title: Zebrafish sperm ATAC-seq - ST_ACI_2

description:
Library name: ST_ACI_2
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.


title: ROI 3 CD68

status: Public on Aug 16 2026

type: protein

city: singapore

first: Lichang

last: Deng

address: singapore

country: Singapore

institute: NUS

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_02.RCC

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing:
Each RCC file represents one nCounter readout lane, and multiple samples are pooled within the same lane to generate the .RCC file. The GeoMx software then separates the readout and assigns the data back to each individual sample (ROI).
The counts file was generated from the nCounter RCC files, and the normalized values were calculated in R(4.4.1) by normalizing the raw digital counts to the total number of nuclei within each segment.

molecule: protein

organism: Homo sapiens

source_name: human ENKTL biopsies

growth_protocol: Not applicable.

extract_protocol: Antibody incubations and Ncounter readout were performed as per standardised Nanostring GeoMX DSP protocol

treatment_protocol: Not applicable.

tag: tissue type

value: human FFPE

tag: segment

value: CD68+ macrophage


title: POP-1: anterior vaginal wall, untreated control, scRNA-seq

type: SRA

city: Taiyuan

first: Xiaochun

last: Liu

state: Shanxi

address: No.99 Longcheng Street, Xiaodian district

department: department of gynecology and obstetrics

country: China

institute: Shanxi Bethune Hospital

description:
Library name: POP-1_sc
GEXSCOPE

library_source: transcriptomic single cell

data_processing:
For scRNA-seq: raw sequencing data were processed using the CeleScope pipeline (v1.9.0, Singleron). Low-quality reads and adapter sequences were trimmed using Cutadapt (v1.17). Clean reads were aligned to the GRCh38 reference genome (Ensembl version 92) using STAR (v2.6.1a). Gene expression counts were generated using featureCounts (v2.0.1). For spatial transcriptomics: data were processed using Space Ranger (10x Genomics) to generate count matrices.
Quality control and clustering were performed using the Seurat R package (v5.0). Cells with fewer than 200 genes or more than the top 2% of gene counts were filtered out. Mitochondrial gene content exceeding 10% was excluded. Batch effects across patient samples were corrected using Seurat v5.0 Reciprocal PCA (RPCA) integration.
For spatial transcriptomics analysis: data were analyzed in Seurat (v5.0) using the Load10X Spatial function. Spots with fewer than 10 UMI counts were filtered out. Integration of scRNA-seq and spatial transcriptomics data was performed using the Seurat integration pipeline. Anchor points were identified with FindTransferAnchors, and cell type labels from scRNA-seq were transferred to spatial spots using TransferData.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text files containing gene expression count matrices for scRNA-seq (filtered feature-barcode matrices) and spatial transcriptomics (spatial count matrices).

molecule: polyA RNA

source_name: anterior vaginal wall

growth_protocol: Not applicable (human tissue biopsy)

extract_protocol:
Fresh vaginal anterior wall tissues were collected during transvaginal reconstructive surgery. Tissues were washed three times with HBSS, minced into small pieces, and digested with 3 mL sCelLiveTM Tissue Dissociation Solution using the Singleron PythoNTM Tissue Dissociation System at 37°C for 15 minutes. The cell suspension was filtered through a 40-μm sterile strainer. Red blood cells were lysed using GEXSCOPE® Red Blood Cell Lysis Buffer (RCLB, Singleron) at a volume ratio of 1:2 (cell pellet:RCLB) for 5-8 minutes at room temperature. The mixture was centrifuged at 300 × g at 4°C for 5 minutes, and the pellet was resuspended in PBS. For spatial transcriptomics: FFPE vaginal tissue sections were cut at 5 μm thickness and mounted onto Visium HD slides (10x Genomics).
For scRNA-seq: single-cell suspensions were adjusted to 2 × 10^5 cells/mL in PBS. Cells were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding beads were collected, and reverse transcription was performed to synthesize cDNA. cDNA was amplified by PCR, fragmented, and ligated with sequencing adapters using the GEXSCOPE® Single Cell RNA Library Kit (Singleron). For spatial transcriptomics: libraries were prepared using the Visium HD Spatial Gene Expression protocol for FFPE (10x Genomics) following manufacturer's instructions.

treatment_protocol: Estrogen-treated group: topical promestriene applied once daily for 6 weeks prior to biopsy. Untreated control group: no estrogen treatment.

tag: tissue

value: anterior vaginal wall

tag: cell type

value: mixed vaginal cells

tag: treatment


title: Mouse F1 heart bulk RNA-seq - PU_FU_22

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

description:
Library name: PU_FU_22
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.

library_source: transcriptomic

data_processing:
Quality control of raw sequencing reads was assessed using FastQC v0.11.9 (Andrews, 2010) and aggregated with MultiQC v1.12 (P. Ewels et al., 2016).
Adapter trimming and quality filtering were performed using Fastp v0.23.2 (Chen et al., 2018).
Mouse samples were aligned to GRCm39.
Reads were aligned to the reference genome using STAR v2.7.10a (Dobin et al., 2013).
Gene-level read counts were generated using featureCounts from the Subread package v2.0.3 (Liao et al., 2014).
Differential expression analysis was conducted in R v4.4.0 using DESeq2 v1.44.0 (Love et al., 2014) with a design formula of ~condition.
Log2 fold change shrinkage was applied using apeglm. Differentially expressed genes required |log2FC| > 1; an additional |log2FC| > 0.58 threshold was applied for volcano plot and pathway analyses.
Genes with adjusted p-value < 0.05 (Benjamini-Hochberg correction) and |log2FC| above the species-specific threshold were considered differentially expressed.
Cross-species pathway analysis: Over-representation analysis (ORA) was performed using clusterProfiler v4.12.2 (Wu et al., 2021; Yu et al., 2012) and ReactomePA v1.48.0, with parallel execution via BiocParallel v1.38.0.
Data visualization was performed using ComplexHeatmap v2.20.0, pheatmap v1.0.12 (Kolde, 2019), ggplot2 v3.5.1 (Wickham, 2016), and ggrepel v0.9.5.
Transcript-level quantification was additionally performed using Salmon v1.9.0 (Patro et al., 2017) in star_salmon mode.
Gene Set Enrichment Analysis (GSEA) was additionally performed.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Gene-level read count matrix (featureCounts).

molecule: total RNA

organism: Mus musculus

source_name: heart (ventricle)

growth_protocol: C57BL/6J mice raised together to weaning (3 wpp) then housed at 4 animals/cage (bred males isolated after first breeding); SPF facility, 20-24C, 12h light/dark, 45-65% RH, food/water ad libitum. Approved under license PROEX 310_19 (Comunidad de Madrid, Spain), conforming to EU Directive 86/609/EEC.

extract_protocol:
Tissues washed in PBS and snap frozen. On the day of RNA extraction, samples were homogenized in TRI Reagent (Sigma-Aldrich) using 21G and 30G syringes (BD Microlance). Following phase separation with 1-bromo-3-chloropropane (Sigma-Aldrich), the aqueous phase was mixed with an equal volume of ethanol, and RNA was purified using the RNA Clean & Concentrator kit (Zymo Research) with on-column DNase I treatment. RNA quantity and quality were assessed using a NanoDrop and a Fragment Analyzer before library preparation and sequencing.
Library preparation and sequencing performed by the Genomics Unit at CNIC (Madrid, Spain).

treatment_protocol: Hearts collected at 3 wpp from adult offspring of uninjured or injured males (cardiac cryoinjury performed at P1). Samples included four control and three experimental males, and two control and three experimental females. Sample 'Injured P0_16' was identified as a PCA outlier and excluded from downstream (but not raw-data) analyses.

value: heart (ventricle)

value: paternal Uninjured P0


title: ROI 4 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_06.RCC

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: Zebrafish sperm ATAC-seq - ST_ACI_1

description:
Library name: ST_ACI_1
Sperm nuclei ATAC-seq (Tn5 tagmentation); library prep/sequencing by NGS Platform, University of Bern. Sequencing run: SP and S1 Reagent Kits v1.5, 200 cycles; 100 bp paired-end.

