellulose according to the manufacturer’s instructions (0.5% methylcellulose in phosphate buffer, pH6.8, 50mM) by daily oral gavage in the morning. Mice were monitored daily and weighed every 2-3 days during treatment. After 14 days of treatment, mice were euthanized by CO2 asphyxiation in the morning

value: liver

tag: age

value: 24 months

tag: gender

value: male

tag: treatment


title: PBMC, library GD009_2, CITE

status: Public on Apr 10 2025

first: Kendall

last: Kearns

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Library name: GD009_2_CITE
GD009_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the GRCh38 human reference genome and gene counting was performed using the multi pipeline in CellRanger (v5.0).
Downstream analyses were performed using Seurat (v5.0.0).
Seurat's MULTIseqDEMUX was used for hashtag demultiplexing and singlet assignment.
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
After overnight resting PBMCs were stimulated with extracts (10 µg/ml) or HDMPP (10 µg/ml), or medium alone as negative control, and incubated for 24h at 37ºC. After the incubation, cells were surface stained with fluorochrome-conjugated antibodies, for 40 minutes at 4°C using: anti-CD3 (AF700) (UCHT1), anti-CD4 (APCef780) (RPA-T4), anti-CD8 (PerCP-Cy5.5) (RPA-T8), anti-CD14 (V500) (M5E2), anti-CD19 (V500) (HIB19), anti-TCRγδ (PE-DA594) (IP26), anti-TCRδ1 (FITC) (TS8.2), anti-TCRδ2 (BV421) (B6), anti-CD137 (APC) (4B4-1), and anti-CD69 (BV605) (FN50) antibodies. TotalSeq-C oligonucleotide-conjugated antibodies (BioLegend) were also added at this step at 0.01mg/mL final concentration (one distinct antibody per sample). After two washes in PBS, cells were resuspended into 500 μl of MACS buffer (PBS containing 2mM EDTA (pH 8.0) and 0.5% BSA) and stored at 4ºC until flow cytometry acquisition. AIM+ (CD69+CD137+) Vδ1 and Vδ2 cells were captured by fluorescence-activated cell sorting (FACS), using a BD FACSAria Fusion cell sorter (Becton Dickinson).
Samples were processed using 10x Genomics 5’ end mRNA capture reagents (5v2.0 single cell gene expression profiling chemistry) as per manufacturer’s recommendations; after droplet generation, and in-droplet based reverse transcription, cDNA was amplified by PCR for 13 cycles and gene expression library preparation followed. After quantification, equal molar concentration of each library was pooled and sequenced using the NovaSeq6000 Illumina sequencing platform to obtain 28- and 100-bp paired-end reads using the following read length: read 1, 100 cycles; read 2, 100 cycles; i7 index, 10 cycles and i5 index 10 cycles. Each gene expression library was sequenced aiming at a minimum mean sequencing depth of 30,000 reads per cell. Separate libraries were prepared to identify the DNA-Barcode that will allow de-multiplexing and linking each cell to a donor. Briefly, amplified DNA generated from antibody-DNA oligos was separated from transcriptomic cDNA based on size-selection following amplification. Antibody-DNA amplified fragments were less than 300 bp. Library preparation was followed in accordance with the manufacturer’s recommendations. Each library was sequenced aiming for 5,000 reads per cell.

value: PBMC


title: irradiation-induced senescent, RG7388, rep 5

growth_protocol: IMR90 primary human fibroblasts were grown at 37°C, 3.5% O2, 5% CO2, in Dulbecco’s modified Eagle’s medium (Gibco 10313-121) with 10% FBS (Corning 35-0-11-CV), 1% penicillin/streptomycin (Gibco 15140-122) and 2 mM glutamine (Gibco 25030-081). Cells were checked routinely for mycoplasma contamination.

tag: cell line

tag: cell type

value: fibroblast

value: wild type


title: irradiation-induced senescent, RG7388, rep 4


title: irradiation-induced senescent, RG7388, rep 3


title: irradiation-induced senescent, RG7388, rep 2


title: irradiation-induced senescent, RG7388, rep 1


title: PBMC, library GD006_1, CITE

description:
Library name: GD006_1_CITE
GD006_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: PBMC, library GD004_2, CITE

description:
Library name: GD004_2_CITE
GD004_2
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: irradiation-induced senescent, DMSO, rep 3

value: DMSO, 20 Gy IR


title: irradiation-induced senescent, DMSO, rep 4


title: PBMC, library GD001_1, CITE

description:
Library name: GD001_1_CITE
GD001_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv


title: irradiation-induced senescent, DMSO, rep 2


title: irradiation-induced senescent, DMSO, rep 1


title: PBMC, library GD006_2, GEX

description:
Library name: GD006_2_GEX
GD006_2
GEX_SCT_counts.tsv
metadata.csv


title: proliferating, DMSO, rep 4

value: DMSO


title: proliferating, DMSO, rep 3


title: HDM201, 20 months, female, rep 4

value: 20 months

value: female


title: IMR90 cells, IR, HDM201, rep 3

data_processing:
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: hg38
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

extract_protocol:
Cells were lysed in Trizol (Ambion 15596026) and RNA was isolated using  a commercial kit (Zymo Directzol)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were split after returning to confluence in 3 days, then treated with MDM2 inhibitors, RG7388 (Selleckchem) and HDM201 (Novartis), starting day 4. Drugs were replaced by media change every 3 days after irradiation (day 4, 7, and 10 after IR) and collected 11 days after IR.

tag: condition

value: IR


title: proliferating, DMSO, rep 2


title: IMR90 cells, IR, HDM201, rep 2


title: IMR90 cells, IR, HDM201, rep 1


title: proliferating, DMSO, rep 1


title: genomic_DNAmethylation_PM77_vc_R4

status: Public on Mar 12 2025

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

extract_protocol: DNA salt extraction & bisulfite conversion

value: Villi

tag: sentrix

tag: Sex

value: M

tag: ga


title: IMR90 cells, IR, RG7388, rep 3


title: IMR90 cells, IR, RG7388, rep 2


title: IMR90 cells, IR, RG7388, rep 1


title: IMR90 cells, IR, DMSO, rep 3


title: IMR90 cells, IR, DMSO, rep 2


title: IMR90 cells, proliferating, HDM201, rep 3

value: proliferating


title: genomic_DNAmethylation_PL158_vc


title: IMR90 cells, proliferating, HDM201, rep 1


title: genomic_DNAmethylation_PL293_v_R1


title: IMR90 cells, proliferating, HDM201, rep 2


title: IMR90 cells, IR, DMSO, rep 1


title: IMR90 cells, proliferating, RG7388, rep 3


title: IMR90 cells, proliferating, DMSO, rep 3


title: IMR90 cells, proliferating, RG7388, rep 2


title: IMR90 cells, proliferating, RG7388, rep 1


title: IMR90 cells, proliferating, DMSO, rep 2


title: APECED patient, Gingival biopsy, post-ruxolitinib (10 mg dosing)

status: Public on Jan 28 2025

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

description: Gingival  biopsy optained from an APECED patient with AIRE mutation after tratment with JAK/STAT inhibitor, ruxolitinib.

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to NCBI/GRCh38  using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (gencode.v39.annotation.gtf.gz) obtained from https://www.gencodegenes.org/human/
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contain RPKM values for each Sample

source_name: Gingival biopsy

extract_protocol:
Total RNA was extracted from whole tissue using TruSeq Stranded Total RNA Kit following manufacturer’s recommendations (Illumina, San Diego, CA).
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA).
Paired-end RNA-seq on NextSeq500 sequencer (Illumina)

treatment_protocol: Standardized 4mm long x 2mm wide gingival collar biopsies and/or 4mm buccal punch biopsies were obtained  from APECED patients (N = 3) and healthy donors (N = 3) under local anesthesia. Healthy donors had no signs of mucosal candidiasis, inflammation, or infection at the time of tissue harvesting. Oral tissue was homogenized using Miltenyi Gentlemacs M tube (cat# 130-093-236).

value: Gingival biopsy

value: AIRE mutation

tag: disease state

value: APECED patient

value: post-ruxolitinib (10 mg dosing)


title: APECED patient, Gingival biopsy, pre-ruxolitinib

description: Gingival  biopsy optained from an APECED patient with AIRE mutation.

value: pre-ruxolitinib


title: APECED patient, Gingival biopsy, post-ruxolitinib (15 mg dosing)

value: post-ruxolitinib (15 mg dosing)


title: APECED patient, Buccal biopsy, AIRE.30

description: Buccal biopsy optained from an APECED patient with AIRE mutation.

source_name: Buccal biopsy

value: Buccal biopsy

value: Baseline


title: Healthy donor, Buccal biopsy, HV076

description: Health buccal biopsy was obtained from an individual that met criteria for oral health.

value: wild-type

value: Healthy donor


title: IMR90 cells, proliferating, DMSO, rep 1

value: fibroblast

value: wild type

value: DMSO


title: genomic_DNAmethylation_PL289_v


title: Spleen, Tregs (GEX)

status: Public on Jan 19 2025

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Library strategy: CITE-seq
For demultiplexing of samples, cellranger (v6.0.0; 10X Genomics) was used with the defualt settings.
CellRanger was used to align gene expression data to the mm10 reference and generate feature barcode expression matrices using the default settings.
cite-seq-count was(v1.4.3) used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 -trim 10.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression feature barcode matrices.  CITEseq feature barcode matrices.  The cite seq hash tags to distinguish different experimental settings.

