title: Br2720-1c_dACC (snRNA-seq)

description: Library name: 1c_dACC


title: Br6432-2c_dACC (snRNA-seq)

status: Public on Sep 02 2025

type: SRA

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

country: USA

institute: Lieber Institute for Brain Development

description: Library name: 2c_dACC

library_source: transcriptomic single cell

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.

molecule: polyA RNA

organism: Homo sapiens

source_name: brain (dACC)

extract_protocol:
dACC was dissected from fresh frozen postmortem human tissue. 100 micron coronal sections of dACC 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.

tag: tissue

value: brain (dACC)


title: Br6471-3c_dACC (snRNA-seq)

description: Library name: 3c_dACC


title: H26/0.9 M NaCl/ 68h Repl 2

status: Public on Sep 01 2025

city: Frankfurt am Main

first: Andreas

last: Borst

address: Max-von-Laue-Str. 9

country: Germany

institute: Goethe-Universität Frankfurt

library_source: transcriptomic

data_processing:
All downstream analysis of the RNA-Seq results were done using the galaxy platform (https://usegalaxy.eu/).
The “FastQC” tool (version 0.11.9) was used for quality control, while the “RNA STAR” tool (2.7.8a) was applied for mapping to the Haloferax volcanii reference genome and soft-clipping of non-matching sequences. Standard parameters were applied, except for the following: “Maximum ratio of mismatches to mapped length”, which was set to 0.04; “Minimum alignment score, normalized to read length” and “Minimum number of matched bases, normalized to read length”, which were set to 0.66, respectively. Afterwards, the tool “htseq-count” (version 0.9.1) was used for counting all mapped reads of annotated genes. An up-to-date annotation file (September 2023) was thankfully provided by Friedhelm Pfeiffer of the the Max Planck Institute of Biochemistry in Martinsried (Munich, Germany). Finally, differential expression was calculated with the “DESeq2” tool (2.11.40.8) and the data exported for further procession using Microsoft Excel. Significance was obtained by filtering for results with adjusted value of p < 0.05 and at least a 2-fold up- or downregulation. For visualization, the “bamCoverage” tool (version 3.5.1.0.0) was used to create normalized bigwig files.
Assembly: published Haloferax volcanii DS2 genome (Hartman, Amber L et al. “The complete genome sequence of Haloferax volcanii DS2, a model archaeon.” PloS one vol. 5,3 e9605. 19 Mar. 2010, doi:10.1371/journal.pone.0009605)
Supplementary files format and content: normalized perstrand genomic coveragecoverage in bigwig files

molecule: total RNA

organism: Haloferax volcanii

growth_protocol: H. volcanii H26 cultures were grown in glucose medium with either 2.1 M or 0.9 M NaCl

extract_protocol:
total RNA was isolated using phenol/chloroform extraction. Afterwards, the RNA was DNase-I (Thermo Fisher Scientific) digested and again purified with phenol/chloroform extraction. The RNA was shipped to StarSEQ GmbH (Mainz, Germany), where after another quality check the rRNA depletion (NEBNext rRNA depletion Kit) and Sequencing was done (Illumina Next Seq 500; 25 mio PE reads with 2x 150 nt).
NEBNext Ultra II directional, dual index library

treatment_protocol: H. volcanii cultures were grown in 45 ml glucose medium with either 2.1 M or 0.9 M NaCl. 10 ml of cell culture was harvested after 26h while 5ml was taken after 68h by centrifugation.

tag: strain

value: strain DS2

tag: cell line

tag: genotype

value: WT (deltapyrE2)

tag: treatment

value: 0.9 M Nacl


title: H26/0.9 M NaCl/ 68h Repl 1


title: H26/2.1 M NaCl/ 26h Repl 2

value: 2.1 M Nacl


title: H26/0.9 M NaCl/ 26h Repl 1


title: H26/2.1 M NaCl/ 26h Repl 1


title: H26/0.9 M NaCl/ 26h Repl 2


title: Senescent + 2uM Ruxolitinib, replicate1

status: Public on Aug 13 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

description: Library name: Sen_Ruxo_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_Palbo.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: IMR90 fibroblasts were exposed to 20 Gy ionizing radiation (IR) over a 10‑minute period. Beginning on day 4 post‑IR, cells were treated with 2 μM Palbociclib or 2 μM Ruxolitinib on days 4, 6, 8, and 10. All samples (IR‑DMSO, IR + Palbociclib, and IR + Ruxolitinib) were harvested on day 11 post‑irradiation.

tag: cell type

value: Human Lung Fibroblasts

value: WT

value: Ruxolitinib, 2uM


title: Senescent + 2uM Ruxolitinib, replicate3

description: Library name: Sen_Ruxo_3


title: Senescent + 2uM Palbocicilb, replicate2

description: Library name: Sen_Palbo_2

value: Palbocilib, 2uM


title: Senescent + 2uM Palbocicilb, replicate3

description: Library name: Sen_Palbo_3


title: Senescent DMSO, replicate2

description: Library name: Sen_DMSO_2

value: DMSO


title: Senescent DMSO, replicate1

description: Library name: Sen_DMSO_1


title: Proliferating replicate 3

description: Library name: Prolif_3

value: No treatment


title: Proliferating replicate 2

description: Library name: Prolif_2


title: Proliferating replicate 1

description: Library name: Prolif_1


title: Senescent CCND1 knockdown, replicate2

description: Library name: Sen_siD1_2

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

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: CCND1 knockdown

value: Irradiation, siRNA knockdown


title: Senescent CCND1 knockdown, replicate3

description: Library name: Sen_siD1_3


title: Senescent CDK4, CDK6 dual knockdown, replicate3

description: Library name: Sen_siK4_K6_3

value: CDK4, CDK6 knockdown


title: Senescent CDK4, CDK6 dual knockdown, replicate2

description: Library name: Sen_siK4_K6_2


title: Senescent CDK4, CDK6 dual knockdown, replicate1

description: Library name: Sen_siK4_K6_1


title: Senescent CDK6 knockdown, replicate1

description: Library name: Sen_siK6_1

value: CDK6 knockdown


title: Senescent CDK6 knockdown, replicate2

description: Library name: Sen_siK6_2


title: Senescent CDK6 knockdown, replicate3

description: Library name: Sen_siK6_3


title: Senescent CDK4 knockdown, replicate3

description: Library name: Sen_siK4_3

value: CDK4 knockdown


title: Senescent CDK4 knockdown, replicate2

description: Library name: Sen_siK4_2


title: Senescent Non targeting#4 knockdown, replicate3

description: Library name: Sen_siNT4_3


title: Senescent Non targeting#4 knockdown, replicate2

description: Library name: Sen_siNT4_2


title: Senescent Non targeting#4 knockdown, replicate1

description: Library name: Sen_siNT4_1


title: Senescent Non targeting#3 knockdown, replicate2

description: Library name: Sen_siNT3_2


title: Senescent Non targeting#3 knockdown, replicate1

description: Library name: Sen_siNT3_1


title: Proliferating replicate2

description: Library name: Prolif_2


title: Proliferating replicate1

description: Library name: Prolif_1


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate3

description: Library name: Ccnd1KO_3

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

organism: Mus musculus

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


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate5

description: Library name: Ccnd1KO_5


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate2

description: Library name: Ccnd1KO_2


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate1

description: Library name: Ccnd1KO_1


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate4

description: Library name: Rosa26KO_4


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate1

description: Library name: Rosa26KO_1


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate3

description: Library name: Rosa26KO_3


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate2

description: Library name: Rosa26KO_2


title: sRNA_83 knockout, 2mM H2O2, biol rep 3

status: Public on Aug 11 2025

first: Emma

last: Dallon

address: 3400 N Charles St Levi 235

department: Biology

institute: Johns Hopkins University

description: Library name: 83C_RNA

data_processing:
Adapters were trimmed using Trim Galore (0.6.4_dev using Cutadapt 1.18)
Trimmed reads were aligned to the Haloferax volcanii DS2 NCBI RefSeq genome (GCF 000025685.1, ASM2568v1) using Bowtie (1.2.3 64-bit) allowing 2 mismatches
Read counts were calculated using featureCounts (v2.0.6)
Assembly: Hv NCBI RefSeq genome (taxonomy identification 2246, GCF 000025685.1, ASM2568v1)
Supplementary files format and content: sample_readcount.txt files are tab delimited text files with raw gene counts for each sample
Supplementary files format and content: Hfx_smORFs.gff is an annotation file with appended sRNAs and smORFs
Supplementary files format and content: Hfx_smORFs.gtf is an annotation file with appended sRNAs and smORFs

growth_protocol: Haloferax volcanii DS2 strain H98 was grown in liquid Hv-YPC supplemented with 40 mg/mL thymidine at 42°C, with shaking, to OD >0.5. Cultures were diluted into fresh media to an OD of 0.01 and grown to OD 0.4-0.6.