library_source: genomic

data_processing:
Adapters trimmed using Trim Galore (Martin, 2011).
Reads aligned to the zebrafish reference genome GRCz11 (Ensembl release 115) using Bowtie2 (Langmead & Salzberg, 2012).
BAM files processed and filtered to a mapping quality threshold of Q30 using SAMtools (Danecek et al., 2021). Duplicates removed and uniquely mapped reads selected using Picard Tools (Broad Institute, 2019). Tn5 offset correction applied (+4 bp forward strand, -5 bp reverse strand).
Peaks called on deduplicated BAM files using MACS2 (FDR 0.05; Zhang et al., 2008), yielding a consensus set of 126,797 peaks.
Differential accessibility analysis performed using DiffBind with DESeq2 normalisation (Love et al., 2014; Ross-Innes et al., 2012), comparing ST_ACI 7dpi vs ST_CACI Uninjured samples, Benjamini-Hochberg correction (padj < 0.05), log2FC thresholds 0.5/1.0/2.0.
Peak annotation with ChIPseeker (Yu et al., 2015). Pathway enrichment via clusterProfiler (Wu et al., 2021; Yu et al., 2012) and ReactomePA (Yu & He, 2016).
Motif enrichment analysis on differential peaks using MEME Suite v5.5.8 (Bailey et al., 2015), specifically XSTREME (Patel & Grant, 2022) against JASPAR 2022 CORE Vertebrate, CIS-BP v1.02, and CIS-BP v2.00 motif databases.
BigWig files generated using deepTools (Ramirez et al., 2016); genomic interval operations performed with BEDTools (Quinlan & Hall, 2010).
Entire preprocessing pipeline executed via nf-core/atacseq (P. A. Ewels et al., 2020) using Nextflow (Tommaso et al., 2017) within Docker containers.
Assembly: Danio rerio GRCz11, Ensembl release 115
Supplementary files format and content: Per-replicate ATAC-seq peak calls (BED format; nf-core/atacseq MACS2 output).

molecule: genomic DNA

organism: Danio rerio

source_name: sperm

growth_protocol: Adult zebrafish maintained at max 5 fish/L, 27.5-28C, 14:10h light:dark, conductivity 650-700 uS/cm, pH 7.5, 10% daily water exchange; fed Artemia + dry food 3x/day. Approved under licenses BE46/19, BE109/2021, BE05/2025 (Canton of Bern, Switzerland).

extract_protocol:
See treatment protocol (nuclei lysis/transposition prep).
ATAC-seq libraries were generated following Buenrostro et al. (2015, Curr. Protoc. Mol. Biol. 109:21.29.1-21.29.9; doi:10.1002/0471142727.mb2129s109), with notable exceptions: the Illumina Tagment DNA Enzyme and Buffer Large Kit (Illumina, 20034198) was used for the transposition step, and Illumina DNA/RNA UD Indexes Set A, Tagmentation (Illumina, 20091654) were used for the PCR amplification step. Resulting libraries were evaluated using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854) and an Agilent Fragment Analyzer with a HS NGS Fragment Kit (Agilent, DNF-474); quantitative PCR library quantification used a JetSeq Library Quantification Lo-ROX kit (Bioline, BIO-68029). Equimolar-pooled libraries were sequenced 100 bp paired-end on an Illumina NovaSeq 6000 instrument using NovaSeq 6000 SP and S1 Reagent Kits v1.5 (200 cycles; Illumina, 20040719 and 20028318). Sequencing run quality was assessed using Illumina Sequencing Analysis Viewer (v2.4.7); base call files were demultiplexed and converted to FASTQ using Illumina bcl2fastq conversion software v2.20. All steps from nuclei preparation to FASTQ generation were carried out at the Next Generation Sequencing Platform, University of Bern (targeting 30-35M reads/sample; each sample retained at least 4.6M and up to 29M reads after quality-control processing).

treatment_protocol: ATAC-seq of spermatozoa was performed following Ruth Williams' protocol (Williams & Sauka-Spengler, 2021). 100,000 spermatozoa were spun down at 500 x g for 5 min at 4C, washed with 50 uL ice-cold PBS, resuspended in 50 uL lysis buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% IGEPAL CA-630), centrifuged again, and the supernatant discarded before the transposition reaction. ST_ACI = 7 dpi (cardiac cryoinjury); ST_CACI = uninjured control.

value: sperm

value: cardiac cryoinjury, 7 dpi


title: ROI 2 CD68

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: RPE-PRPF31.AAV 3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

description: Library name: 20_RPE_PRPF31_AAV_3_S20

data_processing:
Quality control and adapter trimming were processed through FastQC/multiQC and Trimmomatic, respectively. An average of 125 million good quality reads per sample were obtained after the QC trimming (phred QV > 20). Reads were aligned through STAR (default parameters), and  STAR-generated sorted BAM output files were used for assigning read counts to either genes or transcripts with featureCounts under the following parameters: -p -C -M -O --fraction -s 2. Differential Expression analysis was relied on DESeq2 negative binomial distribution model through a local fitting type and a 0.05 FDR threshold. Differential Splicing analysis was performed by rMATs using "--libType fr-firststrand --readLength 150 --variable-read-length –novelSS" options.
Assembly: ENSEMBL Homo_sapiens.GRCh38.109
Supplementary files format and content: readCounts' tables at both gene- and transcript-level are on a tab-delimited plain text format.

source_name: iPSCs-RPE

extract_protocol:
RNA was extracted using the Promega-ReliaPrep RNA Cell Miniprep System kit.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit

value: iPSCs-RPE

tag: cell line

value: Retinal Pigmented Epithelium


title: Mouse F1 heart bulk RNA-seq - PU_FU_21

description:
Library name: PU_FU_21
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: RPE-PRPF31.AAV 2

description: Library name: 19_RPE_PRPF31_AAV_2_S19


title: Mechanically injured rat esophagus, biological replicate 3

city: Heifei

first: Wenyong

last: Wu

state: Anhui

address: No. 632 Furong Road

institute: Anhui Institute of Medicine

description:
Library name: Model-3
Male Sprague-Dawley rat; mechanically injured esophageal tissue collected on day 28.

data_processing:
Raw base-call data were converted to FASTQ format using bcl2fastq v2.20.0.422.
Adapters were removed and low-quality reads were filtered using fastp v0.24.1. Bases with quality scores below 20 or containing N at the 5-prime or 3-prime ends were removed, and reads shorter than 75 bp after trimming were discarded.
Clean paired-end reads were aligned to the Rattus norvegicus Rnor_6.0 reference genome from Ensembl release 104 using HISAT2 v2.2.1 with default parameters.
Gene-level read counts and FPKM expression values were calculated using HTSeq v0.6.1.
Differential expression analysis between the control and model groups was performed using DESeq2 v1.50.2. P values were adjusted using the Benjamini-Hochberg method; genes with adjusted P < 0.05 and absolute log2 fold change >= 1 were considered differentially expressed.
Assembly: Rnor_6.0
Supplementary files format and content: Tab-delimited text file containing Ensembl gene identifiers and raw gene-level read counts for all six samples.

organism: Rattus norvegicus

source_name: esophagus

growth_protocol: Male Sprague-Dawley rats aged 8-10 weeks and weighing 250 +/- 20 g were housed individually at approximately 22 degrees C and 50% relative humidity under a 12-h light/12-h dark cycle, with standard chow and water provided ad libitum.

extract_protocol:
Total RNA was extracted from frozen esophageal tissues using TRIzol reagent according to the manufacturer's instructions. RNA concentration and purity were assessed, and samples with an A260/A280 ratio of 1.8-2.0 were used. One microgram of total RNA per sample was used for library preparation.
Polyadenylated mRNA was enriched using Oligo(dT)-conjugated magnetic beads and fragmented to approximately 150-200 nucleotides. First-strand cDNA was synthesized using random primers and SuperScript II reverse transcriptase, followed by second-strand synthesis using RNase H and DNA polymerase I. Double-stranded cDNA underwent end repair, 3-prime dA-tailing, adapter ligation, size selection and PCR amplification. Library quality was evaluated with an Agilent 2100 Bioanalyzer. Qualified libraries were pooled and sequenced using a 2 x 150-bp paired-end configuration.