source_name: spleen

extract_protocol: Splenocytes were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with Cl. 13. for 16d. T cells were enriched by negative selection. Briefly, single cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with a uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration.A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population. Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: naïve or LCMV infected

value: spleen


title: Healthy donor, Buccal biopsy, HV079


title: 12_female PDMCAO aged #2

status: Public on Jan 09 2025

city: Houston,

first: Gab Seok

last: Kim

state: TX

address: 6431 Fannin St.

department: Department of Neurology

institute: The University of Texas Health Science Center at Houston

description: 10X Genomics

data_processing:
processed by Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Brain

growth_protocol: male and female in young and aged mice

extract_protocol:
brains slice, Miltenyi Adult Brain Dissociation Kitt
10X Genomics

treatment_protocol: sham surgeried or PDCMAO (14 PSD)

value: Brain

value: aged

value: female

value: PDMCAO


title: 10_female PDMCAO young #2

description: 10X Genomics

value: young


title: 5_male PDMCAO young #1

description: 10X Genomics

value: male


title: 8_female PDMCAO aged #1

description: 10X Genomics


title: 7_male PDMCAO aged #1

description: 10X Genomics


title: 6_female PDMCAO young #1

description: 10X Genomics


title: 2_female sham young #1

description: 10X Genomics

value: Young

value: sham


title: 9_male PDMCAO young #2

description: 10X Genomics


title: 1_male sham young #1

description: 10X Genomics


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 4

status: Public on Dec 30 2024

city: Rehovot

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Samples were analyzed using the UTAP pipeline (PMID: 30909881)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm10 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –alignSoftClipAtReferenceEnds No).
Read count extraction (UMI counts) was performed after marking duplicates using HTSeq-count in union mode.
Assembly: mm10
Supplementary files format and content: C2_countsUmiCorrectedMatrix.txt;
Supplementary files format and content: read count matrix

source_name: Mammary gland

growth_protocol: NMuMG-C2 dual reporter cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, 100 unit/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine and 1X MEM non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was produced using the RNeasy mini kit (Qiagen). 50ng of total RNA was used for the construction of sequencing libraries.
Library preparation protocol was bulk-adapted from MARS-seq

treatment_protocol: Cell were plated at 50% confluency in 24-wells plate with DMEM+ 10% FBS and cultured for 24h. Following 24h cells were added with the indicated treatment: BMP4 (31.25ng/ml, R&D), Control- no added ligand, TGFb1 (1.92ng/ml, R&D), or BMP4+ TGFb1 and cultured for additional 6h.

value: Mammary gland

value: Epithel

value: Double reporter cells with BMP RE mCherry and TGFb RE mCitrine


title: 4_female sham aged #1

description: 10X Genomics


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 3


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 2


title: C2 cells, added with TGFb1 and BMP4, 6h, biol rep 1


title: C2 cells, TGFb1 added, 6h, biol rep 2


title: C2 cells, TGFb1 added, 6h, biol rep 3


title: C2 cells, control- no ligand added, 6h, biol rep 4

value: No treatment


title: C2 cells, control- no ligand added, 6h, biol rep 3


title: C2 cells, TGFb1 added, 6h, biol rep 1


title: C2 cells, BMP4 added, 6h, biol rep 3


title: C2 cells, TGFb1 added, 6h, biol rep 4


title: C2 cells, control- no ligand added, 6h, biol rep 1


title: C2 cells, BMP4 added, 6h, biol rep 2


title: C2 cells, control- no ligand added, 6h, biol rep 2


title: C2 cells, BMP4 added, 6h, biol rep 1


title: WGBS_exp5_1TX-3a-R878H

status: Public on Dec 17 2024

city: Saint Louis

first: Andrew

middle: Lee

last: Young

state: MO

address: 660 South Euclid Ave

department: Medicine

institute: Washington University in St. Louis

description: Library name: WGBS_exp5_1TX-3a-R878H

data_processing:
For WGBS, reads were sequenced using NovaSeq platform. Reads were aligned to mm10,  deduplicated and CpG methylation extracted using Bismark.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10
Supplementary files format and content: bw

source_name: KSL

growth_protocol: 200 CD45.2 HSCs of the indicated genotypes were competitively transplanted with competetive 250,000 CD45.1 whole bone marrow cells in lethally irradiated primary recipient mice.  Serial transplant was performed by repeating this process.

extract_protocol:
For WGBS, genomic DNA (gDNA) was prepared from the cells using PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific #K1820-02).
For WGBS, using 200 ng of gDNA and 0.2% lambda DNA was bisulfite treated using EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research #D5042) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries.

treatment_protocol: No treatment

tag: Stage

value: Primary

value: KSL

value: Vav-Cre


title: Exp4_Control1_rep1

description: Library name: Exp4_Control1_rep1


title: Haloferax volcanii cells, rosR deletion strain, rep3

status: Public on Nov 20 2024

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_3

data_processing:
RNA-seq data were processed using the fastp toolkit (Chen et al., 2018) to trim low-quality bases and sequencing adapters from the 3’ end of reads.
STAR (Dobin et al., 2013) RNA-seq alignment tool was used to map trimmed reads to the genome of Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively). Reads aligning to a single genomic location were summarized across genes.
For genes having an overlap of at least 10 reads, gene counts were normalized and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package implemented for the R programming environment. Consistent with the recommendation of the DESeq authors, independent filtering (Ignatiadis et al., 2016) was utilized prior to calculating adjusted p-values (Benjamini Y, 1995) and moderated log2 fold-changes were derived using the ashr package (Stephens, 2017). Genes were considered significantly differentially expressed if the log2 fold change ratio (∆rosR : parent) was >= |1| and adjusted p-value < 0.05.
Assembly: Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively).
Supplementary files format and content: Hfx. mediterranei assembly ASM540632v1 refseq ID = GCF_005406325.1; Hfx. volcanii assembly ASM2568v1 refseq ID = GCF_000025685.1

organism: Haloferax volcanii DS2

source_name: archaeal cells

growth_protocol: Hm∆rosR, Hv∆rosR, and corresponding parent strain cultures were grown in biological triplicate in rich medium to mid-exponential phase.

extract_protocol:
RNA was extracted using an Absolutely RNA Miniprep kit according to manufacturer instructions (Agilent, Santa Clara, CA). RNA quality was measured using RNA 6000 Nano kit on a 2100 Bioanalyzer (Aglient, Santa Clara, CA). PCR to verify lack of DNA contamination was  conducted on 300 ng of RNA sample using species-specific primers listed in Supplementary Table S2. Ribosomal RNA depletion was performed from 300 ng of each sample using NEBNextR RNA Depletion Core Reagent (#E7870 New England Biolabs) according to the manufacturer instructions. The resultant mRNA was purified using NEBNext RNA sample purification beads and eluted in 7 l of nuclease-free water. 1l of each sample was used for quantification and quality verification (free of rRNA) in a second round of Agilent Bioanalyzer analysis using 2100 Prokaryote Total RNA Nano kit (Aglient, Santa Clara, CA).
Libraries were constructed using 5 ml of mRNA using the Ultra II Directional RNA Library Preparation Kit (Agilent, Santa Clara. CA). Indexes were designed according to the kit specifications and obtained from Integrated DNA Technologies. Resultant libraries were tested for quality and quantity by Bioanalyzer using the 2100 expert High Sensitivity DNA Assay chip (Agilent Technologies)

value: archaeal cells

value: deltapyrEdeltaHVOrosR

value: standard growth medium, knockout strain


title: Haloferax volcanii cells, rosR deletion strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_2


title: Haloferax volcanii cells, rosR deletion strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_1


title: Haloferax volcanii cells, pyrE parent control strain, rep3

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_3

value: deltapyrE

value: standard growth medium, control strain


title: Haloferax volcanii cells, pyrE parent control strain, rep2

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_2


title: Haloferax volcanii cells, pyrE parent control strain, rep1

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_1


title: No LDL

status: Public on Nov 01 2024

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

institute: South Dakota State University

data_processing:
20 base sgRNA reads were trimmed using Cutadapt 2.3, where 20bp sequence flanked by cgaaacaccg...gttttagagc was identifed from all fastq files
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9
Counts_24-h_AcLDL_2.txt, Counts_24h_OxLDL.txt were edited to delete 78 sgRNA due to contamination of the cDNA library and the edited files are Counts_24h_AcLDL_2_edited.txt, Counts_24h_OxLDL_edited.txt. List of deleted counts Counts_24h_AcLDL_2_deleted.txt, Counts_24h_OxLDL_deleted.txt.
We used MAGeCK Robust Ranking Aggregation (version 0.5.9) algorithm to indentify and rank list of genes significantly enriched by comparing low and high fluorescence population read counts.
Genome_build: Brie_library
Supplementary_files_format_and_content: Comma separated value files for Brie sgRNA library, read counts, and MAGeCK-RRA analysis

source_name: Bone marrow derived macrophage

growth_protocol: BMDM were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.