extract_protocol:
RNA extraction was performed using a Quick-RNA Miniprep kit (Zymo).
rRNA was depleted using 2.5 µg of DNase-treated RNA and the Ribo-Zero rRNA removal kit for bacteria (Illumina, discontinued). The SMARTer Stranded RNA-Seq kit (Takara Bio) was used to prepare the libraries with 100 ng RNA, dual-index primers, and 12 PCR cycles. For knockout strains, library preparation and sequencing were performed by SeqCenter in Pittsburgh, PA using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom probes.

treatment_protocol: For oxidative stress treatment, cultures were incubated with 2mM H2O2 for one hour at 42°C with shaking

value: sRNA_83 knockout

value: 2mM H2O2


title: sRNA_83 knockout, 2mM H2O2, biol rep 2

description: Library name: 83B_RNA


title: sRNA_83 knockout, 2mM H2O2, biol rep 1

description: Library name: 83A_RNA


title: sRNA_24 knockout, 2mM H2O2, biol rep 1

description: Library name: 24A_RNA

value: sRNA_24 knockout


title: sRNA_20 knockout, 2mM H2O2, biol rep 3

description: Library name: 20C_RNA

value: sRNA_20 knockout


title: sRNA_20 knockout, 2mM H2O2, biol rep 2

description: Library name: 20B_RNA


title: sRNA_20 knockout, 2mM H2O2, biol rep 1

description: Library name: 20A_RNA


title: WT RNA-seq, 2mM H2O2, biol rep 3

description: Library name: WTC_oxi_RNA


title: WT RNA-seq, 2mM H2O2, biol rep 2

description: Library name: WTB_oxi_RNA


title: WT RNA-seq, untreated, biol rep 3

description: Library name: WTC_control_RNA


title: WT RNA-seq, 2mM H2O2, biol rep 1

description: Library name: WTA_oxi_RNA


title: WT RNA-seq, untreated, biol rep 2

description: Library name: WTB_control_RNA


title: WT RNA-seq, untreated, biol rep 1

description: Library name: WTA_control_RNA


title: H98 RNA-seq, 2mM H2O2, biol rep 4

description: Library name: H98H_RNA


title: H98 RNA-seq, 2mM H2O2, biol rep 3

description: Library name: H98F_RNA


title: H98 RNA-seq, 2mM H2O2, biol rep 1

description: Library name: H98B_RNA


title: H98 RNA-seq, untreated, biol rep 3

description: Library name: H98E_RNA


title: H98 RNA-seq, untreated, biol rep 2

description: Library name: H98C_RNA


title: sRNA_24 knockout, 2mM H2O2, biol rep 2

description: Library name: 24B_RNA


title: H98 RNA-seq, untreated, biol rep 1

description: Library name: H98A_RNA


title: NC,WT,60-3

status: Public on Jul 31 2025

city: Kunming, Yunnan

first: fei

last: li

address: Dongwaihuan South Road, University Town, Chenggong District, Kunming City, Yunnan Province

country: China

institute: Yunnan university

description:
Library name: sample15
slam-WT-60-3
featurecounts_nc.txt

data_processing:
SLAM-Seq (thiol(SH)-linked alkylation for the metabolic sequencing of RNA) data were processed using a custom computational pipeline. First, adapter trimming was performed using Trim Galore (v0.6.10) to remove sequencing adapters and low-quality bases. Cleaned reads were then aligned to the reference genome of either Homo sapiens (GRCh38) or the Neurospora crassa using STAR (v2.7.10a) with default parameters, allowing detection of mismatches such as T>C conversions.
Following alignment, SAMtools (v1.15.1) was used to convert, sort, and index the aligned SAM files into BAM format. A custom Python script was then employed to extract reads containing T>C mutations, which are indicative of 4-thiouridine incorporation and subsequent alkylation. This step produced a mutation-specific BAM file consisting only of T>C conversion-containing reads.
To quantify gene-level expression and mutation levels, featureCounts (Subread v2.0.3) was used to separately count:
(1) the number of T>C mutation reads, and
(2) the total reads (mutation-inclusive and -exclusive),
mapped to each gene based on the corresponding genome annotation (GTF file).
Finally, for each gene, a T>C mutation ratio (termed remaining reads percentage) was calculated by dividing the number of T>C mutation reads by the total number of reads, providing a quantitative measure of RNA stability and labeling retention.
Ribosome profiling data for Neurospora crassa (assembly NC12), Mus musculus(GRCm38), and Homo sapiens(GRCh38) were processed according to established pipelines. Raw sequencing reads underwent adapter trimming and size selection (retaining 25-40 nt fragments), followed by rRNA depletion. Filtered reads were aligned using Bowtie to custom genomic references containing the longest transcript per gene plus 100-nt flanking regions at both ends.  Ribosome-protected footprints (RPFs) were stratified by length, with A-site codon assignment to nucleotides 16-18 from the 5' end. Subsequently, the groups of RPFs with a high ratio of in-frame codons (e.g., >70% for N. crassa, >70% for H. sapiens, >80% for M. musculus) are selected for further analysis. These groups include RPFs in the 0 frame, as well as the +1 and -1 frames
Assembly: hg38?nc10
Supplementary files format and content: feature counts for each sample

organism: Neurospora crassa

source_name: fungal cell

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1×penicillin-streptomycin and incubated at 37℃ with 5% concentration of CO2. Neurospora crassa strains were grown in minimal mediu at 25℃ with constant light.

extract_protocol:
total RNA was extracted with Trizol reagent.
1.For SLAM-seq :After alkylation modification with iodoacetamide, 1ug total RNA (HCT116 cell) or 50 ng mRNA (N. crassa) was prepared for library. and library preperation was following the manufacturers protocal of VAHTS Universal V8 RNA-seq Library Prep Kit
2.For Ribo-seq in human cell : 2×10? HCT116 cells were lysed in 300 µL ice-cold lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl?, 1 mM DTT, 100 ?g/mL cycloheximide, 0.5% Triton X-100, 2 U/mL DNase I, 1× protease inhibitor cocktail). Lysates were centrifuged at 10,000 × g for 10 min at 4°C. Supernatants were treated with RNase I (1 U per OD??? unit) for 45 min at 25°C. Total RNA was extracted using TRIzol reagent, precipitated with glycogen, and washed with 80% ethanol. Ribosome-protected fragments (28-34 nt) were resolved on 16% TBE-urea PAGE, excised, and eluted in RNA Gel Extraction Buffer (300 mM NaOAc, 1mM EDTA, 0.25% SDS). RNA was precipitated with 1× volume isopropanol at -20°C overnight. For library preparation, 100-200 ng RNA fragments were adenylated using poly(A) polymerase and PNK (37°C, 30 min). Preadenylated 5' adapter were ligated to ribosome-protected fragments with T4 RNA Ligase 2, truncated KQ (25°C, 2 h). Then purifying the ligation product with Streptavidin magnetic bead. And template-switching primer was used in reverse transcription with SuperScript III reverse (50°C, 30 min), following the library amplification.

treatment_protocol: 100 nM 4sU was added to medium for 2 hours (N. crassa) or 24 hours (K562 cells) labeling. Then cultures were supplied with 10uM uridine to stop further labeling.

value: fungal cell


title: NC,WT,60-2

description:
Library name: sample14
slam-WT-60-2
featurecounts_nc.txt


title: NC,WT,60-1

description:
Library name: sample13
slam-WT-60-1
featurecounts_nc.txt


title: Br6471_V12J03-002_C1 (ST)

description: Library name: Br6471_V12J03-002_C1

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

extract_protocol:
dACC 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 (dACC)


title: NC,WT,40-3

description:
Library name: sample12
slam-WT-40-3
featurecounts_nc.txt

value: WT


title: NC,WT,40-2

description:
Library name: sample11
slam-WT-40-2
featurecounts_nc.txt


title: NC,WT,40-1

description:
Library name: sample10
slam-WT-40-1
featurecounts_nc.txt


title: NC,WT,20-3

description:
Library name: sample9
slam-WT-20-3
featurecounts_nc.txt


title: Br6432_V12N28-331_B1 (ST)

description: Library name: Br6432_V12N28-331_B1


title: Br8667-10c_dACC (snRNA-seq)

description: Library name: 10c_dACC


title: NC,WT,20-2

description:
Library name: sample8
slam-WT-20-2
featurecounts_nc.txt


title: NC,WT,10-3

description:
Library name: sample6
slam-WT-10-3
featurecounts_nc.txt


title: NC,WT,20-1

description:
Library name: sample7
slam-WT-20-1
featurecounts_nc.txt


title: Br6522-4c_dACC (snRNA-seq)

description: Library name: 4c_dACC


title: Br2743-5c_dACC (snRNA-seq)