treatment_protocol: Rats in the model group underwent localized esophageal mechanical injury using a customized 3D-printed device. The device was inserted orally to a depth of approximately 9-10 cm, and 8-10 reciprocating friction cycles of approximately 3-5 s each were performed. Rats in the control group were untreated. Esophageal tissues were collected on day 28 and snap-frozen in liquid nitrogen before storage at -80 degrees C.

value: esophagus

tag: genotype

value: wild type

value: localized mechanical injury using a customized 3D-printed device; tissue collected 28 days after injury


title: ROI 1 CD68

description:
GeoMx DSP protein expression data
raw data file: 20191029_P1001660004151A_P1001660004151A_08.RCC


title: Mouse F1 heart bulk RNA-seq - PU_FU_20

description:
Library name: PU_FU_20
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: Mouse sperm DNA methylation - Ci7 (cardiac cryoinjury (CI), 37wpp)

type: genomic

description: Sperm DNA methylation array (cardiac cryoinjury (CI))

hyb_protocol: Bisulfite-converted DNA was hybridized to the Infinium Mouse Methylation BeadChip (Illumina) following the standard Illumina protocol, performed by the Josep Carreras Leukaemia Research Institute Foundation (Barcelona, Spain).

scan_protocol: The Infinium Mouse Methylation BeadChip was scanned using the Illumina iScan System.

data_processing:
Data analysis was performed using the SeSAMe pipeline in R (Ding et al., 2023; Mani et al., 2022), which sets quality for masked probes, computes p-value using out-of-band probe distribution, and produces Beta methylation scores used for downstream processing (Zhou et al., 2018). Regions detected by Infinium probes were annotated with SeSAMe using the mouse reference genome (Cavalcante & Sartor, 2017). Differentially methylated genes were subjected to GO and pathway enrichment analysis using clusterProfiler (Yu et al., 2012).
Beta value (SeSAMe)

label: Cy3 and Cy5

source_name: Spermatozoa

label_protocol: Samples were sent to the Josep Carreras Leukaemia Research Institute Foundation (Barcelona, Spain), where they were bisulfite converted and labeled using the standard Illumina Infinium protocol.

growth_protocol: C57BL/6J mice raised to weaning (3 wpp) then housed at 4 animals/cage (bred males isolated after first breeding); SPF facility, 20-24C, 12h light/dark, 45-65% RH, food/water ad libitum. Approved under license PROEX 310_19 (Comunidad de Madrid, Spain), conforming to EU Directive 86/609/EEC.

extract_protocol: Motile spermatozoa utilized for methylome analysis were cryopreserved. After thawing, sperm were lysed in lysis buffer (1M Tris pH 8, 5M NaCl, 20% SDS, 1M DTT) containing Proteinase K at 55C for 2 hours and extracted by phenol/chloroform/isoamylalcohol (25:24:1) followed by ethanol precipitation. DNA was resuspended in nuclease-free water to a final concentration of 50 ng/ul min.

treatment_protocol: Cardiac cryoinjury (CI) performed at postnatal day 1 (P1); uninjured age-matched males served as controls. Sperm collected and cryopreserved at 32 wpp (Uninjured) or 37 wpp (CI).

value: Spermatozoa

tag: strain

value: C57BL/6 J (Jackson lab)

tag: age

tag: Sex

value: male

value: cardiac cryoinjury (CI)


title: RPE-PRPF31.AAV 1

description: Library name: 18_RPE_PRPF31_AAV_1_S18


title: Mechanically injured rat esophagus, biological replicate 2

description:
Library name: Model-2
Male Sprague-Dawley rat; mechanically injured esophageal tissue collected on day 28.


title: Mouse sperm DNA methylation - Ci6 (cardiac cryoinjury (CI), 37wpp)


title: RPE-GFP.AAV 3

description: Library name: 17_RPE_GFP_AAV_3_S17


title: Mouse F1 heart bulk RNA-seq - PU_FU_18

description:
Library name: PU_FU_18
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: Mechanically injured rat esophagus, biological replicate 1

description:
Library name: Model-1
Male Sprague-Dawley rat; mechanically injured esophageal tissue collected on day 28.


title: Mouse sperm DNA methylation - CI5 (cardiac cryoinjury (CI), 37wpp)


title: Untreated control rat esophagus, biological replicate 3

description:
Library name: Control-3
Male Sprague-Dawley rat; esophageal tissue collected on day 28.

value: untreated


title: Mouse F1 heart bulk RNA-seq - PI_FU_17

description:
Library name: PI_FU_17
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.

value: paternal Injured P0


title: m15_Null_WD_4

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

country: USA

institute: OMRF

description: Library name: S29

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Mus musculus genome reference (GRCm39/mm39) using STAR and per transcript reads were counted with HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow.
Assembly: GRCm39/mm39
Supplementary files format and content: rawCounts.csv.gz: csv (comma-separated values) file includes ENSEMBL id and raw read counts for each transcript, in each sample

source_name: hepatocytes

extract_protocol:
Total RNA was isolated for approximately 25 mg of liver tissue using RNeasy Mini kit (Cat# 74106) from Qiagen (Valencia, CA, USA) . RNA was quantified using Qubit RNA BR Assay kit (Cat# Q10211,ThermoScientific, Waltham, MA) in a Qubit3.0 fluorometer.
RNA was checked for quality using Agilent’s 4150 Tapestation, and concentrations from ThermoFisher’s NanoDrop readings were used. Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols.  The library construction was done using 1mg of RNA. Each of the libraries was indexed during library construction in order to multiplex for sequencing. Libraries were quantified using Invitrogen’s Qubit 4 fluorometer and checked for size and quality on Agilent’s 4150 Tapestation.  Samples were normalized and pooled onto a 150 paired end run on Illumina HiSeq 2500 Platform to obtain 20M reads per sample.

treatment_protocol: Male Mlklfl/fl mice on a C57BL/6J background were injected with AAV8-TBG-Cre (hepatocyte-specific) or AAV8-TBG-Null  via tail vein at 1.5 months of age to generate hepatocyte-specific Mlkl knockout (MlklHepKO) or control mice. Beginning at 2.5 months of age, mice were fed ad libitum either a control diet (CD) or a Western diet (WD) ) for 4, 8, or 15 months.  Liver was dissected out, RNA isolated using Qiagen RNeasy mini kit and was used for RNA sequencing.

value: hepatocytes

tag: study time

value: 15 months

tag: knockout

tag: diet

value: WD


title: RPE-GFP.AAV 2

description: Library name: 16_RPE_GFP_AAV_2_S16


title: Mouse sperm DNA methylation - Ci4 (cardiac cryoinjury (CI), 37wpp)


title: Untreated control rat esophagus, biological replicate 2

description:
Library name: Control-2
Male Sprague-Dawley rat; esophageal tissue collected on day 28.


title: RPE-GFP.AAV 1

description: Library name: 15_RPE_GFP_AAV_1_S15


title: Mouse sperm DNA methylation - U3 (uninjured control, 32wpp)

description: Sperm DNA methylation array (uninjured control)

value: uninjured control


title: Mouse F1 heart bulk RNA-seq - PI_FU_16

description:
Library name: PI_FU_16
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.

value: heart (ventricle)


title: Untreated control rat esophagus, biological replicate 1

description:
Library name: Control-1
Male Sprague-Dawley rat; esophageal tissue collected on day 28.


title: RO-PRPF31.AAV 3

description: Library name: 14_RO_PRPF31_AAV_3_S14

source_name: iPSCs-RO

value: iPSCs-RO

value: Retinal Organoids


title: Mouse F1 heart bulk RNA-seq - PI_FU_15

description:
Library name: PI_FU_15
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: Mouse sperm DNA methylation - U2 (uninjured control, 32wpp)


title: RO-PRPF31.AAV 2

description: Library name: 13_RO_PRPF31_AAV_2_S13


title: Tissue array: 3 punches

type: RNA

city: Ljubljana

first: Emanuela

last: Boštjančič

address: Korytkova 2, Ljubljana

country: Slovenia

institute: University of Ljubljana, Faculty of Medicine, Institute of Pathology

hyb_protocol: Human Multi-Tissue and Cancer Panel: 377 genes; over-night hybridization followed by rolling circle amplification.