treatment_protocol: BMDM expressing Cas9 were transduced with the Brie library at a low multiplicity of infection (MOI). Approximately 2.5 x10^7  to 5 x10^7  cells were transduced with 8 x 10^6  or 16 x 10^6  transduction units (TUs) to achieve 200-400-fold representation of each sgRNA. After 48 h, cells were selected with puromycin (5 µg/mL) for two days and were cultured for at least seven more days before the neutral lipid assay and cell sorting. Cells were exposed to AcLDL (50 µg/ml) or OxLDL (100 µg/ml) for 24 h. We scrutinized neutral lipid content in two conditions: 1) 24-h LDL exposure and 2) post LDL 36-48-h. For each condition we treated cells with AcLDL for two replicate populations and treated cells with OxLDL for one replicate for each condition. Before group isolation by fluorescence activated cell sorting BMDMs were stained with 5 µM BODIPY (493/503), a neutral lipid dye, diluted in DMEM for 5 mins, washed once with cold DPBS (-Ca/-Mg) and detached with DPBS (-Ca/-Mg). Next, sorting was done by BD FACs JAZZ cell sorter based on low or high BODIPY fluorescence

value: Primary macrophage

tag: time point

value: 48 hr


title: Post OxLDL 48h chase: Low fluorescent (Low_LDD3)


title: Post OxLDL 48h chase: Pre-sort (Pre_LDD3)


title: Post OxLDL 48h chase: High fluorescent (High_LDD3)


title: Post AcLDL 48h chase 2: Input (Input_LDD2)


title: Post AcLDL 48h chase 2: Pre-sort (Pre_LDD2)


title: Post AcLDL 48h chase 2: High fluorescent (High_LDD2)


title: Post AcLDL 48h chase 2: Low fluorescent (Low_LDD2)


title: 3_male sham aged #1

description: 10X Genomics

value: Brain

value: aged

value: male


title: Post AcLDL 48h chase 1: Pre-sort (Pre_LDD1)


title: Post AcLDL 48h chase 1: High fluorescent (High LDD1)


title: Post AcLDL 48h chase 1: Low fluorescent (Low LDD1)


title: 24-h OxLDL: Pre-sort (Pre_LDF3)

value: 24 hr


title: Senescent CDK4 knockdown, replicate1

status: Public on Aug 13 2025

description: Library name: Sen_siK4_1

data_processing:
Trim adapters and low‑quality bases with Trimmomatic 0.38.1.
Align reads to the human hg38 genome with HISAT2 2.2.1.
Count reads per gene using featureCounts 2.0.3.
Generate QC reports (FastQC 0.74, then summarize with MultiQC) and perform PCA for sample relationships.
Perform differential expression analysis and generate Normalized counts with DESeq2 2.11.40.8.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: Normalized_Counts_RNA_seq_IMR90_siRNAKD.csv

growth_protocol: IMR90 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), L-glutamine, and penicillin-streptomycin, and maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
TRIzol extraction: lyse, add chloroform, centrifuge, collect aqueous phase, precipitate with ethanol, wash, air‑dry, resuspend.
PolyA capture

treatment_protocol: siRNA KD (days 4 & 7 post‑IR): use 5 nM siRNA with DharmaFECT in serum‑free media; incubate complexes RT 30 min; add to cells for 18–20 h; then replace with regular media. Harvest day 10.

value: Human Lung Fibroblasts

value: CDK4 knockdown

value: Irradiation, siRNA knockdown


title: 24-h OxLDL: High fluorescent (High_LDF3)


title: 24-h AcLDL 2: High fluorescent (High LDF2)


title: 24-h AcLDL 2: Pre-sort (Pre_LDF2)


title: 24-h AcLDL 2: Low fluorescent (Low LDF2)


title: 24-h AcLDL 1: Pre-sort (Pre_LDF1)


title: 24-h AcLDL 1: High fluorescent (High_LDF1)


title: 24-h AcLDL 1: Low fluorescent (Low_LDF1)


title: shZFPL1-2

status: Public on Oct 19 2024

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

country: China

institute: China Medical University

data_processing:
After screening for CutAdapt-based 3'end adapter sequences or reads with average quality score lower than Q20, the high-quality sequences were compared with the reference genome (Assembly GRCm38). The processed data were then normalized and derepeated. Finally fold change and p-value for Students’ t-test were calculated for control and siZFPL1 groups.
Assembly: GRCm38
Supplementary files format and content: comma-delimited csv  file includes the FPKM for each sample

source_name: xenograpted from human

growth_protocol: Hepatocellular carcinoma cells were extracted  from the tissue

extract_protocol:
We used Trizol Reagent (Invitrogen Life Technologies) to extract total RNA in control group (n=3) and siZFPL1 group (n=3). The sequencing library was prepared using the TruSeq RNA sample preparation kit (Illumina, USA) and sequenced at the Hiseq platform (Illumina) of Shanghai Personal Biotechnology Co. LTD. (Shanghai, China). After screening for CutAdapt-based 3'end adapter sequences or reads with average quality score lower than Q20, the high-quality sequences were compared with the reference genome (Assembly GRCm38). The processed data were then normalized and derepeated. Finally fold change and p-value for Students’ t-test were calculated for control and siZFPL1 groups.
The sequencing library was prepared using the TruSeq RNA sample preparation kit (Illumina, USA) and sequenced at the Hiseq platform (Illumina) of Shanghai Personal Biotechnology Co. LTD. (Shanghai, China).

treatment_protocol: ZFPL1 was knocked down in HUH-7 cell line and afterwards the cell line was transplanted to mouse

value: hepatocellular carninoma


title: shZFPL1-3


title: Senescent Non targeting#3 knockdown, replicate3

description: Library name: Sen_siNT3_3

value: WT


title: Proliferating replicate3

description: Library name: Prolif_3

value: No treatment


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate4

description: Library name: Ccnd1KO_4

data_processing:
Trim adapters and low‑quality bases with Trim Galore 0.6.7.
Align reads to the mouse mm10 genome with HISAT2 2.2.1.
Count reads per gene using featureCounts 2.0.3.
Generate QC reports (FastQC 0.74, then summarize with MultiQC) and perform PCA for sample relationships.
Perform differential expression analysis and generate Normalized counts with DESeq2 2.11.40.8.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Normalized_counts_file_on_data_155_data_154_and_others_Ccnd1KO_3weeks.csv

source_name: Liver

growth_protocol: C57BL/6J mice rested ≥2 weeks upon receipt; maintained on normal chow, 12 h light/12 h dark, ad libitum

extract_protocol:
Flash‑frozen liver piece (m‑lobe) homogenized in TRIzol; total RNA isolated using Zymo Direct‑zol RNA Kit per manufacturer’s instructions
PolyA capture

treatment_protocol: At 17 months, mice received retro‑orbital injection of AAV8‑TBG‑saCas9 carrying either Ccnd1‑targeting sgRNA or Rosa26 control (3×10¹¹ vg/mouse); m‑lobe harvested 3 weeks later, flash‑frozen.

value: Liver

tag: strain


title: shNC-2

value: shNC


title: shNC-1


title: Low-input nephrocyte, control, replicate 2

status: Public on Sep 13 2024

city: Baltimore

first: Hangnoh

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Low-input nephrocyte 2

data_processing:
Nova-seq based sequencing was done by Psomagen (Rockville, MD)
We used STAR aligner 2.7.5c (PMID: 23104886) for the mapping of short reads onto the Drosophila genome.
We quantified RNA-Seq reads using RSEM 1.3.3 (PMID: 21816040)
For the quantification of RNA-Sequencing reads, we used Drosophila gene annotation 6.28 from FlyBase.
Assembly: Berkeley Drosophila Genome Project (BDGP) Release 6
Supplementary files format and content: Text file (compressed with gzip) containing gene expression profiles in transcripts per million reads (TPM).

organism: Drosophila melanogaster

source_name: Nephrocytes

growth_protocol: Flies were crossed, reared, and kept on standard food at 25°C.

extract_protocol:
RNA was harvested using SuperScript™ IV Single Cell/Low‑Input cDNA PreAmp Kit (Thermo Fisher Scientific) from flowcytometry-isolated adult fly nephrocytes.
cDNA libraries for RNA-seq were prepared using SuperScript™ IV Single Cell/Low‑Input cDNA PreAmp Kit (Thermo Fisher Scientific).