description: Library name: 5c_dACC


title: H98 RNA-seq, 2mM H2O2, biol rep 2

description: Library name: H98D_RNA


title: NC,WT,10-2

description:
Library name: sample5
slam-WT-10-2
featurecounts_nc.txt


title: H98 RNA-seq, untreated, biol rep 4

description: Library name: H98G_RNA


title: NC,WT,10-1

description:
Library name: sample4
slam-WT-10-1
featurecounts_nc.txt


title: Senescent + 2uM Ruxolitinib, replicate2

description: Library name: Sen_Ruxo_2

value: Human Lung Fibroblasts

value: Ruxolitinib, 2uM


title: NC,WT,0-1

description:
Library name: sample1
slam-WT-0-1
featurecounts_nc.txt


title: P7_GCM_RNA_2

status: Public on Jul 10 2025

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Library name: Sample12

data_processing:
Raw 3’ RNA-seq data were directly used with Salmon v1.4.0 (Patro et al., 2017) with default parameters and --noLengthCorrection to quantify the expression of GENCODE vM25 features on GRCm38.p6. Gene-level expression estimates were aggregated from transcript-level abundance using tximport v1.16.1 (Soneson et al., 2015).
Alternatively, all reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCm38.p6 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPM values and read counts for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted from cells using a RNeasy Micro kit (QIAGEN, 74004) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification as previously described  (Nakamura et al, 2015). Sequencing libraries were generated from amplified cDNA as described previously   (Nakamura et al, 2015).

value: testis

value: Germ cells


title: NC,WT,0-3

description:
Library name: sample3
slam-WT-0-3
featurecounts_nc.txt


title: NC,WT,0-2

description:
Library name: sample2
slam-WT-0-2
featurecounts_nc.txt


title: P7_GCM_RNA_1

description: Library name: Sample11


title: Senescent DMSO, replicate3

description: Library name: Sen_DMSO_3

value: DMSO


title: Senescent + 2uM Palbocicilb, replicate1

description: Library name: Sen_Palbo_1

value: Palbocilib, 2uM


title: tumor resection tissue, patient 12

status: Public on Jul 09 2025

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

institute: TGen

description: 10X genomics

data_processing:
data as run through cellranger count using 10X's provided reference genome (2020A), using the 'include-introns' option
Assembly: GRCh38, as downloaded from 10X genomics (2020A)
Supplementary files format and content: cellranger counts output matrices

molecule: nuclear RNA

source_name: resected lung tumor tissue

growth_protocol: N/A, cells were obtained directly from human lung

extract_protocol:
Single nuclei were isolated from whole lung tissue; briefly, tissue was mechanically dissociated, and nuclei were retrieved, washed, DAPI stained, and sorted to remove debris. Sorted single nuclei were loaded directly into 10x Genomics 5' chip K for polyA tagging, using the manufacturer's recommendation.
10x Genomics 5' V2

treatment_protocol: N/A, tissue samples were obtained directly from human lung, and directly used for sequencing experiments, upon thawing and processing.

tag: patient diagnosis

value: NSCLC

value: resected lung tumor tissue


title: tumor resection tissue, patient 10

description: 10X genomics


title: tumor resection tissue, patient 9

description: 10X genomics


title: tumor resection tissue, patient 8

description: 10X genomics


title: tumor resection tissue, patient 7

description: 10X genomics


title: tumor resection tissue, patient 5

description: 10X genomics


title: Senescent CCND1 knockdown, replicate1

description: Library name: Sen_siD1_1

value: CCND1 knockdown

value: Irradiation, siRNA knockdown


title: PBMC, pre-tumor resection, patient 14, cell surface antibody barcode library

description:
also sequenced on Illumina NovaSeq X Plus
processed data included in matrix available on related GEX sample.

library_source: other

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs

growth_protocol: N/A, cells were obtained directly from human whole blood.

extract_protocol:
PBMCs were isolated from whole blood via density gradient separation, frozen viably, and stored in liquid nitrogen. For sequencing experiments, cells were thawed, counted, stained with CITE-seq antibodies, and loaded directly into 10x Genomics 5' chip K for polyA tagging, using the manufacturer's recommendation.
10x Genomics 5' V2

treatment_protocol: N/A, cells were obtained directly from human whole blood, and directly used for scRNA and CITE-seq experiments, upon thawing.

value: PBMCs

value: circulating peripheral mononuclear immune cells

tag: library type

value: ADT

tag: adt

value: TotalSeq™-C0083 anti-human CD16, TotalSeq™-C0084 anti-human CD56,  TotalSeq™-C0090 Mouse IgG1, κ isotype


title: tumor resection tissue, patient 2

description: 10X genomics


title: tumor resection tissue, patient 4

description: 10X genomics


title: PBMC, post-tumor resection, patient 12, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 12, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 9, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 14, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 8, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 10, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 7, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 8, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 7, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 6, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 5, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 4, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 2, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 5, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 2, cell surface antibody barcode library


title: PBMC, post-tumor resection, patient 14, VDJ recombination library

description: also sequenced on Illumina NovaSeq X Plus

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample
Library strategy: scVDJ-seq

value: mRNA


title: PBMC, pre-tumor resection, patient 4, cell surface antibody barcode library


title: PBMC, pre-tumor resection, patient 14, VDJ recombination library


title: PBMC, post-tumor resection, patient 12, VDJ recombination library


title: PBMC, pre-tumor resection, patient 12, VDJ recombination library


title: PBMC, pre-tumor resection, patient 10, VDJ recombination library


title: PBMC, post-tumor resection, patient 9, VDJ recombination library


title: PBMC, pre-tumor resection, patient 9, VDJ recombination library


title: PBMC, pre-tumor resection, patient 8, VDJ recombination library


title: PBMC, post-tumor resection, patient 7, VDJ recombination library


title: PBMC, pre-tumor resection, patient 7, VDJ recombination library


title: PBMC, post-tumor resection, patient 6, VDJ recombination library


title: PBMC, pre-tumor resection, patient 6, VDJ recombination library


title: PBMC, post-tumor resection, patient 5, VDJ recombination library


title: PBMC, pre-tumor resection, patient 4, VDJ recombination library


title: PBMC, post-tumor resection, patient 2, VDJ recombination library


title: PBMC, pre-tumor resection, patient 14, gene expression library

description:
also sequenced on Illumina NovaSeq X Plus
processed data matrix also includes data for ADT

data_processing:
fastq files from GEX, VDJ and CSP were processed together using cellranger multi. CSP was processed using uploaded feature_README.txt file for CSP barocodes. GEX and VDJ were processed using reference downloaded from 10X's website (v. 2020A)
Assembly: GRCh38, builds downloaded from 10X's website specfic to GEX and VDJ data (v. 2020A)
Supplementary files format and content: feature, barcode and counts matrices from cellranger multi, run on combined dataset from GEX, CSP and VDJ data for each sample


title: PBMC, pre-tumor resection, patient 12, gene expression library


title: PBMC, pre-tumor resection, patient 10, gene expression library


title: PBMC, pre-tumor resection, patient 9, gene expression library


title: PBMC, post-tumor resection, patient 8, gene expression library


title: PBMC, pre-tumor resection, patient 7, gene expression library


title: PBMC, pre-tumor resection, patient 6, gene expression library


title: PBMC, post-tumor resection, patient 6, gene expression library


title: PBMC, pre-tumor resection, patient 5, gene expression library


title: PBMC, pre-tumor resection, patient 4, gene expression library


title: PBMC, post-tumor resection, patient 2, gene expression library


title: PBMC, pre-tumor resection, patient 2, gene expression library


title: extracellular vesicle RNA, NK cell derived, pool of donors without any diagnosed cancer at the time of collection

data_processing:
fastq files  were aligned to the human genome using STAR with a custom transcriptome that includes additional lncRNAs from lncpedia
count tables were generated from the STAR alignments using featureCounts
counts from featureCounts were collapsed into a single raw counts table
Assembly: GRCh38
Supplementary files format and content: Raw counts table with sample IDs as columns and ENSEMBL IDs as rows

growth_protocol: After thawing and isolation, NK cells were maintained in growth medium (X-Vivo, Lonza, 5% human AB serum, heat inactivated, Il-2, Il-15) for 12 days, with occasional counting and medium addition; at day 12, cells were retrieved, centrifuged to remove the medium, and resuspended in EV medium (X-Vivo, Lonza, 5% human AB serum EV depleted, heat inactivated, Il-2, Il-15, Il-21) and medium was retrieved every 2 days, and frozen. Medium was then thawed, and size exclusion chromatography was used to isolate the extracellular vesicles (EVs).