scan_protocol: xenium analyser: automatic image processing, decoding, analysis of quality, cell segmentation.

data_processing: Xenium Explorer 2.0

label: Xenium probe set

source_name: larynx; hypopharynx

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE: tissue array, 5 µm thick slice placed on Xenium slide, dried and permeabilized.

value: larynx; hypopharynx

tag: tissue preservation method

value: FFPE


title: Mouse F1 heart bulk RNA-seq - PI_FU_14

description:
Library name: PI_FU_14
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: Mouse sperm DNA methylation - U1 (uninjured control, 32wpp)


title: Mouse F1 heart bulk RNA-seq - PI_FU_13

description:
Library name: PI_FU_13
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: RO-PRPF31.AAV 1

description: Library name: 12_RO_PRPF31_AAV_1_S12


title: siMLKL-3_S9

description: Library name: S6

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Homo sapiens (human) genome reference GRCh38 (hg38)  using STAR and per transcript reads were counted with HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow.
Assembly: GRCh38 (hg38)
Supplementary files format and content: raw_counts_matrix.tsv.gz: tab-separated values file includes ENSEMBL gene id and raw read counts for each transcript, in each sample

growth_protocol: HepG2 (HB-8065, ATCC) cells were grown in EMEM medium (30-2003, ATCC) supplemented with 10% fetal bovine serum (FBS) and 1X Penicillin-Streptomycin (15-070-063, Gibco) at 37oC with 5% CO2.

extract_protocol:
Total RNA was isolated  using RNeasy Mini kit (Cat. No. 74106, Qiagen). RNA was quantified using Qubit RNA BR Assay kit (Cat. No. Q10211,ThermoScientific) in a Qubit3.0 fluorometer.
RNA was checked for quality using Agilent’s 4150 Tapestation, and concentrations from ThermoFisher’s NanoDrop readings were used. Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols.  The library construction was done using 1mg of RNA. Each of the libraries was indexed during library construction in order to multiplex for sequencing. Libraries were quantified using Invitrogen’s Qubit 4 fluorometer and checked for size and quality on Agilent’s 4150 Tapestation.  Samples were normalized and pooled onto a 150 paired end run on Illumina HiSeq 2500 Platform to obtain 20M reads per sample.

treatment_protocol: MLKL was knocked down in HepG2 cells by transfecting with 100nM of siControl (Silencer Select Negative Control No.1 siRNA, Cat. No. 4390843, Invitrogen) or siMLKL (Silencer Select siRNA against human MLKL, Cat. No. 4392420, Invitrogen) for 48h using Lipofectamine RNAimax transfection reagent (13778150, Invitrogen).

value: MLKL


title: Tissue array: 8 punches


title: mir-52;mir-54-56 mutant strain, L4, Rep3

city: Bethesda

first: Kasuen

last: Kotagama

state: MD

address: 50 South Dr

department: NIDDK

institute: National Institutes of Health

description:
Library name: sKK82
150 bp PE

data_processing:
Sequenced reads were preprocessed using cutadapt (v2.7) to remove adaptor and low quality sequence, then mapped to worm whole genome (ws277) using hisat2 v2.1.0 with default parameters. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Assembly: worm WS277
Supplementary files format and content: tab-delimited text files include gene count values for each sample.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: To isolate L4 staged worms, we first synchronized worms to L1 by hypochlorite treatment and ~2000 worms were placed per seeded 10cm plate and grown at 25°C. At time points when most of the population was at the L4 stage (48hrs for wild-type; 96hr for mir-52; mir-54-56 mutants), worms were washed three times with water to remove bacteria and plated on NGM plates without bacteria. Distal tip cell migration was then used to identify L4 individuals, which were picked directly into Trizol (500 worms per sample).

extract_protocol:
Trizol and acid phenol-chloroform
A minimum of 0.5ug of total RNA was used for library preperation. Library kit: TruSeq stranded Total RNA with Ribo-Zero Human/Mouse/Rat.

value: Whole worm

tag: sample group

value: mir-52;mir-54-56 mutant strain, L4


title: RO-GFP.AAV 3

description: Library name: 11_RO_GFPAAV_3_S11


title: Mouse F1 heart bulk RNA-seq - PI_FU_12

description:
Library name: PI_FU_12
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.


title: siMLKL-2_S8

description: Library name: S5


title: Control, L4, Rep3

description:
Library name: sKK81
150 bp PE

value: Control, L4


title: S. elongatus PCC 7942 D1339 input DNA, biological replicate 2

city: Jinan

first: Guoyan

last: Zhao

state: Shandon

address: ShanDong Normal University

institute: ShanDong Normal University

description:
Library name: In_D1339_2
Non-immunoprecipitated input genomic DNA from D1339 biological replicate 2; paired ChIP library: IP_D1339_2.

data_processing:
Raw reads were quality assessed using FastQC v0.11.5 and filtered using Trimmomatic v0.36 with parameters ILLUMINACLIP:adapters.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:20.
Filtered reads were aligned to the Synechococcus elongatus PCC 7942 reference genome (CP000100.1) using BWA v0.7.15-r1140.
Duplicate reads were removed, uniquely mapped reads were retained, and genome-wide coverage signals were generated in bigWig format for each ChIP and input library.
Enriched regions were identified for each ChIP sample relative to its matched input control using MACS v2.1.1.20160309 with a significance threshold of P < 0.001.
Peak-associated genomic features and genes were annotated using the ChIPseeker R package, and enriched sequence motifs were identified using HOMER v3.
Assembly: Synechococcus elongatus PCC 7942 reference genome, GenBank accession CP000100.1
Supplementary files format and content: BigWig files contain genome-wide sequencing coverage signals for each ChIP and matched input library.
Supplementary files format and content: BED files contain MACS peak intervals for each ChIP library relative to its matched input control; columns contain chromosome accession, start coordinate, end coordinate, peak identifier, and a quantitative peak score.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cyanobacterial cells

growth_protocol: Synechococcus elongatus PCC 7942 cells were cultured in BG-11 medium (pH 8.0) at 30 degrees C under continuous illumination of 40 micromol photons m-2 s-1 and harvested during logarithmic growth.

extract_protocol:
Chromatin from the NsrC-mNG-FLAG strain was crosslinked with formaldehyde, quenched with glycine, washed with pre-chilled PBS, lysed, and sonicated. An aliquot was retained as input DNA. Immunoprecipitation was performed with anti-FLAG antibody (F1804-1MG, Sigma-Aldrich). Bound DNA was eluted, reverse crosslinked, purified, and assessed by Qubit.
Sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, size selection, PCR amplification, and purification. Libraries were sequenced as paired-end 2 x 150 bp reads on an Illumina NovaSeq 6000 instrument.

treatment_protocol: No additional treatment was applied; cultures were harvested during logarithmic growth for ChIP-seq.

value: cyanobacterial cells

value: NsrC-mNG-FLAG strain (D1339)

value: none; cells harvested during logarithmic growth


title: RO-GFP.AAV 2

description: Library name: 10_RO_GFPAAV_2_S10


title: Control, L4, Rep2

description:
Library name: sKK80
150 bp PE


title: RO-GFP.AAV 1

description: Library name: 9_RO_GFPAAV_1_S9


title: siMLKL-1_S7

description: Library name: S4


title: S. elongatus PCC 7942 D1339 ChIP DNA, biological replicate 2

description:
Library name: IP_D1339_2
Chromatin-immunoprecipitated genomic DNA from D1339 biological replicate 2; paired input library: In_D1339_2.


title: mir-52;mir-54-56 mutant strain, L4, Rep2

description:
Library name: sKK79
150 bp PE


title: siControl-3_S6

description: Library name: S3

value: Control


title: ENKTL CosMx slide 2

description: CosMx 6k spatial transcriptomic data for ENKTL slide 2. Supplementary files include a cell-by-gene expression matrix, cell level metadata, decoded transcript coordinates, field of view positions, and cell segmentation polygons.

hyb_protocol: CosMx RNA probes were hybridized to the tissue sections according to the NanoString CosMx SMI protocol using the CosMx 6k RNA panel.

scan_protocol: Slides were imaged using the NanoString CosMx Spatial Molecular Imager. A preview scan was performed, fields of view were selected over the tissue regions, and cyclic reporter hybridization and fluorescence imaging were conducted to decode the spatial locations of RNA transcripts.

data_processing:
Images were registered across imaging cycles, RNA transcripts were decoded, cells were segmented using fine-tuned cellpose, and detected transcripts were assigned to individual cells.Downstream analyses of the CosMx 6k spatial transcriptomics data were performed using Seurat v5 pipelines.
Processed data files: Library size normalized and log1p-transformed transcript abundance per cell
Original CosMx output tx_file.csv file has been renamed to transcript.csv to clarify that each row represents an individual transcript

source_name: ENKTL lymphoma tissue (FFPE tissue section)

label_protocol: Tissue morphology was labeled using PanCK, CD45, CD3, DAPI and CD298. RNA targets were detected using the CosMx 6k RNA probe panel according to the NanoString CosMx SMI protocol.