treatment_protocol: normal diet, contains 6% sucrose

value: Nephrocytes

value: Hand-GFP; Klf15-Gal4, UAS-RFP/CyO

value: normal diet, contains 6% sucrose


title: Low-input nephrocyte, control, replicate 1

description: Low-input nephrocyte 1


title: Endometrial stromal cells from ESC_58

status: Public on Sep 01 2024

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

data_processing:
Low quality sequencing reads and contaminating HiSeq Illumina adaptor sequences were trimmed using Trimmomatic v0.36
Trimmed reads were aligned to the human reference genome (Ensembl Homosapiens GRCh38 relesse 84) using with HISAT2 v2.05
Assembled into transcripts and counted using StringTie v1.3.1 and the EnsemblHomo sapiensGRCh38 release 91 reference assembly
Lowly expressed genes with counts per million (CPM) <0.22 (~10 counts) and expressed in <90% of the samples, were removed
Counts were normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM) using the edgeR R package v3.22.3
Assembly: hg38
Supplementary files format and content: csv file containing raw counts for each sample
Supplementary files format and content: csv file containing counts normalized using the Trimmed Mean of M (TMM) method, converted to CPM and log2 transformed (log2-CPM)

source_name: endometrial stromal cells

growth_protocol: Endometrial stromal cells were maintained in IMEM with 10% fetal calf serum and 1% antibiotics in a humidified atmosphere and 5% C02

extract_protocol:
Total RNA was isolated via the AllprepDNA/RNA Mini kit. RNA was treated with Turbo DNA-free kit.
Stranded RNA-seq libraries were prepared using the Illumina Tru-seq Strandard Total RNA Gold protocol, including ribosomal depletion (Illumina, USA)

treatment_protocol: No treatment was performed

value: endometrial stromal cells

tag: menstrual cycle_phase

value: Proliferative

tag: passage

tag: flowcell

tag: lane


title: Endometrial stromal cells from ESC_59

value: Peri-ovulatory


title: Endometrial stromal cells from ESC_57

value: Amenorrheic


title: Endometrial stromal cells from ESC_56


title: Endometrial stromal cells from ESC_54

value: Secretory


title: Endometrial stromal cells from ESC_52


title: Endometrial stromal cells from ESC_50


title: shNC-4

tag: tissue


title: Spleen, CD8 (HTO)

molecule: protein

tag: genotype

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

value: LCMV infected only

value: spleen


title: Endometrial stromal cells from ESC_49


title: Endometrial stromal cells from ESC_48


title: Endometrial stromal cells from ESC_45


title: Endometrial stromal cells from ESC_44


title: Endometrial stromal cells from ESC_43


title: Endometrial stromal cells from ESC_42


title: Endometrial stromal cells from ESC_41


title: Endometrial stromal cells from ESC_46


title: Endometrial stromal cells from ESC_40


title: Endometrial stromal cells from ESC_39


title: 24-h AcLDL 2: Input (Input LDF2)

value: Primary macrophage

value: 24 hr


title: 24-h OxLDL: Low fluorescent (Low_LDF3)


title: 24-h AcLDL 1: Input (Input_LDF1)


title: Endometrial stromal cells from ESC_38


title: Endometrial stromal cells from ESC_37


title: Endometrial stromal cells from ESC_35


title: shZFPL1-4

value: hepatocellular carninoma

tag: treatment


title: Endometrial stromal cells from ESC_34

tag: cell type


title: Endometrial stromal cells from ESC_36


title: Endometrial stromal cells from ESC_33


title: shNC-3


title: shZFPL1-1


title: Endometrial stromal cells from ESC_32


title: Endometrial stromal cells from ESC_31


title: Endometrial stromal cells from ESC_30


title: Endometrial stromal cells from ESC_29


title: Endometrial stromal cells from ESC_28


title: Endometrial stromal cells from ESC_26


title: Endometrial stromal cells from ESC_27


title: Low-input nephrocyte, control, replicate 3

description: Low-input nephrocyte 3


title: Endometrial stromal cells from ESC_23


title: Endometrial stromal cells from ESC_25


title: Endometrial stromal cells from ESC_24


title: Endometrial stromal cells from ESC_22


title: Endometrial stromal cells from ESC_20


title: Endometrial stromal cells from ESC_19


title: Endometrial stromal cells from ESC_18


title: Endometrial stromal cells from ESC_17


title: Endometrial stromal cells from ESC_16


title: Endometrial stromal cells from ESC_15


title: Endometrial stromal cells from ESC_55


title: Endometrial stromal cells from ESC_14


title: Endometrial stromal cells from ESC_13


title: Endometrial stromal cells from ESC_12


title: Endometrial stromal cells from ESC_53


title: Endometrial stromal cells from ESC_11


title: Endometrial stromal cells from ESC_10


title: Endometrial stromal cells from ESC_9


title: Endometrial stromal cells from ESC_8


title: Endometrial stromal cells from ESC_7


title: Endometrial stromal cells from ESC_51


title: Endometrial stromal cells from ESC_6


title: Endometrial stromal cells from ESC_5


title: Endometrial stromal cells from ESC_4


title: Endometrial stromal cells from ESC_3


title: Endometrial stromal cells from ESC_1


title: RV1B d4, rep 3

status: Public on Aug 25 2024

city: Ann Arbor

first: Marc

last: Hershenson

state: Michigan

address: 1150 E. Medical Center Drive

department: Pediatrics

institute: University of Michigan

description:
9578-JB-6
instrument model: Illumina NovaSeq X Plus

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.
The reads were trimmed using Cutadapt v2.3. The reads were evaluated with FastQC (v0.11.8) to determine quality of the data and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011)..
Alignment options followed ENCODE standards for RNA-seq. QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL 102) using STAR v2/7.8a and assigned count estimates to genes with RSEM v1/3.3
Supplementary files format and content: Tab-deliminated text file includes a complete matrix of gene expected count totals for all Samples.

source_name: lung

extract_protocol:
Total RNA was prepared using Trizol extraction.  RNA was double purified using RNEasy spin columns and enriched for mRNA using a Poly(A) mRNA Magnetic Isolation Module.
cDNA libraries for next generation sequencing were prepared with a xGen Broad-range RNA Library Prep with xGen Normalase UDI Primers.
Samples were subjected to 151 bp paired-end sequencing using a NovaSeq S4 or NaveSeq X Plus flow cell according to the Illumina NovaSeq manufacturer’s protocol.

treatment_protocol: Mice were treated intranasally with sham LLC-MK2 cell lysate, 100,000 TCID50 units HCoV-NL63, or 1,000,000 PFU RV-A1B. At 48h their lungs were harvested for RNA.

value: lung

value: RV1B d4


title: RV1B d4, rep 2

description:
9578-JB-5
instrument model: Illumina NovaSeq X Plus


title: Endometrial stromal cells from ESC_2


title: RV1B d4, rep 1

description:
9578-JB-4
instrument model: Illumina NovaSeq X Plus


title: NL63 d4, rep 3

description:
9578-JB-3
instrument model: Illumina NovaSeq X Plus

value: NL63 d4


title: NL63 d4, rep 1

description:
9578-JB-1
instrument model: Illumina NovaSeq X Plus


title: NL63 d4, rep 2

description:
9578-JB-2
instrument model: Illumina NovaSeq X Plus


title: NL63 d2, rep 3

value: NL63 d2


title: sham d2, rep 3

value: Sham d2


title: RV1B d6 NL63 d2, rep 3

value: RV1B d6 NL63 d2


title: NL63 d2, rep 2


title: Sham d2, rep 2


title: RV1B d6 NL63 d2, rep 2


title: NL63 d2, rep 1


title: Sham d2, rep 1


title: RV1B d2, rep 3

value: RV1B d2


title: RV1Bd2, rep 1


title: RV1B d2, rep 2


title: RV1B d6 NL63 d2, rep 1


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 9_DHIRA_Sen3

status: Public on Aug 13 2024

description: RNA extraction

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks, then transferred to TPM
Assembly: hg38
Supplementary files format and content: TPM matrix contains TPM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

source_name: Human primary lung fibroblasts IMR90

growth_protocol: To culture the cells and induce senescence, primary human IMR90 fibroblasts were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, and 2 mM glutamine at 37°C in a humidified atmosphere with 5% CO2 and 3.5% oxygen. To induce senescence, cells were treated with etoposide, a DNA damaging agent, at a concentration of 25 or 50 μM for 24 hours. Following this treatment, the etoposide-containing media was replaced with complete media.  After eight days, the cells were harvested for senescence assays

extract_protocol:
The TRIzol method was used to extract total RNA according to the manufacturer's instructions (Invitrogen™ TRIzol™ Reagent, Catalog number: 15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Senescence was induced by 50 µM Etoposide, a DNA damaging agent.

tag: growing state

value: Senescence

value: Mutant HIRA


title: Endometrial stromal cells from ESC_47

value: endometrial stromal cells

value: Proliferative


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 7_DHIRA_Sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 6_EV_Sen3

description: RNA extraction

value: Empty Vector


title: Human primary lung fibroblasts IMR90 - Senescent Mutant HIRA (pQCXIP-HA-HIRA (520-1017)) 8_DHIRA_Sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 5_EV_Sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 3_EV_Prolif3

description: RNA extraction

value: Proliferating


title: Human primary lung fibroblasts IMR90 - Senescent Empty vector control (pQCXIP) 4_EV_Sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 2_EV_Prolif2

description: RNA extraction


title: Human primary lung fibroblasts IMR90 - Proliferating Empty vector control (pQCXIP) 1_EV_Prolif1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-15_shPML-Sen3

description: RNA extraction

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Assembly: hg19
Supplementary files format and content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary files format and content: Raw count matrix contains raw counts for each sample and each gene

treatment_protocol: Senescence was induced by 50 µM Etoposide, a DNA damaging agent. Infected with lentivirus containing non targeting sequences and short hairpin sequences to knock-down HIRA and PML.