extract_protocol:
The isolated Evs were treated for total RNA extraction using a commercial kit, according to the manufacturer's instructions. Plasma/serum circulating and exosomal RNA purification mini kit (Norgen Biotek) was used, followed by DNA digestion with TURBO DNA-free (ThermoFisher) and treatment with RNeasy MinElute Cleanup (Qiagen). RNA was quantified with Ribogreen Quant-iT (ThermoFisher) before library preparation.
Libraries were constructed using a workflow optimized for low input, low quality RNA sources, as is appropriate for Evs. Using the Smart-er Stranded Total RNAseq kit v3 for pico inputs (Takara Bio), RNA was converted into cDNA, PCR-amplified with unique barcodes, and treated with ribosomal RNA probes for ribosomal RNA depletion. The libraries were size selected via magnetic bead separation, PCR amplified again, size-selected again, and eluted in water. The resulting libraries were stranded, with unique molecular indices.

treatment_protocol: N/A, Evs were retrieved and used for RNAseq experiments after thawing without additional treatment.

value: extracellular vesicled derived from cultured NK cells

value: extracellular vesicled derived from cultured human primary NK cells

value: cells were kept in extracellular vesicle free medium prior to retrieval of extracellular vesicles


title: extracellular vesicle RNA, NK cell derived, patient 14, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 14, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 12, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 12, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 10, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 9, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 9, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 8, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 10, pre tumor resection sample


title: PBMC, pre-tumor resection, patient 9, cell surface antibody barcode library


title: extracellular vesicle RNA, NK cell derived, patient 8, post tumor resection sample


title: PBMC, post-tumor resection, patient 6, cell surface antibody barcode library


title: extracellular vesicle RNA, NK cell derived, patient 7, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 7, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 6, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 6, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 5, pre tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 5, post tumor resection sample


title: PBMC, post-tumor resection, patient 8, VDJ recombination library


title: extracellular vesicle RNA, NK cell derived, patient 4, pre tumor resection sample


title: PBMC, post-tumor resection, patient 4, VDJ recombination library


title: extracellular vesicle RNA, NK cell derived, patient 4, post tumor resection sample


title: extracellular vesicle RNA, NK cell derived, patient 2, pre tumor resection sample


title: PBMC, post-tumor resection, patient 12, gene expression library


title: extracellular vesicle RNA, NK cell derived, patient 2, post tumor resection sample


title: Blood of tumor-bearing (KP) mice (scATAC-seq)

status: Public on Jul 07 2025

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description: 10x Genomics

library_source: genomic single cell

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10; Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).

molecule: genomic DNA

source_name: Blood

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scRNA-seq, cells were encapsulated following 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 protocol. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Human: CD45positive cells after sorting or bead-based enrichment were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC Kit v1.1 or Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. For human NSCLC sample multiome assays, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.
Human: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol:
Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.
Human: CD45 positive cells were bead-enriched from processed tissues (Lung Tumor/Lung adjacent normal/PBMC) of patients with NSCLC. In one patient, viable CD45 positive cells were sorted from respective tissues (Lung Tumor/Lung adjacent normal/PBMC), based on surface markers described in Methods section.

value: Blood

value: immune

value: Tumor-bearing

tag: time

value: late


title: Lung of tumor-bearing (KP) mice replicate 1 (scATAC-seq)

description: 10x Genomics

source_name: Lung tumor

value: Lung tumor


title: PBMC, post-tumor resection, patient 14, gene expression library


title: Lung of naive mice (scATAC-seq)

description: 10x Genomics

source_name: Lung naive

value: Lung naive

value: Naive


title: PBMC, pre-tumor resection, patient 2, VDJ recombination library


title: Bone marrow of tumor-bearing (KP) mice replicate 1 (scATAC-seq)

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow


title: Adjacent normal lung cells from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu954_filtered_feature_bc_matrix.h5

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10; Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).
Library strategy: multiome (RNA + ATAC)

source_name: Lung adjacent normal

value: Lung adjacent normal


title: PBMC, post-tumor resection, patient 9, gene expression library

value: PBMCs


title: Bone marrow of tumor-bearing (KP) mice replicate 2 (scATAC-seq)

description: 10x Genomics


title: Adjacent normal lung cells from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu941_filtered_feature_bc_matrix.h5


title: PBMC, post-tumor resection, patient 7, gene expression library

value: circulating peripheral mononuclear immune cells


title: Bone marrow of naive mice replicate 1 (scATAC-seq)

description: 10x Genomics


title: Adjacent normal lung cells from NSCLC Patient Lu952 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu952_filtered_feature_bc_matrix.h5


title: Tumor cells from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu979_filtered_feature_bc_matrix.h5


title: PBMC, pre-tumor resection, patient 8, gene expression library


title: PBMC, post-tumor resection, patient 5, gene expression library


title: Adjacent normal lung cells from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu979_filtered_feature_bc_matrix.h5


title: Tumor cells from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu954_filtered_feature_bc_matrix.h5


title: Adjacent normal lung cells from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_AdjacentNormal_Lu927_filtered_feature_bc_matrix.h5


title: Tumor cells from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu941_filtered_feature_bc_matrix.h5


title: Tumor cells from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu927_filtered_feature_bc_matrix.h5


title: PBMCs from NSCLC Patient Lu979 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu979_filtered_feature_bc_matrix.h5


title: PBMCs from NSCLC Patient Lu941 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu941_filtered_feature_bc_matrix.h5


title: Adjacent normal lung cells from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])

library_source: genomic


title: Adjacent normal lung cells from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])


title: PBMCs from NSCLC Patient Lu927 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu927_filtered_feature_bc_matrix.h5


title: PBMCs from NSCLC Patient Lu954 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu954_filtered_feature_bc_matrix.h5


title: Adjacent normal lung cells from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])


title: PBMC, post-tumor resection, patient 4, gene expression library


title: Tumor cells from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])


title: Tumor cells from NSCLC Patient Lu952 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_Tumor_Lu952_filtered_feature_bc_matrix.h5


title: Adjacent normal lung cells from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])


title: Adjacent normal lung cells from NSCLC Patient Lu952 ATAC (Multiome [RNA + ATAC])


title: Tumor cells from NSCLC Patient Lu952 ATAC (Multiome [RNA + ATAC])


title: D0_Mll2-KO_H3K27me3_repB

status: Public on Oct 01 2025

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 46

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimgalore(v0.6.7).
Reads were mapped to the mm10 reference genome with STAR v2.6.1d (--outSAMtype BAM Unsorted --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --readFilesCommand zcat).
Duplicate reads were marked with picard tool (3.1.1)
Bigwig files were generated with deepTools v3.5.1 using bamCoverage (--normalizeUsing 'RPGC').
Assembly: mm10

source_name: Mll2-KO mESC

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Approximately 10 million and 40 million cells were used for histone PTMs and COMPASS subunits ChIPs, respectively.  For histone modification ChIP assays, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature (RT) before being quenched with 0.125 M glycine for another 10 minutes, while for COMPASS subunits ChIP assays cells were double crosslinked with ChIP cross-link Gold (Diagenode, C01019027) and 1% formaldehyde according to the manufactor’s instructions. Chromatin was isolated through sequential incubation with three distinct lysis buffers: LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin sonication was carried out in LB3 using an EpiShearTM sonicator (Active Motif; 4-5 minutes, 20 seconds ON and 30 seconds OFF at 25% amplitude). The sheared chromatin was then incubated O/N at 4 °C with either 5 or 10 μg of antibody for histone PTMs or COMPASS subunits respectively.
DNA libraries were prepared using the TruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

value: Mll2-KO mESC

value: mESC

value: H3K27me3 antibody (Active Motif, 39155)


title: Tumor cells from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])


title: PBMCs from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])


title: Tumor cells from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])


title: PBMCs from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: D0_double-KO_H3K4me1_repB

description: Library name: Sample 51

source_name: Double-KO mESC

value: Double-KO mESC

value: Double-KO

value: H3K4me1 antibody (Active Motif, 39297)


title: PBMCs from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])

value: Blood


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: D0_Mll2-KO_H3K4me1_repB

description: Library name: Sample 38


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu895 (scATAC-seq)

description: 10x Genomics


title: sRNA_24 knockout, 2mM H2O2, biol rep 3

description: Library name: 24C_RNA

value: sRNA_24 knockout

value: 2mM H2O2


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu895 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu936 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu934 (scATAC-seq)

description: 10x Genomics


title: Tumor cells from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu929 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu931 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu898 (scATAC-seq)

description: 10x Genomics


title: PBMCs from NSCLC Patient Lu895 (scATAC-seq)

description: 10x Genomics


title: D0_Mll1-KO_H3K4me3_repB

description: Library name: Sample 29

source_name: Mll1-KO mESC

value: Mll1-KO mESC

value: H3K3me3 antibdy (Active Motif, 39159)


title: Aged_5w_Sham_OB_5

status: Public on Jun 27 2025

first: Hangnoh

last: Lee

state: MD

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Library name: Aged_5w_Sham_OB_5

data_processing:
The sequencing company used CASAVA version 1.8.2 (Illumina, San Diego, CA) was for the base calling
We used STAR 2.7.5c (Dobin et al., 2013, PMID: 23104886) with the default parameters for alignment of the short reads to the reference genome.
We used the GENCODE mouse gene annotation, version M33, for alignment and quantification.
We used RSEM version 1.3.3 (PMID: 21816040) for the gene and RNA-isoform level quantifications.
Assembly: Mouse reference genome GRCm39 (Ensembl release 100)
Supplementary files format and content: These are tab-limited, gzipped text files that contain Ensembl gene IDs and gene expression levels in FPKM (fragments per kilobase of transcript per million mapped reads) and TPM (transcripts per million).