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

value: ENKTL FFPE sample


title: S. elongatus PCC 7942 D1339 input DNA, biological replicate 1

description:
Library name: In_D1339_1
Non-immunoprecipitated input genomic DNA from D1339 biological replicate 1; paired ChIP library: IP_D1339_1.


title: siControl-2_S5

description: Library name: S2


title: Control, L4, Rep1

description:
Library name: sKK78
150 bp PE


title: ENKTL CosMx slide 1

description: CosMx 6k spatial transcriptomic data for ENKTL slide 1. Supplementary files include a cell-by-gene expression matrix, cell level metadata, decoded transcript coordinates, field of view positions, and cell segmentation polygons.


title: S. elongatus PCC 7942 D1339 ChIP DNA, biological replicate 1

description:
Library name: IP_D1339_1
Chromatin-immunoprecipitated genomic DNA from D1339 biological replicate 1; paired input library: In_D1339_1.


title: Septin2 Mutant, Third Instar Larvae, Rep3

status: Public on Aug 15 2026

city: Istanbul

first: Arzu

last: Celik

state: İstanbul

address: Bebek Yolu Sokağı, Kuzey Kampüs, Kuzey Park Binası 304, Etiler

department: Department of Molecular Biology and Genetics

country: Turkey

institute: Bogazici University

description: Library name: Sep2.2_rep3

data_processing:
Quality control of raw paired-end reads was performed using FastQC (v0.11.9).
Adaptor sequences and low-quality bases were removed using Cutadapt (v3.5). Cleaned reads were aligned to the BDGP6 reference genome using STAR (v2.7.11b) in two-pass mode with Ensembl gene annotations.
Sorted BAM files were generated and gene-level read counts were obtained using STAR's quant mode. Differential expression analysis was performed in R using edgeR v3.40. Counts were filtered using filterByExpr, normalised with TMM, and modelled with a quasi-likelihood negative binomial GLM (~0 + genotype design). Contrasts were tested using glmQLFTest.
GO enrichment analysis was performed using clusterProfiler v4.6 against org.Dm.eg.db with BH correction, pvalueCutoff=0.05, qvalueCutoff=0.05.
Assembly: dm6 (BDGP6, Ensembl release 107)
Supplementary files format and content: Dmelanogaster_log2CPM_Septin_alleles_normalized.csv: TMM-normalised log2 CPM expression matrix; rows = genes (FBgn ID + symbol), columns = samples

organism: Drosophila melanogaster

source_name: whole third instar larvae

growth_protocol: Adult Drosophila melanogaster flies were maintained on standard cornmeal-yeast-agar medium at 25°C under a 12h light/dark cycle.

extract_protocol:
Total RNA was extracted from whole adult flies using TRIzol reagent (Thermo Fisher Scientific) followed by RNeasy Mini Kit (Qiagen) cleanup with on-column DNase I digestion. RNA integrity was assessed by Bioanalyzer (Agilent); samples with RIN > 8 were used.
Watchmaker mRNA Library Prep

treatment_protocol: No treatment was applied. Flies were collected within 3 days of eclosion.

value: whole third instar larvae

value: third instar larvae

value: whole organism


title: Septin2 Mutant, Third Instar Larvae, Rep2

description: Library name: Sep2.2_rep2


title: mir-52;mir-54-56 mutant strain, L4, Rep1

description:
Library name: sKK77
150 bp PE


title: Septin2 Mutant, Third Instar Larvae, Rep1

description: Library name: Sep2.2_rep1


title: siControl-1_S4

description: Library name: S1


title: Septin5 Mutant, Third Instar Larvae, Rep3

description: Library name: Sep5.2_rep3


title: Septin5 Mutant, Third Instar Larvae, Rep2

description: Library name: Sep5.2_rep2


title: Septin5 Mutant, Third Instar Larvae, Rep1

description: Library name: Sep5.2_rep1


title: Septin2/5 Double Mutant, Third Instar Larvae, Rep4

description: Library name: Sep2.2_Sep5.2_DM_rep4


title: Septin2/5 Double Mutant, Third Instar Larvae, Rep3

description: Library name: Sep2.2_Sep5.2_DM_rep3


title: Septin2/5 Double Mutant, Third Instar Larvae, Rep2

description: Library name: Sep2.2_Sep5.2_DM_rep2


title: Septin2/5 Double Mutant, Third Instar Larvae, Rep1

description: Library name: Sep2.2_Sep5.2_DM_rep1


title: Control, Third Instar Larvae, Rep4

description: Library name: w1118_rep4


title: Control, Third Instar Larvae, Rep2

description: Library name: w1118_rep2


title: Control, Third Instar Larvae, Rep1

description: Library name: w1118_rep1


title: Control, Third Instar Larvae, Rep3

description: Library name: w1118_rep3


title: Col-0, polysomal RNA, replicate 3

city: Canberra

first: Diep

middle: R

last: Ganguly

state: ACT

address: 46 Sullivans Creek Rd

department: Research School of Biology

country: Australia

institute: The Australian National University

description: Library name: WT-polysome-rep3

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality base calls with Trim Galore v2.3.0.
Trimmed reads were used for transcript quantification with Kallisto v0.52.0 (Bray et al., 2016). A transcript index was generated from TAIR10 coding sequences (Ensembl Plants Release 59) using kallisto index -k 21, and transcript abundances were estimated using kallisto quant --rf-stranded --bias.
Gene-level transcript per million (TPM) values and length-scaled estimated counts were then generated using Tximport v1.40.0 with type = “kallisto” and countsFromAbundance = “lengthScaledTPM” (Soneson et al., 2016).
Assembly: TAIR10
Supplementary files format and content: .h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length.
Supplementary files format and content: Counts_all_samples.csv: gene-level length-scaled estimated counts for all samples
Supplementary files format and content: TPM_all_samples.csv: gene-level TPM matrix for all samples.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seedlings were was grown on half-strength Murashige and Skoog medium (Phytotech Labs, Lenexa, KS, USA) at 22 °C under a 16-h-light (100-150 µmol m-2 s-1)/8-h-dark photoperiod.