value: shPML


title: Human primary lung fibroblasts IMR90-14_shPML-Sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-13_shPML-Sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-12_sh2HIRA-sen3

description: RNA extraction


title: Human primary lung fibroblasts IMR90-11_sh2HIRA-sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-10_sh2HIRA-sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-09_sh1HIRA-sen3

description: RNA extraction


title: Human primary lung fibroblasts IMR90-08_sh1HIRA-sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-07_sh1HIRA-sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-06_TRC-Sen3

description: RNA extraction

value: TRC


title: Human primary lung fibroblasts IMR90-05_TRC-Sen2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-04_TRC-Sen1

description: RNA extraction


title: Human primary lung fibroblasts IMR90-03_TRC-Pro3

description: RNA extraction


title: Human primary lung fibroblasts IMR90-02_TRC-Pro2

description: RNA extraction


title: Human primary lung fibroblasts IMR90-01_TRC-Pro1

description: RNA extraction


title: Islets_ndLN_HTO

status: Public on Aug 10 2024

description: HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.

library_source: other

data_processing:
*library strategy: CITE-seq, TCR-seq
CellRanger v6.0.1, along with its count and vdj functions, and cite-seq-count v1.4.3 were utilized to aggregate reads across sequencing samples, resulting in unified sets of corresponding readouts.
Assembly: mm10
Supplementary files format and content: CellRanger output files:  GEX_barcodes.tsv.gz,GEX_features.tsv.gz, GEX_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TCR_filtered_contig_annotations.csv
Supplementary files format and content: cite-seq-count output files:  HTO_barcodes.tsv.gz, HTO_features.tsv.gz, HTO_matrix.mtx.gz

source_name: islet and lymph nodes

extract_protocol:
Regulatory T cells and conventional CD4 T cells (Tconvs) were isolated from the islets and ndLN 6 Foxp3CRE-GFP.NOD and 6 Rosa26+/LSL-Ametrine-Nrp1Foxp3CRE-GFP.NOD (6-week females).
Cells were loaded into Single Cell Chip at a a goal of 50:50 ratio of Tregs:Tconvs. Cells were then processed through 10X controller for droplet generation and Library preparation.
The CITE-seq and hashing protocol were employed to produce a hashtag oligo library and a 5' gene expression library.

value: islet and lymph nodes

value: wild type and Rosa^Nrp1^L/+

value: CD4 Tconv and Treg

tag: library type

value: HTO

tag: hto


title: Islets_ndLN_TCR

description: TCR library, read 1 contains barcode and UMI information, and read 2 containsTCR sequences

molecule: other

value: TCR


title: Islets_ndLN_GEX

description: GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript

value: mRNA


title: pMEL CD8 cells citeseq hashtages

status: Public on Aug 07 2024

description:
Hashtag-derived oligonucleotides
HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.
pMEL_HTO

data_processing:
After library preparation and quantification, samples were pooled and sequenced on a NovaSeq 6000 using S1 v1.5 kits (150 cycles), with sequencing parameters adjusted for v1 and v2 Chemistry.
Demultiplexing, barcode processing, gene counting, and aggregation were conducted using Cell Ranger software version 6.1.2 and CITE-seq-Count version 1.4.4.
Assembly: mm10
Supplementary files format and content: CellRanger output files: polyclonal_GEX_barcodes.tsv.gz, polyclonal_GEX_features.tsv.gz, polyclonal_GEX_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: polyclonal_TCR_filtered_contig_annotations.csv
Supplementary files format and content: CellRanger output files: pMEL_GEX_barcodes.tsv.gz, pMEL_GEX_features.tsv.gz, pMEL_GEX_matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count output files: polyclonal_HTO_barcodes.tsv.gz, polyclonal_HTO_features.tsv.gz, polyclonal_HTO_matrix.mtx.gz
Supplementary files format and content: CITE-seq-Count output files: pMEL_HTO_barcodes.tsv.gz, pMEL_HTO_features.tsv.gz, pMEL_HTO_matrix.mtx.gz

source_name: Tumor

extract_protocol:
Single-cell libraries were prepared from sorted live CD8+ T cells derived from either polyclonal mice or CD8+ pMEL cells from an antigen-specific system, utilizing Chromium Single Cell 5’ Reagent (v1 Chemistry) or Chromium Next GEM Single Cell 5’ Reagent (v2 Chemistry Dual Index) immediately post-cell isolation.
Sample multiplexing was achieved via CITEseq, wherein cells were stained with TotalSeq-C anti-mouse hashtag antibodies and additional surface flow cytometry antibodies (TCRβ, CD8). Sorted cells, tagged with uniquely barcoded TotalSeq-C antibodies, were pooled and loaded into parallel lanes for droplet generation, targeting a recovery of 2,000 cells per sample. After droplet partitioning, cells underwent lysis and reverse transcription within droplets.
cDNA was isolated, bulk amplified, and selected with SPRIselect beads. Adaptors were ligated, sample indices were added through PCR, and samples underwent another selection using SPRIselect beads. Library concentration was determined via PCR with KAPA DNA Quantification.

value: Tumor

tag: cell line

value: m_totalseq_1, Pdcd1L/L Lag3L/L-yfp (WT) - Tumor; m_totalseq_2, Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_3, Pdcd1L/L E8ICre.GFP - Tumor; m_totalseq_4, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - Tumor.


title: pMEL CD8 cells gene expression

description:
polyA RNA
GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript
pMEL_GEX


title: polyclonal CD8 cells TCR seq

description:
TCR seq
TCR library, read 1 contains barcode and UMI information, and read 2 containsTCR sequences
polyclonal_TCR

source_name: Tumor and lymph node

value: Tumor and lymph node


title: polyclonal CD8 cells citeseq hashtages

description:
Hashtag-derived oligonucleotides
HTO library, Read 1 contains cell barcode and UMI.Read 2 contains the15 bp hashtag.
polyclonal_HTO

value: m_totalseq_1, Pdcd1L/L Lag3L/L-yfp (WT) - Tumor; m_totalseq_2, E8ICre.GFP (WT) - Tumor; m_totalseq_3, Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_4, Pdcd1L/L E8ICre.GFP - Tumor; m_totalseq_5, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - Tumor; m_totalseq_6, Pdcd1L/L Lag3L/L-yfp (WT) - ndLN; m_totalseq_7, E8ICre.GFP (WT) - ndLN; m_totalseq_8, Lag3L/L-yfp E8ICre.GFP - ndLN; m_totalseq_9, Pdcd1L/L E8ICre.GFP - ndLN; m_totalseq_10, Pdcd1L/L Lag3L/L-yfp E8ICre.GFP - ndLN.


title: polyclonal CD8 cells gene expression

description:
polyA RNA
GEX (5' mRNA) library,Read 1 contains the cell barcode and UMI, and Read 2 contains the transcript
polyclonal_GEX


title: Male microglia, pMCAO, Day 3

status: Public on Jul 01 2024

first: Wei

last: Yang

state: United States

address: 300 Duke Street

description:
10X Genomics
M_Stroke

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of all 4 samples , using 10X Cellranger v7.1.0 with default parameters.
Assembly: mm10-2020-A custome ref with ZsGreen seq added
Supplementary files format and content: raw read counts in gene-barcode matrix

source_name: brain

extract_protocol:
Mice were intubated, anesthesized with isoflurane and transcardially perfused. Brains were immediately harvested and only the ipsilateral hemisphere was proccessed. Brain tissue was dissociated by mechanical dissociation, filtered (70 um). A percoll gradient  were used to isolate enriched microglial cells yield (pellet) after centrifugation . Samples were resuspended in FASC buffer (RPMI1640, 2% FBS, and 2 mM EDTA). Four samples per condition were combined at this step. Next, live ZsGreen+ cells were sorted using fluorescence-activated cell sorting (BD FACSAria II) and immediately after sequenced (Novaseq 6000).
10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) was used to generate single-cell gel beads with reverse transcription (RT) reagents in emulsions (GEMs). After GEM-RT was performed, the single-strand cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). The cDNA was then amplified and purified. Indexed sequencing libraries were constructed using the Chromium Single-Cell 3’ v3.1 Library Kit following the manufacture’s instruction. The barcoded sequencing libraries were quantified and loaded on a Novaseq 6000 (Illumina, San Diego, CA, USA) for sequencing.

treatment_protocol: pMCAO was performed by permanent ligation of the right middle cerebral artery. Body temperature was monitored during the entire surgical process. Sham mice underwent similar surgical procedure without ligation of the middle cerebral artery.