source_name: Olfactory Bulb

extract_protocol:
Following euthanasia 24 hours and 5 weeks after GA/OP, mice were perfused with 50 mL of ice-cold saline. Total RNA was isolated from the OB and hippocampus (HI) of both sham and GA/OP mice using a miRNeasy isolation kit (Cat# 217084, Qiagen). In brief, approximately 600ul of Buffer RLT were added to each sample and disrupted in a Precellys 24 Touch homogenizer. The aqueous phase containing RNA was collected, mixed with ethanol, and applied to a silica membrane spin column. After a series of washes to remove contaminants, RNA was eluted in RNase-free water. A minimum of 100ng was sent to the University of Maryland Institute for Genome Sciences and Novogene for downstream sequencing assays.
Library preparations were performed by the University of Maryland Institute for Genome Sciences (Baltimore, MD) and Novogene (Sacramento, CA) for sequencing on the Illumina platform (paired-end, 150 bp). mRNA was enriched using poly-A pulldown

value: Olfactory Bulb

tag: developmental stage

value: Adult

tag: age

value: 18 to 25 months

tag: Sex

value: male

value: Sham

tag: time point

value: 5 weeks after General Anesthesia and Operation

tag: biological replicate


title: PBMCs from NSCLC Patient Lu881 (scATAC-seq)

description: 10x Genomics


title: Aged_5w_Sham_OB_4

description: Library name: Aged_5w_Sham_OB_4


title: Aged_5w_Sham_OB_3

description: Library name: Aged_5w_Sham_OB_3


title: Aged_5w_Sham_OB_2

description: Library name: Aged_5w_Sham_OB_2


title: Aged_5w_Sham_OB_1

description: Library name: Aged_5w_Sham_OB_1


title: Aged_5w_Sham_Hi_5

description: Library name: Aged_5w_Sham_Hi_5

source_name: Hippocampus

value: Hippocampus


title: Aged_5w_Sham_Hi_2

description: Library name: Aged_5w_Sham_Hi_2


title: Aged_5w_Sham_Hi_4

description: Library name: Aged_5w_Sham_Hi_4


title: Aged_5w_Sham_Hi_1

description: Library name: Aged_5w_Sham_Hi_1


title: Aged_5w_IsoOP_OB_5

description: Library name: Aged_5w_IsoOP_OB_5

value: 2% isoflurane (2hr) and midline laparotomy


title: Aged_5w_Sham_Hi_3

description: Library name: Aged_5w_Sham_Hi_3


title: Aged_5w_IsoOP_OB_3

description: Library name: Aged_5w_IsoOP_OB_3


title: Aged_5w_IsoOP_OB_4

description: Library name: Aged_5w_IsoOP_OB_4


title: Aged_5w_IsoOP_OB_1

description: Library name: Aged_5w_IsoOP_OB_1


title: Aged_5w_IsoOP_OB_2

description: Library name: Aged_5w_IsoOP_OB_2


title: Aged_5w_IsoOP_Hi_5

description: Library name: Aged_5w_IsoOP_Hi_5


title: Aged_5w_IsoOP_Hi_4

description: Library name: Aged_5w_IsoOP_Hi_4


title: Aged_5w_IsoOP_Hi_3

description: Library name: Aged_5w_IsoOP_Hi_3


title: Aged_5w_IsoOP_Hi_2

description: Library name: Aged_5w_IsoOP_Hi_2


title: Aged_2h_Iso_Op_OB_5

description: Library name: Aged_2h_Iso_Op_OB_5

value: 24 hours after General Anesthesia and Operation


title: Aged_2h_Iso_Op_OB_6

description: Library name: Aged_2h_Iso_Op_OB_6


title: Aged_2h_Iso_Op_OB_7

description: Library name: Aged_2h_Iso_Op_OB_7


title: Aged_2h_Iso_Op_OB_1

description: Library name: Aged_2h_Iso_Op_OB_1


title: Aged_Sham_OB_6

description: Library name: Aged_Sham_OB_6


title: Aged_2h_Iso_Op_OB_3

description: Library name: Aged_2h_Iso_Op_OB_3


title: Aged_5w_IsoOP_Hi_1

description: Library name: Aged_5w_IsoOP_Hi_1


title: Aged_2h_Iso_Op_OB_2

description: Library name: Aged_2h_Iso_Op_OB_2


title: Aged_Sham_OB_5

description: Library name: Aged_Sham_OB_5


title: Aged_Sham_OB_3

description: Library name: Aged_Sham_OB_3


title: Aged_2h_Iso_Op_OB_4

description: Library name: Aged_2h_Iso_Op_OB_4


title: Aged_Sham_OB_2

description: Library name: Aged_Sham_OB_2


title: Aged_Sham_OB_4

description: Library name: Aged_Sham_OB_4


title: Aged_Sham_OB_1

description: Library name: Aged_Sham_OB_1


title: Aged_2h_Iso_Op_Hi_5

description: Library name: Aged_2h_Iso_Op_Hi_5


title: Aged_2h_Iso_Op_Hi_6

description: Library name: Aged_2h_Iso_Op_Hi_6


title: Aged_2h_Iso_Op_Hi_7

description: Library name: Aged_2h_Iso_Op_Hi_7


title: D0_Mll1-KO_H3K4me1_repA

description: Library name: Sample 24

value: mESC


title: Aged_2h_Iso_Op_Hi_3

description: Library name: Aged_2h_Iso_Op_Hi_3


title: Aged_Sham_Hi_6

description: Library name: Aged_Sham_Hi_6


title: Aged_2h_Iso_Op_Hi_4

description: Library name: Aged_2h_Iso_Op_Hi_4


title: Aged_Sham_Hi_3

description: Library name: Aged_Sham_Hi_3


title: Aged_2h_Iso_Op_Hi_2

description: Library name: Aged_2h_Iso_Op_Hi_2


title: Young_2h_Iso_Op_OB_12

description: Library name: Young_2h_Iso_Op_OB_12

value: 10 to 12 weeks


title: Aged_Sham_Hi_5

description: Library name: Aged_Sham_Hi_5


title: Aged_2h_Iso_Op_Hi_1

description: Library name: Aged_2h_Iso_Op_Hi_1


title: Young_2h_Iso_Op_OB_3

description: Library name: Young_2h_Iso_Op_OB_3


title: Aged_Sham_Hi_4

description: Library name: Aged_Sham_Hi_4


title: Adjacent normal Patient Lung cells from NSCLC Patient Lu912 (scATAC-seq)

description: 10x Genomics

value: Lung adjacent normal


title: Aged_Sham_Hi_2

description: Library name: Aged_Sham_Hi_2


title: Aged_Sham_Hi_1

description: Library name: Aged_Sham_Hi_1


title: Young_2h_Iso_Op_OB_5

description: Library name: Young_2h_Iso_Op_OB_5


title: Young_2h_Iso_Op_OB_2

description: Library name: Young_2h_Iso_Op_OB_2


title: Young_2h_Iso_Op_OB_1

description: Library name: Young_2h_Iso_Op_OB_1


title: Young_Sham_OB_11

description: Library name: Young_Sham_OB_11


title: Young_Sham_OB_13

description: Library name: Young_Sham_OB_13


title: Young_Sham_OB_4

description: Library name: Young_Sham_OB_4


title: Young_Sham_OB_8

description: Library name: Young_Sham_OB_8


title: Young_2h_Iso_Op_Hi_5

description: Library name: Young_2h_Iso_Op_Hi_5


title: Young_Sham_OB_10

description: Library name: Young_Sham_OB_10


title: Young_2h_Iso_Op_Hi_3

description: Library name: Young_2h_Iso_Op_Hi_3


title: Young_2h_Iso_Op_Hi_2

description: Library name: Young_2h_Iso_Op_Hi_2


title: Young_2h_Iso_Op_Hi_1

description: Library name: Young_2h_Iso_Op_Hi_1


title: Young_2h_Iso_Op_Hi_12

description: Library name: Young_2h_Iso_Op_Hi_12


title: Young_Sham_Hi_10

description: Library name: Young_Sham_Hi_10


title: Young_Sham_Hi_13

description: Library name: Young_Sham_Hi_13


title: Young_Sham_Hi_8

description: Library name: Young_Sham_Hi_8


title: Young_Sham_Hi_11

description: Library name: Young_Sham_Hi_11


title: 4wk NT Rep 1 FLEX single nuclei-RNA-seq

status: Public on Jun 24 2025

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description:
Library name: 3-5_4wk_NT
10x Genomics FLEX BC001,3-5,4-week-NT