extract_protocol:
Polysome profiling was performed on 14-day old plate-grown seedlings using an adapted protocol (Smith et al., 2024). Briefly, 200 mg of seedlings were homogenized in 800 µl of extraction buffer (160 mM Tris-Cl [pH 7.6], 80 mM KCl, 5 mM MgCl2, 5.36 mM EGTA [pH 8], 0.5% IGEPAL CA-630, 40 U ml-1 RNasin Plus RNase inhibitor [Promega], 150 µg ml-1 cycloheximide and 150 µg ml-1 chloramphenicol) and incubated on ice for 10 min. Samples were repeatedly centrifuged at 16,000 × g for 5 min at 4 °C until the supernatant was clear. 700 µl of supernatant was loaded onto a sucrose gradient, consisting of layers of 50% (1.68 ml), 35% (3.32 ml), 20% (3.32 ml) and 20% (1.68 ml), with the two 20% layers added separately. The buffer used in the gradients consisted of 400 mM Tris-Cl (pH 8.4), 200 mM KCl, 100 mM MgCl2, 10.12 µg ml-1 cycloheximide and 10.12 µg ml-1 chloramphenicol. Gradients were centrifuged at 36,000 × g with an SW41Ti rotor for 3.5 h at 4 °C. Each gradient was passed through a spectrophotometer from the highest to lowest density and absorbance at 256 nm was recorded, with 1 ml fractions collected using a Gradient Piston Fractionator (BioComp Instruments, Tatamagouche, NS, Canada). Sucrose gradient fractions were collected based on the observation of peaks representing 1 ribosome (monosomes), 2 ribosomes (disomes), and 3 or more ribosomes (polysomes). Total RNA was isolated from the polysome fractions (polysome RNA) and from an aliquot of lysate collected prior to sucrose gradient fractionation (input RNA) by adding an equal volume of 5:1 (v/v) acid phenol:chloroform. After centrifugation at 16,000 × g for 10 min, the aqueous layer was extracted a second time using a one-fifth volume of chloroform, followed by precipitation of RNA in equal-volume isopropanol. The precipitated RNA was washed twice with 70% ethanol and resuspended in nuclease-free water. Five micrograms of RNA were treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) for 30 min at 37°C, followed by paramagnetic bead-based purification at a ratio of 1.8×bead: sample (Sera-Mag, GE Healthcare, Chicago, IL, USA). RNA was quantified with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and RNA quality was assessed on the GX Touch (PerkinElmer, Shelton, CT, USA).
Libraries were prepared using the Illumina Stranded mRNA Prep (Ligation) kit according to the manufacturer’s guidelines and sequenced on a NextSeq 2000 (Illumina) to generate 2 × 50 bp paired-end reads.

value: Seedlings

value: wild-type, Col-0


title: Col-0, polysomal RNA, replicate 1

description: Library name: WT-polysome-rep1


title: Col-0, input RNA, replicate 1

description: Library name: WT-input-rep1


title: Col-0, input RNA, replicate 3

description: Library name: WT-input-rep3


title: Col-0, input RNA, replicate 2

description: Library name: WT-input-rep2


title: dxo1-2, polysomal RNA, replicate 3

description: Library name: dxo1-polysome-rep3


title: Col-0, polysomal RNA, replicate 2

description: Library name: WT-polysome-rep2


title: dxo1-2, polysomal RNA, replicate 1

description: Library name: dxo1-polysome-rep1


title: dxo1-2, input RNA, replicate 3

description: Library name: dxo1-input-rep3


title: dxo1-2, input RNA, replicate 2

description: Library name: dxo1-input-rep2


title: dxo1-2, polysomal RNA, replicate 2

description: Library name: dxo1-polysome-rep2


title: dxo1-2, input RNA, replicate 1

description: Library name: dxo1-input-rep1


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 3d-ON/8d-OFF, Rep2

city: Boston

first: Alex

last: Plesa

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: S385
Donor age 79, Passage 14, Batch 8

data_processing:
To minimize variability arising from differences in sequencing depth, FASTQ files for all libraries (except LIB058979, LIB092645, and LIB083102) were downsampled to 20 million reads using Seqtk-1.3.
Raw RNA-seq reads were aligned to the GRCh38/GRCm39 reference genome using STAR v2.5.2b and checked for quality control using FastQC v0.11.5
Alignment files were indexed using SAMtools v1.3.154 and gene-level counts were obtained using featureCounts from the Subread v2.0.1 package
Assembly: GRCh38, GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: NHDFs were maintained in low-glucose DMEM supplemented with 15% fetal bovine serum (FBS) and 1% Pen-strep (P/S) in humidified atmosphere with 5% CO2 and 5% O2, at 37C. iPSCs were maintained in mTESR+supplement in humidified atmosphre with 5% CO2 at 37C.

extract_protocol:
Cells were lysed using the Monarch DNA/RNA Protection Reagent (NEB T2011) and stored at -80°C until RNA extraction. Total RNA was extrqacted using the Monarch Total RNA Miniprep kit (NEB T2010). Mouse tissues were processed by Novogene.
Libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the polyA mRNA workflow according to manufacturer's instructions. LIB058979 was genereated using the Tecan MagicPrepRevelo mRNA-seq kit acoording to manufacturare's instructions. LIB083102 was generated by Novogene using a directional mRNA library preparation method.

treatment_protocol: Transgene was induced using doxycycline at the specified concentration for the specified amount of time. Similarly, rapamycin was added to the media at the 100nM for the specified amount of time.