value: brain

tag: Sex

value: Male

value: microglial cells

value: pMCAO


title: Female microglia, pMCAO, Day 3

description:
10X Genomics
F_Stroke

value: Female


title: Male microglia, Sham, Day 3

description:
10X Genomics
M_Sham

value: Sham surgery


title: Female microglia, Sham, Day 3

description:
10X Genomics
F_Sham


title: SIC_182_561_1_heart

status: Public on Jun 22 2024

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: GRCh38
Supplementary files format and content: combined_tissue_data.h5ad includes the counts for all cells that passed QC in .h5 format
Supplementary files format and content: combined_pbmc_data.h5ad includes the counts for all demultiplexed cells that passed QC in .h5 format
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format
Supplementary files format and content: all_contig_annotations_tcr.csv files include the TCR data for the associated samples
Supplementary files format and content: fbc.csv files contains data for featured barcodes for applicable samples (all PBMC samples)
Supplementary files format and content: hashing_info.csv includes information about which samples correspond to which fbc hashtags in the PBMC samples
Supplementary files format and content: cite_info.csv includes information about the antibodies included in the FBC pool

source_name: Heart tissue

extract_protocol:
Tissue samples obtained by biopsy or autopsy were immediately placed in ice-cold HypoThermosol solution (BioLife Solutions, Bothell, WA) and kept on ice during transfer to the research facility. Tissue was then washed twice with cold phosphate buffered saline. Tissue was then dissociated using the human tumor dissociation kit according to the manufacturer’s instructions (Miltenyi Biotic, Bergisch Gladbach, Germany) with modification such that calcium chloride was added to the enzymatic cocktail to a final concentration of 1.25 mM. Tubes containing tissue fragments in the enzymatic cocktail were placed in a heated shaker at 37° C with shaking at 750 RPM for 25 minutes with the machine placed on its side to prevent tissue fragments from settling. Following incubation, the reaction was quenched through the addition of 100 µl human serum. The mixture was further dissociated through manual trituration followed by filtration through 70 µm mesh. Following centrifugation at 350 x g for 12 minutes, the supernatant was removed and RBC lysis was performed (ACK lysing buffer, Lonza, Basel, Switzerland). Following a wash step, cells were resuspended in phenol-free RPMI with 2% (v/v) human AB serum.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart tissue

tag: age

value: male

tag: group

value: control


title: Brain_Ipsi_Stroke_3day_Cells

status: Public on May 22 2024

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Count matrices were generated for each library using the 10X Genomics CellRanger v3.0.2 pipeline. First, raw reads were demultiplexed to produce fastq files. Second, reads were aligned to the mouse reference genome (GRCm38) and quantified. Resultantly, two unique molecule identifiers (UMI) based expression matrices were generated each for the ipsilateral and contralateral conditions which were pre-processed and analysed using the Seurat v3 package in R
Assembly: GRCm38
Supplementary files format and content: Seurat object

extract_protocol:
Cells were extracted from brains using a no-enzyme cold processing approach in Hank's balanced salt solution to avoid activation of immune cells due to warm enzyme processing.
Single cell 3’ gene expression (mRNA) and cell surface hashtag-oligonucleotide (HTO) libraries were prepared according to the Chromium Single Cell 3ʹ with Feature Barcoding technology for Cell Surface Protein Reagent Kit v3 protocol (10X Genomics) with modifications for incorporation of TotalSeq™-A HTO antibodies (clones M1/42; 30-F11, BioLegend). Briefly, generation of gel beads in emulsion (GEM) partitioned with single cells, reverse transcription to generate cDNA and HTO-barcoded DNA, and DNA amplification were performed according to manufacturer instructions with the addition of HTO primers during DNA amplification. Amplified cDNA and HTO-derived DNA were separated by size selection, fragmented and libraries constructed.

value: Brain

value: Immune cells

value: WT


title: Brain_Contra_Stroke_3day_Cells


title: H9-DE, dRNA-ONT

status: Public on May 08 2024

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

description: Direct RNA sequencing (SQK-RNA002 Kit) for Library prepration; R9.4.1 flow cell for sequencing

data_processing:
For ONT long-read RNA-seq, only the long reads with a quality score (qscore ≥7, passed reads) are used for our study, and these passed reads are uploaded to NCBI GEO.  For Illumina short-read RNA-seq, sequencing adapters are trimmed by Cutadapt (v1.8.1)  with the parameter “-q 20,20 -m 20 --max-n 0.01 --trim-n”.
ReDD (v1.0.0) with sample-specific model is run separately on the ONT direct RNA seq data to obtain the A-to-I editing sites and editing level.
REDItools2 (v2.0.0) is run on the Illumina RNA-seq data to obtain the A-to-I editing sites and editing level.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by ReDD.
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by REDItools2.

growth_protocol: Definitive endoderm (DE) and pharyngeal endoderm (PE), and primordial germ cell-like cells (PGC) (reference: PMID: 37709760) are differentiated from human ESC (H1-hESC cell line), respectively. See the details in the manuscripts: (1)  DOI: https://doi.org/10.1101/2022.06.26.497457 (from ESC to DE and PE); and (2) PMID: 37709760 (from ESC to PGC).

extract_protocol:
Total RNA is extracted by TRIzol Reagent (Thermo Fisher Scientific), followed by polyA+ RNA enrichment using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific).
For H1-ESC, H1-PE, H1-DE, H1-PGC,H9-hESC,H9-PE,H9-DE and HEK293T, ONT sequencing libraries are prepared using the SQK-RNA002 Kit for direct RNA sequencing (dRNA-ONT). ONT sequencing is conducted using MiniON/GridION flow cells with R9.4.1 chemistry, with real-time base calling performed by the Guppy software. The library preparation and sequencing of Illumina RNA-seq data are conducted by Novogene company.

value: H9-hESC derived definitive endoderm


title: H9-PE, dRNA-ONT

value: H9-hESC derived pharyngeal endoderm


title: H9-hESC, dRNA-ONT

value: H9 human embryonic stem cells


title: H1-PGC, dRNA-ONT

value: H1-hESC derived primordial germ cell-like cells


title: H1-DE, dRNA-ONT

value: H1-hESC derived definitive endoderm


title: H1-hESC, dRNA-ONT

value: H1 human embryonic stem cells


title: H1-PE, dRNA-ONT

value: H1-hESC derived pharyngeal endoderm


title: HEK293T_WT, dRNA-ONT

value: human epithelial like cells


title: H9-PE, Illumina, rep 3


title: HEK293T_dMut, dRNA-ONT


title: H9-PE, Illumina, rep 1


title: H9-PE, Illumina, rep 2


title: APECED patient, Buccal biopsy, AIRE.23c

status: Public on Jan 28 2025

description: Buccal biopsy optained from an APECED patient with AIRE mutation.

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to NCBI/GRCh38  using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (gencode.v39.annotation.gtf.gz) obtained from https://www.gencodegenes.org/human/
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contain RPKM values for each Sample

source_name: Buccal biopsy

extract_protocol:
Total RNA was extracted from whole tissue using TruSeq Stranded Total RNA Kit following manufacturer’s recommendations (Illumina, San Diego, CA).
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA).
Paired-end RNA-seq on NextSeq500 sequencer (Illumina)

value: Buccal biopsy

value: AIRE mutation

tag: disease state

value: APECED patient

value: Baseline


title: H9-DE, Illumina, rep 3


title: H9-DE, Illumina, rep 2


title: H9-hESC, Illumina, rep 3


title: Spleen, Tregs (HTO)

status: Public on Jan 19 2025

data_processing:
Library strategy: CITE-seq
For demultiplexing of samples, cellranger (v6.0.0; 10X Genomics) was used with the defualt settings.
CellRanger was used to align gene expression data to the mm10 reference and generate feature barcode expression matrices using the default settings.
cite-seq-count was(v1.4.3) used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 -trim 10.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression feature barcode matrices.  CITEseq feature barcode matrices.  The cite seq hash tags to distinguish different experimental settings.

source_name: spleen

extract_protocol: Splenocytes were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with Cl. 13. for 16d. T cells were enriched by negative selection. Briefly, single cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with a uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration.A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population. Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: naïve or LCMV infected

value: spleen


title: 11_male PDMCAO aged #2

status: Public on Jan 09 2025

description: 10X Genomics

data_processing:
processed by Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Brain

extract_protocol:
brains slice, Miltenyi Adult Brain Dissociation Kitt
10X Genomics

value: Brain

value: aged

value: male

value: PDMCAO


title: H9-DE, Illumina, rep 1

value: H9-hESC derived definitive endoderm


title: H9-hESC, Illumina, rep 2

value: H9 human embryonic stem cells


title: H1-PGC, Illumina, rep 3

value: H1-hESC derived primordial germ cell-like cells


title: H9-hESC, Illumina, rep 1


title: H1-PGC, Illumina, rep 2


title: H1-PE, Illumina, rep 3


title: H1-PE, Illumina, rep 1


title: H1-PE, Illumina, rep 2


title: H1-DE, Illumina, rep 3

value: H1-hESC derived definitive endoderm


title: H1-PGC, Illumina, rep 1


title: H1-DE, Illumina, rep 2


title: H1-hESC, Illumina, rep 3

value: H1 human embryonic stem cells


title: HEK293T_dMut, Illumina, rep 3

value: human epithelial like cells


title: H1-hESC, Illumina, rep 1


title: H1-DE, Illumina, rep 1


title: HEK293T_dMut, Illumina, rep 1


title: HEK293T_dMut, Illumina, rep 2


title: HEK293T_WT, Illumina, rep 3


title: HEK293T_WT, Illumina, rep 2


title: Postculture1_screen4_03

status: Public on May 01 2024

data_processing:
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9.2
We used a paired MAGeCK test so we could analyze data from four independent CRISPR screens
Assembly: Brie Library
Supplementary files format and content: Counts.csv file contains frequency per sgRNA in each CRISPR screen per condition
Supplementary files format and content: rra_paired.gene_summary.txt contains the MAGeCK RRA analysis output comparing input to post-culture sgRNA read frequencies from counts.csv

source_name: Bone-marrow

growth_protocol: Following bone-marrow cell isolation, cells were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.
The parameters for how the library sequenced - chip: 75 high fidelity read