data_processing:
Raw reads and cell barcode demultiplexed to generate count matrix using CellRanger software (v7.1.0) using a value of 9000 for the force_cells parameter.
The obtained count matrices for each sample were merged and filtered for based on number of features expressed and number of mitochondrial genes.
Downstream analyses with Seurat (v3.1.5) include normalization, dimension reduction by principal component analysis (‘RunPCA’) using the top 3000 variable features, uniform manifold approximation and projection (‘RunUMAP’), Shared Nearest Neighbor (SNN) Graph construction (‘FindNeighbors’), and finally Louvain clustering (‘FindClusters’) using the first 20 principal components and a resolution of 0.20 to determine cluster assignment.
To identify cell type markers and differentially expressed genes between different conditions, Wilcoxon rank sum test was used (‘FindMarkers’)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain, male, 4-week

extract_protocol:
Fresh frozen tissue were OCT embedded, snap frozen over isopentane bath immersed in liquid nitrogen and ~700uM of 30uM sections of tissue were collected. Sections were fixed for 21 hours with 4% PFA and dissociated using Liberase TL (postnatal day 0) or Liberse TH (4-week and 12-week) and processed with the 10x Genomics Chromium Fixed RNA Profiling kit according to manufacter's instructions. Tissue was then dissoaciated with a gentleMACS OctoDissociator and cell quality and number evaluated.
Probe hybiridization and library construction were performed with the 10x Genomics Single Cell Gene Expression FLEX according to the manufacter's instructions. 4 samples were multiplexed and 2 samples singleplex. After probe hybridization, nuclei were pooled (if multiplexed), partitioned into GEMs and ligation and extension was in GEMs  Samples were sequenced with the Illumina NovaSeq system with a target sequenciong depth of at least 30,000/nuclei.

value: Brain, male, 4-week

value: Non-transgenic (NT)

tag: batch


title: 4wk R62 Rep 1 FLEX single nuclei-RNA-seq

description:
Library name: 1-6_4wk_R62
10x Genomics FLEX BC001,1-6,4-week-HD

value: Transgenic (R62)


title: melb-a cells, lenti- shHIRA II biol rep4

status: Public on Jun 11 2025

data_processing:
FASTQs were generated using bcl2fastq.
Read pseudo-alignment was completed with Kallisto read-mapping software v0.46.2.
Transcript-level counts and abundance data were imported into R using the TxImport package
TPM normalized using the package edgeR.
Assembly: mm10
Supplementary files format and content: File includes raw counts for each sample
Supplementary files format and content: File includes TPM values for each sample

source_name: melb-a cells

growth_protocol: melb-a cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 10ng/ml SCF, 40 pM Fgf2, 25U/ml penicillin, and 25 μg/ml streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using TRIzol and Direct-zol RNA MiniPrep Plus kit (Zymo R2072).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).

treatment_protocol: melb-a cells were splitted to a confluency of ~50%. Lentivirus was diluted in 1 ml growth medium per 3.5 cm well and incubated with 8 μg/ml polybrene for 16 hours. The infected cells were selected using 1 μg/ml puromycin.

value: melb-a cells

value: melanoblasts

value: wt

value: lenti- shHIRA II


title: melb-a cells, lenti- shHIRA II biol rep3


title: melb-a cells, lenti- shHIRA II biol rep2


title: melb-a cells, lenti- shHIRA II biol rep1


title: melb-a cells, lenti- shHIRA I biol rep4

value: lenti- shHIRA I


title: PBMCs from NSCLC Patient Lu883 (scATAC-seq)

description: 10x Genomics

value: Blood


title: Young_Sham_Hi_4

description: Library name: Young_Sham_Hi_4

value: Adult

value: male

value: Sham


title: melb-a cells, lenti- shHIRA I biol rep2


title: melb-a cells, lenti- shHIRA I biol rep3


title: melb-a cells, lenti- shScramble biol rep2

value: lenti- shScramble


title: melb-a cells, lenti- shScramble biol rep3


title: melb-a cells, lenti- shScramble biol rep1


title: melb-a cells, lenti- shHIRA I biol rep1


title: melb-a cells, parental biol rep3

value: parental


title: melb-a cells, lenti- shScramble biol rep4


title: melb-a cells, lenti- shLuciferase biol rep4

value: lenti- shLuciferase


title: melb-a cells, lenti- shLuciferase biol rep2


title: melb-a cells, lenti- shLuciferase biol rep3


title: melb-a cells, lenti- shLuciferase biol rep1


title: melb-a cells, parental biol rep4


title: melb-a cells, parental biol rep2


title: FJ02_HIRA knockout

data_processing:
A novel mm10 reference genome including sequences for tdTom and Cre was created as per the 10X genomics guidelines.
Count matrices were produced for each sample using Cellranger software version 2.2.0 with the following parameters: --transcriptome=./refdata-cellranger-mm10-1.2.0.Cre-tdTom --localcores=58 --localmem=112GB
Genome_build: mm10
Supplementary_files_format_and_content: barcode, genes and matrix files per sample

source_name: HIRA knockout_E15.5 Skin

extract_protocol:
Tissue harvesting: Embryos were harvested at E15.5 then washed in ice cold HBSS. Trunk skin was then removed, rinsed in HBSS and digested in 300ul of 0.2 U/ml dispase and 0.5mg/ml DnaseI in HBSS for 45 minutes at 37 degrees celcius. Digestion was halted by the addition of 5mM EDTA/PBS.
dissociation protocol: Skin suspensions were dissociated by passing through 18G then 21G needles, then filtered through 50 um filter membranes. Cell suspensions were centrifuged at 300g for 5 minutes at 4 degrees celcius, before being resuspended in sorting buffer (1% FBS, 5mM EDTA and 25mM HEPES in PBS).
cell sorting protocol: tdTomato negative skins were used as a negative control for gating and 1 ug/ml DAPI was used as a dead cell marker prior to sorting. TdTomato positive live cells were sorted using a BD FACSAria cell sorter.
Approximately 7000-10000 cells per sample were used for single cell RNA isolation, cDNA synthesis and library preparation using a 10X Genomics Chromium Single Cell 3’ Reagent kit as per the manufacturer’s protocol. Libraries were sequenced using an Illumina HiSeq4000 sequencer.

tag: strain background

value: mixed; close (~99.9%) to C57BL/6J

tag: genotype/variation

value: HIRA knockout

value: skin


title: FJ01_Wild type

source_name: WT_E15.5 Skin

value: Wild type

tag: tissue


title: FJ03_HIRA knockout


title: S1_FJ_Wild type


title: FJ04_Wild type


title: melb-a cells, parental biol rep1

tag: cell line


title: S2_FJ_HIRA knockout


title: melb-a cells, lenti- shScramble

data_processing:
Reads were trimmed using Cutadapt v2.3 and then aligned against chrM mm10 using Bowtie2.
Duplicate reads were removed using Picard MarkDuplicates v2.22.0.
MACS2 v2.2.9.1 was used to call peaks.
Reproducible peaks for replicates (n=2) were determined using IDR v2.0.4.2.
Differential accessibility of peaks were tested using edgeR v3.38.4
Assembly: mm10
Supplementary files format and content: Differential peaks with tag count, p-value and fold change.

extract_protocol:
DNA was extracted from cells using the ATAC-seq kit (Active Motif, 53150)
ATAC libraries were prepared using the ATAC-seq kit (Active Motif, 53150) following the manufacturer's protocol.

tag: genotype


title: melb-a cells, lenti- shHIRA II

tag: treatment


title: melb-a cells, lenti- shLuciferase

tag: cell type


title: melb-a cells, lenti- shHIRA I


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 10 with MuInactive Leaf 3, Plant ND59-3

status: Public on May 09 2025

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

description:
Library name: L83_10xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 10 with MuSeq2 Leaf sample from MuInactive plant ND59-3

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.