value: Fibroblast

value: Dox_1000ng/mL, 3d-ON/8d-OFF

tag: batch


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 3d-ON, Rep2

description:
Library name: S383
Donor age 79, Passage 13, Batch 8

value: Dox_1000ng/mL, 3d-ON


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 3d-ON, Rep1

description:
Library name: S382
Donor age 79, Passage 13, Batch 8


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 3d-ON/8d-OFF, Rep2

description:
Library name: S381
Donor age 79, Passage 14, Batch 8


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 3d-ON/8d-OFF, Rep1

description:
Library name: S380
Donor age 79, Passage 14, Batch 8


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep1

description:
Library name: S376
Donor age 79, Passage 14, Batch 5

value: Dox_1000ng/mL, 1d-ON/8d-OFF


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep2

description:
Library name: S377
Donor age 79, Passage 14, Batch 5


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 3d-ON, Rep1

description:
Library name: S378
Donor age 79, Passage 13, Batch 8


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 1d-ON, Rep2

description:
Library name: S375
Donor age 79, Passage 13, Batch 5

value: Dox_1000ng/mL, 1d-ON


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 3d-ON, Rep2

description:
Library name: S379
Donor age 79, Passage 13, Batch 8


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 1d-ON, Rep1

description:
Library name: S374
Donor age 79, Passage 13, Batch 5


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep2

description:
Library name: S373
Donor age 79, Passage 14, Batch 5


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep1

description:
Library name: S372
Donor age 79, Passage 14, Batch 5


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 1d-ON, Rep2

description:
Library name: S371
Donor age 79, Passage 13, Batch 5


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 1d-ON, Rep1

description:
Library name: S370
Donor age 79, Passage 13, Batch 5


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 3d-ON/16d-OFF, Rep2

description:
Library name: S369
Donor age 79, Passage 15, Batch 12

value: Dox_1000ng/mL, 3d-ON/16d-OFF


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 3d-ON/16d-OFF, Rep1

description:
Library name: S368
Donor age 79, Passage 15, Batch 12


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 3d-ON/16d-OFF, Rep2

description:
Library name: S367
Donor age 79, Passage 15, Batch 12


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 3d-ON/16d-OFF, Rep1

description:
Library name: S366
Donor age 79, Passage 15, Batch 12


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 3d-ON, Rep2

description:
Library name: S365
Donor age 55, Passage 12, Batch 12


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 3d-ON, Rep1

description:
Library name: S364
Donor age 55, Passage 12, Batch 12


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 3d-ON, Rep2

description:
Library name: S363
Donor age 55, Passage 12, Batch 12


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 3d-ON, Rep1

description:
Library name: S362
Donor age 55, Passage 12, Batch 12


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 3d-ON, Rep2

description:
Library name: S361
Donor age 79, Passage 13, Batch 11

value: OSKM


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep2

description:
Library name: S359
Donor age 79, Passage 14, Batch 11

value: Dox_1000ng/mL, 2d-ON/8d-OFF


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep1

description:
Library name: S358
Donor age 79, Passage 14, Batch 11


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 3d-ON, Rep2

description:
Library name: S357
Donor age 55, Passage 12, Batch 11


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 3d-ON, Rep1

description:
Library name: S356
Donor age 55, Passage 12, Batch 11


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 3d-ON, Rep1

description:
Library name: S360
Donor age 79, Passage 13, Batch 11


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 2d-ON/16d-OFF, Rep1

description:
Library name: S352
Donor age 55, Passage 14, Batch 4

value: Dox_1000ng/mL, 2d-ON/16d-OFF


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep2

description:
Library name: S355
Donor age 55, Passage 13, Batch 11


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep1

description:
Library name: S354
Donor age 55, Passage 13, Batch 11


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 2d-ON/16d-OFF, Rep2

description:
Library name: S353
Donor age 55, Passage 14, Batch 4


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep1

description:
Library name: S350
Donor age 55, Passage 13, Batch 4


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep2

description:
Library name: S351
Donor age 55, Passage 13, Batch 4


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 2d-ON/16d-OFF, Rep2

description:
Library name: S349
Donor age 55, Passage 14, Batch 4


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 2d-ON/16d-OFF, Rep1

description:
Library name: S348
Donor age 55, Passage 14, Batch 4


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep2

description:
Library name: S347
Donor age 55, Passage 13, Batch 4


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 2d-ON/8d-OFF, Rep1

description:
Library name: S346
Donor age 55, Passage 13, Batch 4


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 2d-ON, Rep2

description:
Library name: S345
Donor age 55, Passage 12, Batch 3

value: Dox_1000ng/mL, 2d-ON


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep1

description:
Library name: S342
Donor age 55, Passage 14, Batch 3

value: Dox_1000ng/mL, 1d-ON/16d-OFF


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 2d-ON, Rep1

description:
Library name: S340
Donor age 55, Passage 12, Batch 3


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 2d-ON, Rep1

description:
Library name: S344
Donor age 55, Passage 12, Batch 3


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep1

description:
Library name: S338
Donor age 55, Passage 14, Batch 3


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep2

description:
Library name: S343
Donor age 55, Passage 14, Batch 3


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 2d-ON, Rep2

description:
Library name: S341
Donor age 55, Passage 12, Batch 3


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep2

description:
Library name: S339
Donor age 55, Passage 14, Batch 3


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep2

description:
Library name: S335
Donor age 79, Passage 15, Batch 6


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep1

description:
Library name: S334
Donor age 79, Passage 15, Batch 6


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 2d-ON, Rep1

description:
Library name: S336
Donor age 79, Passage 13, Batch 6


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 2d-ON, Rep2

description:
Library name: S333
Donor age 79, Passage 13, Batch 6


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep1

description:
Library name: S330
Donor age 79, Passage 15, Batch 6


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 2d-ON, Rep2

description:
Library name: S337
Donor age 79, Passage 13, Batch 6


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 2d-ON, Rep1

description:
Library name: S332
Donor age 79, Passage 13, Batch 6


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep2

description:
Library name: S331
Donor age 79, Passage 15, Batch 6


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 2d-ON/16d-OFF, Rep2

description:
Library name: S329
Donor age 79, Passage 15, Batch 7


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep2

description:
Library name: S327
Donor age 79, Passage 14, Batch 7


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P15, 2d-ON/16d-OFF, Rep1

description:
Library name: S328
Donor age 79, Passage 15, Batch 7


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 2d-ON/16d-OFF, Rep2

description:
Library name: S325
Donor age 79, Passage 15, Batch 7


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep1

description:
Library name: S326
Donor age 79, Passage 14, Batch 7


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P15, 2d-ON/16d-OFF, Rep1

description:
Library name: S324
Donor age 79, Passage 15, Batch 7


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep2

description:
Library name: S323
Donor age 79, Passage 14, Batch 7


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 2d-ON/8d-OFF, Rep1

description:
Library name: S322
Donor age 79, Passage 14, Batch 7


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 1d-ON, Rep2

description:
Library name: S319
Donor age 55, Passage 12, Batch 2


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep1

description:
Library name: S316
Donor age 55, Passage 13, Batch 2


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep2

description:
Library name: S321
Donor age 55, Passage 13, Batch 2


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep2

description:
Library name: S317
Donor age 55, Passage 13, Batch 2


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P12, 1d-ON, Rep1

description:
Library name: S318
Donor age 55, Passage 12, Batch 2


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 1d-ON, Rep1

description:
Library name: S314
Donor age 55, Passage 12, Batch 2


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 2d-ON, Rep2

description:
Library name: S313
Donor age 79, Passage 13, Batch 10


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep1

description:
Library name: S320
Donor age 55, Passage 13, Batch 2


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P12, 1d-ON, Rep2

description:
Library name: S315
Donor age 55, Passage 12, Batch 2


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep2

description:
Library name: S311
Donor age 79, Passage 15, Batch 10


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 2d-ON, Rep1

description:
Library name: S312
Donor age 79, Passage 13, Batch 10


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 2d-ON, Rep1

description:
Library name: S308
Donor age 55, Passage 12, Batch 10


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 3d-ON/8d-OFF, Rep1

description:
Library name: S384
Donor age 79, Passage 14, Batch 8


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep2

description:
Library name: S307
Donor age 55, Passage 14, Batch 10


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P15, 1d-ON/16d-OFF, Rep1

description:
Library name: S310
Donor age 79, Passage 15, Batch 10


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 3d-ON/16d-OFF, Rep1

description:
Library name: S303
Donor age 55, Passage 14, Batch 1


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 3d-ON/8d-OFF, Rep1

description:
Library name: S301
Donor age 55, Passage 13, Batch 1


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 3d-ON/16d-OFF, Rep1

description:
Library name: S299
Donor age 55, Passage 14, Batch 1


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 1d-ON/16d-OFF, Rep1

description:
Library name: S306
Donor age 55, Passage 14, Batch 10


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 3d-ON/8d-OFF, Rep2

description:
Library name: S304
Donor age 55, Passage 13, Batch 1


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep1

description:
Library name: S296
Donor age 79, Passage 14, Batch 9


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 1d-ON, Rep2

description:
Library name: S295
Donor age 79, Passage 13, Batch 9


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 1d-ON, Rep1

description:
Library name: S294
Donor age 79, Passage 13, Batch 9


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 1d-ON, Rep2

description:
Library name: S291
Donor age 55, Passage 12, Batch 9


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P14, 1d-ON/8d-OFF, Rep2

description:
Library name: S297
Donor age 79, Passage 14, Batch 9


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P14, 3d-ON/16d-OFF, Rep2

description:
Library name: S302
Donor age 55, Passage 14, Batch 1


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P14, 3d-ON/16d-OFF, Rep2

description:
Library name: S298
Donor age 55, Passage 14, Batch 1


title: M79 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P10, Rep3

description:
Library name: S288
Donor age 79, Passage 10

value: NTg

value: Dox_1000ng/mL, 3days


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep2

description:
Library name: S293
Donor age 55, Passage 13, Batch 9


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, 1d-ON/8d-OFF, Rep1

description:
Library name: S292
Donor age 55, Passage 13, Batch 9


title: M65 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P5, Rep3

description:
Library name: S286
Donor age 65, Passage 5


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 1d-ON, Rep1

description:
Library name: S290
Donor age 55, Passage 12, Batch 9


title: M65 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P11, Rep2

description:
Library name: S283
Donor age 65, Passage 11


title: M79 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P10, Rep4

description:
Library name: S289
Donor age 79, Passage 10


title: M65 line with Dox-inducible NTg transgene, Dox_0ng/mL, P7, Rep4

description:
Library name: S281
Donor age 65, Passage 7

value: WT

value: NT


title: M69 line with Dox-inducible NTg transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S279
Donor age 69, Passage 9

value: Dox_2000ng/mL, 3days


title: M55 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P9, Rep4

description:
Library name: S285
Donor age 55, Passage 9


title: M69 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S277
Donor age 69, Passage 12


title: M55 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P9, Rep3

description:
Library name: S284
Donor age 55, Passage 9


title: M69 line with Dox-inducible NTg transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S278
Donor age 69, Passage 9


title: M69 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S274
Donor age 69, Passage 12


title: M65 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P11, Rep1

description:
Library name: S282
Donor age 65, Passage 11


title: M69 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S273
Donor age 69, Passage 12


title: M69 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S276
Donor age 69, Passage 12


title: M69 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S272
Donor age 69, Passage 12


title: Mouse F1 heart bulk RNA-seq - PU_FU_19

description:
Library name: PU_FU_19
F1 offspring heart bulk RNA-seq; library prep/sequencing by Genomics Unit, CNIC. Sequencing run: Instrument not stated in the Methods for this specific dataset (marked as unresolved in the manuscript draft itself); inferred from the same CNIC Genomics Unit and approximate timeframe as the Bulk_RNA-seq_testes_M dataset, which explicitly used a NextSeq 2000.