treatment_protocol: Primary Macrophages expressing Cas9 were transduced with the Brie Library plasmids (Input) packaged in lentivirus at low multiplicity of infection (MOI) (0.3) to achieve 50 fold representation of each sgRNA in the Brie Mouse library.  After 48 h, transduced cells were selected with 5 ug/ml puromycin for 2 days and cultured another 12-14 days (post-culture)

value: Bone-marrow

value: Primary Macrophage

tag: molecule type

value: PCR amplicon from genomic DNA


title: HEK293T_WT, Illumina, rep 1


title: Postculture1_screen4_02


title: Postculture1_screen4_04


title: Postculture1_screen4_01


title: Input_screen4_04


title: Input_screen4_02


title: Input_screen4_01


title: Input_screen4_03


title: Endometrial stromal cells from ESC_21

value: endometrial stromal cells

tag: menstrual cycle_phase

value: Proliferative

tag: passage


title: Postculture1_screen3_04


title: Postculture1_screen3_02


title: Postculture1_screen3_03


title: Input_screen3_04


title: Postculture1_screen3_01


title: Input_screen3_02


title: Input_screen3_01


title: Postculture1_screen2_04


title: Input_screen3_03


title: Postculture1_screen2_03


title: Input_screen2_03


title: Input_screen2_02


title: Input_screen2_01


title: Haloferax volcanii cells, rosR deletion strain, rep4

status: Public on Nov 20 2024

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_rosR_4

data_processing:
RNA-seq data were processed using the fastp toolkit (Chen et al., 2018) to trim low-quality bases and sequencing adapters from the 3’ end of reads.
STAR (Dobin et al., 2013) RNA-seq alignment tool was used to map trimmed reads to the genome of Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively). Reads aligning to a single genomic location were summarized across genes.
For genes having an overlap of at least 10 reads, gene counts were normalized and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package implemented for the R programming environment. Consistent with the recommendation of the DESeq authors, independent filtering (Ignatiadis et al., 2016) was utilized prior to calculating adjusted p-values (Benjamini Y, 1995) and moderated log2 fold-changes were derived using the ashr package (Stephens, 2017). Genes were considered significantly differentially expressed if the log2 fold change ratio (∆rosR : parent) was >= |1| and adjusted p-value < 0.05.
Assembly: Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively).
Supplementary files format and content: Hfx. mediterranei assembly ASM540632v1 refseq ID = GCF_005406325.1; Hfx. volcanii assembly ASM2568v1 refseq ID = GCF_000025685.1

source_name: archaeal cells

extract_protocol:
RNA was extracted using an Absolutely RNA Miniprep kit according to manufacturer instructions (Agilent, Santa Clara, CA). RNA quality was measured using RNA 6000 Nano kit on a 2100 Bioanalyzer (Aglient, Santa Clara, CA). PCR to verify lack of DNA contamination was  conducted on 300 ng of RNA sample using species-specific primers listed in Supplementary Table S2. Ribosomal RNA depletion was performed from 300 ng of each sample using NEBNextR RNA Depletion Core Reagent (#E7870 New England Biolabs) according to the manufacturer instructions. The resultant mRNA was purified using NEBNext RNA sample purification beads and eluted in 7 l of nuclease-free water. 1l of each sample was used for quantification and quality verification (free of rRNA) in a second round of Agilent Bioanalyzer analysis using 2100 Prokaryote Total RNA Nano kit (Aglient, Santa Clara, CA).
Libraries were constructed using 5 ml of mRNA using the Ultra II Directional RNA Library Preparation Kit (Agilent, Santa Clara. CA). Indexes were designed according to the kit specifications and obtained from Integrated DNA Technologies. Resultant libraries were tested for quality and quantity by Bioanalyzer using the 2100 expert High Sensitivity DNA Assay chip (Agilent Technologies)

value: archaeal cells

value: deltapyrEdeltaHVOrosR

value: standard growth medium, knockout strain


title: Postculture1_screen2_02


title: Postculture1_screen1_04


title: Postculture1_screen2_01


title: Input_screen2_04


title: Postculture1_screen1_02


title: Postculture1_screen1_01


title: Postculture1_screen1_03


title: Input_screen1_04


title: Input_screen1_03


title: Input_screen1_01


title: Input_screen1_02


title: Br8325_VSPG

status: Public on Apr 27 2024

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: brain (hippocampus)

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (hippocampus)


title: Br8492


title: Br8325


title: Br6471


title: Br6522


title: Br8667


title: Br6423


title: Br6432


title: Br2743


title: Br2720


title: 39c_scp

data_processing:
FASTQ files were pre-processed with the 10x CellRanger pipeline
Reads were aligned to reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Raw FASTQ files and data processed with the 10x CellRanger pipeline with barcode, feature, and matrix files for each donor.

extract_protocol:
Anterior hippocampus was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of hippocampus from fresh frozen postmortem human tissue were obtained by cryosectioning. Nuclei were isolated and barcoded with 10x Genomics Chromium.
Libraries were prepared using 10x Chromium Next GEM Single Cell 3’ v3.1 (dual-index) kit according to manufacturer's instructions.
single-nucleus RNA-sequencing


title: 38c_scp


title: 32c_scp


title: 27c_scp


title: 37c_scp


title: 36c_scp


title: 33c_scp


title: 26c_scp


title: 24c_scp


title: 25c_scp


title: 23c_scp


title: 22c_scp


title: 20c_scp


title: 19c_scp


title: 21c_scp


title: 17c_scp


title: 18c_scp


title: 15c_scp


title: 14c_scp


title: 11c_scp


title: 16c_scp


title: 13c_scp


title: 2c_scp


title: 12c_scp


title: 10c_scp


title: control, RCC4 [shCTRL_rep2]

status: Public on Apr 23 2024

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine.
Sequencing adapters were removed using trimmomatic v0.39.
Trimmed sequence reads were mapped to the human genome assembly GRCh38 (hg38) using the STAR aligner.
Annotation of genomic features was performed using the featureCounts tool v1.6.4 using the last GENCODE release for RNA-seq. Differential gene expression was evaluated in R/BioConductor using the DESeq2 package vs 1.30.1
Assembly: hg38
Supplementary files format and content: tab delimited text of normalized counts

growth_protocol: Cells were cultured in DMEM supplemented with 1% penicillin/streptomycin and 10% 10% tetracycline-free FBS.

extract_protocol:
RNA was isolated with QIAGEN RNeasy Plus Micro Kit
RNA libraries were prepared using the TruSeq stranded mRNA protocol (Illumina).

treatment_protocol: Silencing of PML was performed via lentiviral shRNA

value: Human kidney cancer

value: control

value: shCTRL


title: PML knockdown, RCC4 [shPML_rep1]

value: PML knockdown

value: shPML


title: Old High Fat Diet Batch2 rep5

status: Public on Apr 17 2024

first: Peter

last: Adams

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Raw reads quality were checked using FastQC v0.11.8
Reads were aligned to mm10 using STAR v2.7.3a with GDC 2-step pass pipeline.
Raw read counts per gene were generated using HTSeq v0.11.2
Batch correction was done using sva(Surrogate Variable Analysis) ComBat v3.40.0.
Batch corrected FPKMs were then generated using R package countToFPKM 1.0
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample after batch correction

source_name: Isolated hepatocytes

extract_protocol:
Isolated hepatocytes were purified and snap frozen in LN2. RNA was derived using trizol chloroform RNA extraction methadology
PolyA capture

treatment_protocol: Mice were rested for at least 2 weeks prior to initiation of diet for 9-weeks. Diets were provided ad libitum and changes weekly. High fat diet 58y1 was purchased from TestDiet consisting of 60% nergy from fat. Normal diet was purchased from Teklad global 18% protein. Mice were maintained on diets for 9-weeks then euthanized using CO2 upon which 2-step liver perfusion was conducted to isolate hepatocytes.

value: Isolated hepatocytes

tag: strain

value: male

tag: age (months)

value: High fat diet


title: Old High Fat Diet Batch2 rep6

tag: tissue


title: control, RCC4 [shCTRL_rep1]

tag: genotype

tag: treatment


title: PML knockdown, RCC4 [shPML_rep2]

tag: cell type


title: 1c_scp


title: Old High Fat Diet Batch1 rep2


title: Old High Fat Diet Batch2 rep4


title: Old High Fat Diet Batch1 rep1


title: Old High Fat Diet Batch1 rep3


title: Old Normal Diet Batch2 rep6

value: Normal Diet


title: Old Normal Diet Batch2 rep5


title: Old Normal Diet Batch2 rep4


title: Young High Fat Diet Batch2 rep5


title: Old Normal Diet Batch1 rep2


title: Young High Fat Diet Batch1 rep3


title: Young High Fat Diet Batch2 rep6


title: Young High Fat Diet Batch2 rep4


title: Old Normal Diet Batch2 rep3


title: Young Normal Diet Batch2 rep6

value: Normal diet


title: Old Normal Diet Batch1 rep1


title: Young High Fat Diet Batch1 rep1


title: Young Normal Diet Batch1 rep3


title: Young Normal Diet Batch1 rep1


title: m4 Old Rep4 ATAC

description: m4 Old technical rep2, biological rep2

data_processing:
Raw reads quality were checked using FastQC v0.10.0
Raw reads were trimmed with threshold quality score > 20 using Trimgalore v0.3.0
Trimmed reads were aligned to mm9 using bowtie2
Duplicated reads were marked using Picard Tools v1.98.
Peaks were called using macs2 with parameter --nomodel
Assembly: mm9
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: liver

extract_protocol:
Nuclei were extracted from whole liver and lysed using diluted 10x (LB): 100mM Tris.Hcl pH 7.5, 100mM NaCl, 30mM MgCl2, 1% Igepal CA-630 with 2% BSA and protease inhibitor diluted in PBS.
Tagmentation reaction was for 30 minutes at 37C then DNA was isolated and 6-PCR cycles (72C 3m, 95C 30s, (95C for 10s, 63C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C) with i5xx and i7xx primers followed by a gel size selection of 220-1000bp.