organism: Zea mays

source_name: Leaf

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

value: Leaf

value: W22 Mu-Active, W22 Mu-Inactive


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 30 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_30xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 30 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: CUT&Run (IgG) of sorted pachytene/diplotene cells from adult testis

status: Public on May 10 2025

city: Stockholm

first: Masomeh

last: Askari

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

description: Library name: CUT_RUN_IgG_PD

data_processing:
Adapter sequences were trimmed and low-quality reads were removed from the raw paired-end CUT&RUN reads using Fastp (v0.24.0; {Chen et al., 2018, #251424}). Reads were then aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.4; {Langmead and Salzberg, 2012, #21255}) with parameters —local —very-sensitive —no-unal —no-mixed —no-discordant -|10 -X700. Subsequently, SAM files were converted to BAM format using SAMtools (v1.20; {Danecek et al., 2021, #260227}), and alignments whose quality is less than 20 were removed. BAM files were then sorted and indexed, and multiple aligning read pairs were removed. Thereafter, duplicate reads were removed using MarkDuplicates function from picard-tools (v.3.3.0; {Toolkit, 2019, #210533}). Bigwig files were generated using bamCoverage function from deepTools (v3.3.2; {Ramírez et al., 2016, #143661}) and normalized to reads per million (RPM).
Assembly: mm10
Supplementary files format and content: Bigwig normalized by RPM
Library strategy: CUT&Run

source_name: Testis

extract_protocol:
FACS purified spermatogonia (SpG), leptotene & zygotene (L/Z), and pachytene & diplotene (P/D) cells.
CUT&RUN libraries were prepared using the Active Motif kit according to the manufacturer's protocol.

value: Testis

tag: strain

value: WT


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 10 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_10xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 10 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 30 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L83_30xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 30 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: Leaf 83, MuActive Plant ND58-83 diluted 1 part in 3 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L83_3xDilution
MuSeq2 Leaf sample from MuActive plant ND58-83 diluted 1 in 3 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: Root 75, MuActive Plant ND58-75

description:
MuSeq2 Root sample from MuActive plant ND58-75
Library name: R75

source_name: Root

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.

value: Root

value: W22 MuActive


title: Leaf 79, MuActive Plant ND58-79 diluted 1 part in 3 with MuInactive Leaf 3, Plant ND59-3

description:
Library name: L79_3xDilution
MuSeq2 Leaf sample from MuActive plant ND58-79 diluted 1 in 3 with MuSeq2 Leaf sample from MuInactive plant ND59-3


title: Root 74, MuActive Plant ND58-74

description:
MuSeq2 Root sample from MuActive plant ND58-74
Library name: R74


title: Root 69, MuActive Plant ND58-69

description:
MuSeq2 Root sample from MuActive plant ND58-69
Library name: R69


title: Root 63, MuActive Plant ND58-63

description:
MuSeq2 Root sample from MuActive plant ND58-63
Library name: R63


title: Root 65, MuActive Plant ND58-65

description:
MuSeq2 Root sample from MuActive plant ND58-65
Library name: R65


title: Root 61, MuActive Plant ND58-61

description:
MuSeq2 Root sample from MuActive plant ND58-61
Library name: R61


title: Pollen 99, MuActive Plant ND58-85

description:
MuSeq2 Pollen sample from MuActive plant ND58-99
Library name: P99

source_name: Pollen

value: Pollen


title: Pollen 85, MuActive Plant ND58-85

description:
MuSeq2 Pollen sample from MuActive plant ND58-85
Library name: P85


title: Pollen 83, MuActive Plant ND58-83

description:
MuSeq2 Pollen sample from MuActive plant ND58-83
Library name: P83


title: Pollen 79 Technical Replciate, MuActive Plant ND58-79

description:
MuSeq2 Pollen sample Technical Replicate split after DNA shearing from MuActive plant ND58-79
Library name: P79T


title: Pollen 78, MuActive Plant ND58-78

description:
MuSeq2 Pollen sample from MuActive plant ND58-78
Library name: P78


title: Pollen 79, MuActive Plant ND58-79

description:
MuSeq2 Pollen sample from MuActive plant ND58-79
Library name: P79


title: Pollen 76, MuActive Plant ND58-76

description:
MuSeq2 Pollen sample from MuActive plant ND58-76
Library name: P76


title: Pollen 75, MuActive Plant ND58-75

description:
MuSeq2 Pollen sample from MuActive plant ND58-75
Library name: P75


title: Pollen 42, MuActive Plant ND67-42

description:
MuSeq2 Pollen sample from MuActive plant ND67-42
Library name: P42


title: Pollen 69, MuActive Plant ND58-69

description:
MuSeq2 Pollen sample from MuActive plant ND67-69
Library name: P69


title: Pollen 107, MuActive Plant ND58-107

description:
MuSeq2 Pollen sample from MuActive plant ND58-107
Library name: P107


title: Pollen 52, MuActive Plant ND67-52

description:
MuSeq2 Pollen sample from MuActive plant ND67-52
Library name: P52


title: Pollen 74, MuActive Plant ND58-74

description:
MuSeq2 Pollen sample from MuActive plant ND58-74
Library name: P74


title: Pollen 106, MuActive Plant ND58-106

description:
MuSeq2 Pollen sample from MuActive plant ND58-106
Library name: P106


title: Pollen 105, MuActive Plant ND58-105

description:
MuSeq2 Pollen sample from MuActive plant ND58-105
Library name: P105


title: MuInactive Leaf 3 Technical Replicate, Plant ND59-3

description:
MuSeq2 Leaf sample Technical Replicate split after DNA shearing from MuInactive plant ND59-3
Library name: MI3T

source_name: MuInactive Leaf

value: MuInactive Leaf

value: W22 Mu-Inactive


title: MuInactive Leaf 3, Plant ND59-3

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-3
Library name: MI3


title: Leaf 83, MuActive plant ND58-83

description:
MuSeq2 Leaf sample from MuActive plant ND58-83
Library name: L83

source_name: Primary Leaf

value: Primary Leaf


title: MuInactive Leaf 1, Plant ND59-1

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-1
Library name: MI1


title: MuInactive Leaf 2, Plant ND59-2

description:
MuSeq2 Leaf sample from MuInactive plan5 ND59-2
Library name: MI2


title: Leaf 78, MuActive Plant ND58-78

description:
MuSeq2 Leaf sample from MuActive plant ND58-78
Library name: L78


title: Leaf 79, MuActive Plant ND58-79

description:
MuSeq2 Leaf sample from MuActive plant ND58-79
Library name: L79


title: Leaf 76, MuActive Plant ND58-76

description:
MuSeq2 Leaf sample from MuActive plant ND58-76
Library name: L76


title: Leaf 75 Technical Replicate, MuActive Plant ND58-76

description:
MuSeq2 Leaf sample Technical Replicate, split after DNA shearing from MuActive plant ND58-75
Library name: L75T


title: Leaf 74 Technical Replicate, MuActive Plant ND58-74

description:
MuSeq2 Leaf sample Technical Replicate, split after DNA shearing from MuActive plant ND58-74
Library name: L74T


title: Leaf 75, MuActive Plant ND58-75

description:
MuSeq2 Leaf sample from MuActive plant ND58-75
Library name: L75


title: Endosperm 99, MuActive plant ND58-99

description:
MuSeq2 Endosperm chip from MuActive plant ND58-99
Library name: E99

source_name: Endosperm

value: Endosperm


title: Endosperm 85, MuActive plant ND58-85

description:
MuSeq2 Endosperm chip from MuActive plant ND58-85
Library name: E85


title: Endosperm 79, MuActive plant ND58-79

description:
MuSeq2 Endosperm chip from MuActive plant ND58-79
Library name: E79


title: Leaf 74, MuActive plant ND58-74

description:
MuSeq2 Leaf sample from MuActive plant ND58-74
Library name: L74


title: Endosperm 83, MuActive plant ND58-83

description:
MuSeq2 Endosperm chip from MuActive plant ND58-83
Library name: E83


title: Endosperm 75, MuActive plant ND58-75

description:
MuSeq2 Endosperm chip from MuActive plant ND58-75
Library name: E75


title: Endosperm 74, MuActive plant ND58-74

description:
MuSeq2 Endosperm chip from MuActive plant ND58-74
Library name: E74

value: B73 MuKiller & W22 MuActive


title: Endosperm 78, MuActive plant ND58-78

description:
MuSeq2 Endosperm chip from MuActive plant ND58-78
Library name: E78


title: Endosperm 65, MuActive plant ND58-65

description:
MuSeq2 Endosperm chip from MuActive plant ND58-65
Library name: E65


title: Endosperm 69, MuActive plant ND58-69

description:
MuSeq2 Endosperm chip from MuActive plant ND58-69
Library name: E69


title: Endosperm 63 MuActive plant ND58-63

description:
MuSeq2 Endosperm chip from MuActive plant ND58-63
Library name: E63


title: Endosperm 52, MuActive plant ND67-52

description:
MuSeq2 Endosperm chip from MuActive plant ND67-52
Library name: E52


title: Endosperm 61, MuActive plant ND58-61

description:
MuSeq2 Endosperm chip from MuActive plant ND58-61
Library name: E61

value: W22 MuActive & B73 MuKiller


title: Endosperm 106, MuActive plant ND58-106

description:
MuSeq2 Endosperm chip from MuActive plant ND58-106
Library name: E106


title: Endosperm 107, MuActive plant ND58-107

description:
MuSeq2 Endosperm chip from MuActive plant ND58-107
Library name: E107


title: Endosperm 105, MuActive plant ND58-105

description:
MuSeq2 Endosperm chip from MuActive plant ND58-105
Library name: E105


title: PBMC, library GD009_1, 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_1_CITE
GD009_1
processed data in the Market Exchange (MEX) format for HTO is available on associated GEX sample.
HTO_normalized_counts.tsv
metadata.csv