treatment_protocol: Mice were aged for 6 and 23 months under IACUC supervision and provided normal CHOW (Teklad global 18% protein)

value: liver

value: Aging


title: m3 Old Rep2 ATAC

description: m3 Old technical rep2, biological rep1


title: m2 Young Rep4 ATAC

description: m2 Young technical rep2, biological rep2


title: m1 Young Rep2 ATAC

description: m1 Young technical rep2, biological rep1


title: m1 Young Rep1 ATAC

description: m1 Young technical rep1, biological rep1


title: EC-3h-ΔΔ, replicate 1, scRNA-seq

status: Public on Feb 20 2024

city: Wuhan

first: Xiaodan

last: Yan

state: Hubei Province

address: Donghu Road, No. 115, Wuchang District,

department: Medical Research Institute

institute: Wuhan University

description:
RiboD-mSPLiT
Result of correlation analysis between mSPLiT and RiboD-mSPLiT.xlsx
0427-3
ECOLI rRNA and mRNA reads.txt

data_processing:
The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq data were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples of the same species

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cell

extract_protocol:
For RiboD-mSPLiT, all  cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-mSPLiT, library was performed accarding to the Materials and Methods section;

value: bacterial cell

value: WT

value: exponential growth phase


title: Set1 Knockdown rep 1

status: Public on Jan 03 2024

data_processing:
The short reads were mapped using STAR aligner version 2.7.10a (PMID: 23104886) with the --alignIntronMax 250000 --alignMatesGapMax 1000000 parameters.
The mapped reads were then counted using RSEM version 1.3.3 with its default parameters (PMID: 21816040).
For the mapping and counting processes, the Drosophila gene annotation from Ensembl (Release 100, corresponding to Flybase 6.28) was used with the Berkeley Drosophila Genome Project (BDGP) reference genome release 6.
Berkeley Drosophila Genome Project (BDGP) reference genome release 6
Supplementary files format and content: Tab-delimited text files include Flybase gene IDs and corresponding expression levels in TPM (transcripts per kilobase million) for each sample.

source_name: Heart

extract_protocol:
For each of the heart samples,50 one-week old adult fly hearts were dissected and collected into ice-cold TRIzol LS reagent. Total RNA extraction followed the manufacturer's instructions (Direct-zol RNA Microprep, Zymo Research). The quality and concentration of RNA were assessed using agarose gel electrophoresis, NanoDrop 8000 Spectrophotometer, and Agilent 2100.
The preparation of RNA libraries was conducted by Novogene (Beijing, China) using standard Illumina protocols.

treatment_protocol: twi-Gal4 was applied to tissue specifically knockdown (RNAi) targeting Set1, trx, or trr. Hand-GFP was used to visualize the heart cells (labels the nuclei). Fly hearts were dissected from 50 one-week-old adult female flies.

value: Heart

value: trx-IR


title: Trx Knockdown rep 2

value: trr-IR


title: Young Normal Diet Batch2 rep4

city: La Jolla


title: Trx Knockdown rep 1


title: Young Normal Diet Batch2 rep5


title: Young Normal Diet Batch1 rep2


title: m2 Young Rep3 ATAC

description: m2 Young technical rep1, biological rep2


title: H1-hESC, Illumina, rep 2

value: H1 human embryonic stem cells


title: Young High Fat Diet Batch1 rep2


title: WTM2

status: Public on Dec 06 2023

city: Nanchang

first: Yanni

last: Lv

address: Yongwai street No. 17

institute: The First Affiliated Hospital of Nanchang University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: brain

value: Wild-type mice following MCAO/R


title: Br3942_VSPG

value: brain (hippocampus)


title: WTM1


title: Trr Knockdown rep 1


title: Set1 Knockdown rep 2


title: Trr Knockdown rep 3


title: WTC3

value: Wild-type mice following sham surgery


title: Control

value: control

value: Hand-GFP;twi-Gal4+/- (Gal4 crossed with w1118)


title: WTC1


title: WT_c_glu

status: Public on Dec 01 2023

address: 124 Science Dr

data_processing:
Merged FASTQ files for samples that were loaded onto multiple lanes of a given flowcell, respecting read pair assignment. Ex) cat *_L001_R1_001.fastq.gz *_L002_R1_001.fastq.gz
Adapter sequences were removed with Trim_galore! 0.4.3, cutadapt 2.3, and and sample quality assessed with FastQC 0.11.7 using default parameters.
Reads were aligned to the Haloferax volcanii DS2 reference genome (GCA_000025685.1, accessed 2023-09-11) with Bowtie2 2.3.5.1. Alignment by Bowtie2 required stand-specific read orientation for libraries constructed in the 2021 experiment. Only pairs aligning concordantly in the --rf orientation were considered.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.10.
Reads (for samples from 2019) or read paris (2021 samples) aligning to ORFs were counted using featureCounts 2.0.1 with arguments -p -B -s 2 and the DS2 reference genome  annotation (GCA_000025685.1, accessed 2023-09-11). For 2021 samples, fragments were required to align concordantly in the correct strand orientation (reverse) to be tallied.
In R, counts from 2019 and 2021 experiments were normalized relative to library size and batch corrected with DeSeq2 1.34.0. Pairwise correlations were computed using normalized counts for samples within each genotype+condition group, and samples with average R < 0.7  were considered outliers and were not used in downstream analyses.
Assembly: GCA_000025685.1
Supplementary files format and content: Text file of fragments mapping to genes. Each column is a sample, and rows are counts mapping to a given gene.

source_name: H26 ∆pyrE2

growth_protocol: Four single colonies of DF60 and ASK133 or AKS319 from 10-day old plates were inoculated in 5 mL YPC23 medium supplemented with 0.1% glucose and grown aerobically (250 rpm shaking) at 37C to stationary phase (optical density at 600nm ~ 4). Cells were washed twice with Hh-CA medium without glucose and transferred into fresh 50 mL Hh-CA with or without 0.1\% glucose at an initial optical density of ~ 0.4. After 24 hours cultures were collected and flash frozen with liquid nitrogen.

extract_protocol:
After 24 hours storage in -80C, RNA was extracted from cell pellets using Absolutely RNA Miniprep kit (Agilent Technologies, Santa Clara, CA).  For all samples, the absence of DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR and total RNA was quantified using Agilent Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Santa Clara, CA). For 2019 samples,  ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit (now discontinued, Illumina, San Diego, CA). For 2021 samples, extraction was followed by additional DNAse treatment with Turbo DNAse (Invitrogen), and ribosomal RNA was removed from total RNA with the PanArchaea riboPOOL kit according to the manufacturer protocol (siTOOLs Biotech, Germany) and checked for depletion using Agilent Bioanalyzer RNA Nano 6000 chip as described as described in Pastor et al. 2022.
For 2019 samples, rRNA-depleted RNA was used to construct the sequencing libraries with KAPA Stranded RNA-seq Library preparation (Kapa Biosystems) following manufacturer protocol. Fragment size of final libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on Illumina HiSeq4000 at the Duke Sequencing and Genomic Technologies Core Facility at Duke University (Durham, NC). For 2021 samples, sequencing libraries were constructed with NEBNext UltraII Directional RNA Library Preparation Kit (New England BioLabs, #E7760). The fragment size of all libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on NovaSeq6000 at the Center for Genomic and Computational Biology at Duke University (Durham, NC).

value: H26 {delta}pyrE2

value: archaeal cell culture

value: HvCA + uracil + 0.1% glucose (w/v)

tag: time

tag: year-flowcell


title: m4 Old Rep3 ATAC

description: m4 Old technical rep1, biological rep2

value: liver

value: male

value: Aging


title: WT_b_glu


title: WT_d_glu


title: Trr Knockdown rep 2


title: WT_b_noglu

value: HvCA + uracil


title: Set1 Knockdown rep 3

value: Heart


title: WT_a_glu


title: WT_a_noglu


title: WTC2


title: Br3942


title: Trx Knockdown rep 3


title: trmB_a_noglu

source_name: H26 ∆pyrE2∆trmB

value: H26 {delta}pyrE2{delta}trmB


title: WT_d_noglu


title: tbsP_e_glu

source_name: H26 ∆pyrE2∆tbsP (HVO_2861)

value: H26 {delta}pyrE2{delta}tbsP (HVO_2861)


title: trmB_a_glu


title: tbsP_d_noglu


title: tbsP_c_glu