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

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: PBMC, library GD007_1, CITE

description:
Library name: GD007_1_CITE
GD007_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 GD007_2, CITE

description:
Library name: GD007_2_CITE
GD007_2
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 GD006_2, CITE

description:
Library name: GD006_2_CITE
GD006_2
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 GD005_2, CITE

description:
Library name: GD005_2_CITE
GD005_2
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 GD005_1, CITE

description:
Library name: GD005_1_CITE
GD005_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_1, CITE

description:
Library name: GD004_1_CITE
GD004_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 GD009_2, GEX

description:
Library name: GD009_2_GEX
GD009_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD009_1, GEX

description:
Library name: GD009_1_GEX
GD009_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD001_2, CITE

description:
Library name: GD001_2_CITE
GD001_2
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 GD007_1, GEX

description:
Library name: GD007_1_GEX
GD007_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD002, CITE

description:
Library name: GD002_CITE
GD002
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 GD007_2, GEX

description:
Library name: GD007_2_GEX
GD007_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD005_2, GEX

description:
Library name: GD005_2_GEX
GD005_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD004_2, GEX

description:
Library name: GD004_2_GEX
GD004_2
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD005_1, GEX

description:
Library name: GD005_1_GEX
GD005_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD006_1, GEX

description:
Library name: GD006_1_GEX
GD006_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD004_1, GEX

description:
Library name: GD004_1_GEX
GD004_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD002, GEX

description:
Library name: GD002_GEX
GD002
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD001_1, GEX

description:
Library name: GD001_1_GEX
GD001_1
GEX_SCT_counts.tsv
metadata.csv


title: PBMC, library GD001_2, GEX

description:
Library name: GD001_2_GEX
GD001_2
GEX_SCT_counts.tsv
metadata.csv


title: genomic_DNAmethylation_PL295_v

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

value: F

tag: ga


title: genomic_DNAmethylation_PL149_vc


title: genomic_DNAmethylation_PL284_vc

value: M


title: genomic_DNAmethylation_PM161_vc_R1


title: genomic_DNAmethylation_FT54_vc


title: genomic_DNAmethylation_FT58_vc


title: genomic_DNAmethylation_FT101_vc


title: genomic_DNAmethylation_PL148_vc


title: genomic_DNAmethylation_FT42_vc


title: genomic_DNAmethylation_PL294_v


title: genomic_DNAmethylation_FT89_vc


title: genomic_DNAmethylation_FT98_vc


title: genomic_DNAmethylation_FT60_vc


title: genomic_DNAmethylation_FT47_vc


title: genomic_DNAmethylation_PL292_v


title: genomic_DNAmethylation_FT40_vc


title: genomic_DNAmethylation_FT100_vc


title: genomic_DNAmethylation_FT82_vc


title: genomic_DNAmethylation_PM332_vc


title: genomic_DNAmethylation_PM344_vc


title: genomic_DNAmethylation_PL296_v


title: IMR90 cells, IR, 53BP1 OE, rep 3

status: Public on Feb 11 2025

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: 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

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.

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: For 53BP1 exogenous expression, lentivirus was generated from 293T cells. Concentrated virus was titrated to the minimum amount required for >90% cell viability after puromycin selection. Cells were infected overnight with 8 ug/mL polybrene. IR senescence was induced by 20 Gray x-ray irradiation of 20-30% confluent cells. Cells were split after returning to confluence in 3 days.

value: fibroblast

value: 53BP1 OE

value: 10 days post 20 Gy IR


title: IMR90 cells, IR, 53BP1 OE, rep 2


title: IMR90 cells, IR, empty vector, rep 3

value: empty vector


title: IMR90 cells, IR, empty vector, rep 2


title: IMR90 cells, IR, empty vector, rep 1


title: IMR90 cells, IR, 53BP1 OE, rep 1


title: IMR90 cells, proliferating, 53BP1 OE, rep 3

value: Cultured 10 days


title: IMR90 cells, proliferating, 53BP1 OE, rep 2


title: IMR90 cells, proliferating, empty vector, rep 3


title: IMR90 cells, proliferating, empty vector, rep 2


title: IMR90 cells, proliferating, 53BP1 OE, rep 1


title: vehicle, 5 months, female, rep 5

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

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

value: 5 months

tag: gender

value: female

value: Vehicle


title: vehicle, 5 months, female, rep 4


title: 16-20 h embryo, w[1118], Replicate 3, NovaSeq 6000 (ChIP)

status: Public on Sep 25 2025

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description: Library name: 16-20 h embryo, w[1118], Replicate 3 (ChIP)

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.33 with default settings.  ChIP-seq reads were algined to dm6 genome using Burrows-Wheeler Aligner v0.7.16a with default settings. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequnced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format using HOMER 4.11.1.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <= 0.01 and were annotated with ChIPseeker and motifs identified with HOMER v4.11.1.
Assembly: dm6
Supplementary files format and content: bigWig, narrowPeak, bed

organism: Drosophila melanogaster

source_name: 16-20 h embryo

growth_protocol: Drosophila were reared at 25C on standard fly food.  Embryos were collected and aged at 25C on grape juice agar plates.

extract_protocol:
Embryos were collected for 4 hrs, aged for 16 hrs at 25C, and dechorionated in 50% bleach.  Eye-brain complexes were dissected from 3rd instar larvae in ice-cold PBS.  Tissues were crosslinked in 2 mM EGS for 45 min, followed by paraformaldehyde for 15 min, quenched, washed, flash frozen in liquid nitrogen and stored at -80C until use.  50 ml settled embryos or 100 eye-brain complexes were used per sample.  Crosslinked tissues were homogenized by douncing, followed by nuclear lysis and sonication of the genomic DNA using a Bioruptor or Qsonica Q700 sonicator.  Fragmented chromatin was incubated with anti-GFP or anti-FLAG antibodies and precipitated using MagnaChIP A+G beads or Dynabeads G.
ChIP-seq libraries were prepared from 10 ng DNA.  DNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends.  Size selection was performed with AMPure beads to limit the fragment size to 150-700 bp.  Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: 16-20 h embryo

tag: chip antibody

value: a-GFP (ab290)


title: 16-20 h embryo, w[1118], Replicate 2, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, w[1118], Replicate 2 (ChIP)


title: vehicle, 5 months, female, rep 2

tag: age


title: vehicle, 5 months, male, rep 5

value: male


title: vehicle, 5 months, female, rep 1


title: vehicle, 5 months, female, rep 3


title: vehicle, 5 months, male, rep 3


title: vehicle, 5 months, male, rep 2


title: vehicle, 5 months, male, rep 1


title: HDM201, 24 months, male, rep 5

value: 24 months


title: HDM201, 24 months, male, rep 4


title: HDM201, 24 months, male, rep 3


title: HDM201, 24 months, male, rep 1


title: vehicle, 24 months, male, rep 5


title: vehicle, 24 months, male, rep 2


title: vehicle, 24 months, male, rep 3


title: vehicle, 24 months, male, rep 4


title: vehicle, 24 months, male, rep 1


title: HDM201, 20 months, female, rep 5

value: 20 months


title: HDM201, 20 months, female, rep 2


title: HDM201, 20 months, female, rep 3


title: HDM201, 20 months, female, rep 1


title: IMR90 cells, proliferating, empty vector, rep 1


title: vehicle, 20 months, female, rep 4


title: vehicle, 20 months, female, rep 3


title: vehicle, 20 months, female, rep 2


title: vehicle, 20 months, female, rep 1


title: Ionizing radiation-induced senescence, rep 6

data_processing:
Raw reads were trimmed using Lianti analysis toolkit
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.
LIANTI

treatment_protocol: IR senescence was induced by 20 Gray x-ray irradiation of 20-30% confluent cells. Cells were split after returning to confluence in 3 days and collected 10 days after IR.

value: wild type

value: 20 Gy irradiation


title: Ionizing radiation-induced senescence, rep 5


title: Ionizing radiation-induced senescence, rep 4


title: Ionizing radiation-induced senescence, rep 3


title: Ionizing radiation-induced senescence, rep 2


title: Ionizing radiation-induced senescence, rep 1


title: Proliferating, rep 2


title: Endosperm 76, MuActive plant ND58-76

description:
MuSeq2 Endosperm chip from MuActive plant ND58-76
Library name: E76

value: Endosperm

value: W22 MuActive


title: Proliferating, rep 1

value: fibroblast