value: heart (ventricle)

value: paternal Uninjured P0


title: M69 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S271
Donor age 69, Passage 12

value: Fibroblast


title: M69 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S268
Donor age 69, Passage 12


title: M69 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S267
Donor age 69, Passage 12

value: RNASEL


title: M69 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S266
Donor age 69, Passage 12


title: M69 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S264
Donor age 69, Passage 12


title: M69 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S265
Donor age 69, Passage 12


title: M69 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S263
Donor age 69, Passage 12


title: M69 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S261
Donor age 69, Passage 12

value: OGT


title: M69 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S259
Donor age 69, Passage 12


title: M69 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S258
Donor age 69, Passage 12


title: M69 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S260
Donor age 69, Passage 12


title: M68 line with Dox-inducible NTg transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S257
Donor age 68, Passage 9


title: M68 line with Dox-inducible NTg transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S256
Donor age 68, Passage 9


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S255
Donor age 68, Passage 12


title: M68 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S254
Donor age 68, Passage 12


title: M68 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S252
Donor age 68, Passage 12


title: M68 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S253
Donor age 68, Passage 12


title: M68 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S251
Donor age 68, Passage 12


title: M68 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S249
Donor age 68, Passage 12


title: M68 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S248
Donor age 68, Passage 12


title: M68 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S247
Donor age 68, Passage 12


title: M68 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S250
Donor age 68, Passage 12


title: M55 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P12, 2d-ON, Rep2

description:
Library name: S309
Donor age 55, Passage 12, Batch 10


title: M68 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S246
Donor age 68, Passage 12


title: M68 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S245
Donor age 68, Passage 12


title: M68 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S244
Donor age 68, Passage 12


title: M68 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S243
Donor age 68, Passage 12


title: M55 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, 3d-ON/8d-OFF, Rep1

description:
Library name: S305
Donor age 55, Passage 13, Batch 1

value: Dox_1000ng/mL, 3d-ON/8d-OFF


title: M68 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S241
Donor age 68, Passage 12


title: M68 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S242
Donor age 68, Passage 12


title: M68 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S240
Donor age 68, Passage 12


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, 3d-ON/8d-OFF, Rep2

description:
Library name: S300
Donor age 55, Passage 13, Batch 1


title: M68 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S239
Donor age 68, Passage 12


title: M68 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S238
Donor age 68, Passage 12


title: M68 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S237
Donor age 68, Passage 12


title: M68 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S236
Donor age 68, Passage 12


title: M55 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep4

description:
Library name: S233
Donor age 55, Passage 9


title: M79 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep3

description:
Library name: S234
Donor age 79, Passage 9


title: M79 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep4

description:
Library name: S235
Donor age 79, Passage 9


title: M67 line with Dox-inducible NTg transgene, Dox_0ng/mL, P5, Rep1

description:
Library name: S230
Donor age 67, Passage 5


title: M55 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep3

description:
Library name: S232
Donor age 55, Passage 9


title: M67 line with Dox-inducible NTg transgene, Dox_0ng/mL, P5, Rep2

description:
Library name: S231
Donor age 67, Passage 5


title: M67 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S229
Donor age 67, Passage 8


title: M67 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S228
Donor age 67, Passage 8


title: M67 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S226
Donor age 67, Passage 8


title: M67 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S227
Donor age 67, Passage 8


title: M67 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S222
Donor age 67, Passage 8


title: M65 line with Dox-inducible NTg transgene, Dox_0ng/mL, P7, Rep3

description:
Library name: S280
Donor age 65, Passage 7


title: M67 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S221
Donor age 67, Passage 8


title: M67 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S223
Donor age 67, Passage 8


title: M67 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S225
Donor age 67, Passage 8


title: M67 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S219
Donor age 67, Passage 8


title: M67 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S220
Donor age 67, Passage 8


title: M67 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S217
Donor age 67, Passage 8


title: M69 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S275
Donor age 69, Passage 12


title: M67 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S218
Donor age 67, Passage 8


title: M67 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S224
Donor age 67, Passage 8


title: M67 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S216
Donor age 67, Passage 8


title: M67 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S215
Donor age 67, Passage 8


title: M67 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S214
Donor age 67, Passage 8


title: M69 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P12, Rep2

description:
Library name: S269
Donor age 69, Passage 12


title: M69 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S270
Donor age 69, Passage 12


title: M67 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S213
Donor age 67, Passage 8


title: M67 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S212
Donor age 67, Passage 8


title: M67 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S211
Donor age 67, Passage 8


title: M79 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep2

description:
Library name: S133
Donor age 79, Passage 9


title: M67 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S210
Donor age 67, Passage 8


title: M79 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep1

description:
Library name: S132
Donor age 79, Passage 9


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S131
Donor age 79, Passage 13


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S130
Donor age 79, Passage 13


title: M79 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S129
Donor age 79, Passage 13


title: M79 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S128
Donor age 79, Passage 13


title: M79 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S127
Donor age 79, Passage 13


title: M79 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S126
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S125
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S124
Donor age 79, Passage 13


title: M79 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P15, Rep2

description:
Library name: S123
Donor age 79, Passage 15


title: M79 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P15, Rep1

description:
Library name: S122
Donor age 79, Passage 15


title: M69 line with Dox-inducible OSKM transgene, Dox_2000ng/mL, P12, Rep1

description:
Library name: S262
Donor age 69, Passage 12


title: M79 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S119
Donor age 79, Passage 13


title: M79 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S120
Donor age 79, Passage 13


title: M79 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S117
Donor age 79, Passage 13


title: M79 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S115
Donor age 79, Passage 13


title: M79 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S116
Donor age 79, Passage 13


title: M79 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S114
Donor age 79, Passage 13


title: M65 line with Dox-inducible NTg transgene, Dox_0ng/mL, P7, Rep1

description:
Library name: S112
Donor age 65, Passage 7


title: M65 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S111
Donor age 65, Passage 9


title: M65 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S110
Donor age 65, Passage 9


title: M65 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S108
Donor age 65, Passage 9


title: M65 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S106
Donor age 65, Passage 9


title: M65 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S104
Donor age 65, Passage 9


title: M65 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S103
Donor age 65, Passage 9


title: M65 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P9, Rep1

description:
Library name: S102
Donor age 65, Passage 9


title: M65 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S109
Donor age 65, Passage 9


title: M65 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S101
Donor age 65, Passage 8


title: M65 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S105
Donor age 65, Passage 9


title: M65 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P9, Rep2

description:
Library name: S107
Donor age 65, Passage 9


title: M65 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S99
Donor age 65, Passage 8


title: M65 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S98
Donor age 65, Passage 8


title: M65 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S97
Donor age 65, Passage 8


title: M65 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S96
Donor age 65, Passage 8


title: M65 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P8, Rep2

description:
Library name: S95
Donor age 65, Passage 8


title: M65 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S94
Donor age 65, Passage 8


title: M55 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep1

description:
Library name: S92
Donor age 55, Passage 9


title: M55 line with Dox-inducible NTg transgene, Dox_0ng/mL, P9, Rep2

description:
Library name: S93
Donor age 55, Passage 9


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P11, Rep2

description:
Library name: S91
Donor age 55, Passage 11


title: M55 line with Dox-inducible mTagBFP2 transgene, Dox_2000ng/mL, P11, Rep1

description:
Library name: S90
Donor age 55, Passage 11


title: M55 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P11, Rep1

description:
Library name: S88
Donor age 55, Passage 11


title: M55 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P11, Rep1

description:
Library name: S86
Donor age 55, Passage 11


title: M55 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P11, Rep2

description:
Library name: S85
Donor age 55, Passage 11


title: M55 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P11, Rep2

description:
Library name: S83
Donor age 55, Passage 11


title: M55 line with Dox-inducible SLC2A13 transgene, Dox_2000ng/mL, P11, Rep1

description:
Library name: S84
Donor age 55, Passage 11


title: M55 line with Dox-inducible SRSF1 transgene, Dox_2000ng/mL, P11, Rep2

description:
Library name: S87
Donor age 55, Passage 11


title: M55 line with Dox-inducible SIRT1 transgene, Dox_2000ng/mL, P11, Rep1

description:
Library name: S82
Donor age 55, Passage 11


title: M55 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P10, Rep2

description:
Library name: S81
Donor age 55, Passage 10


title: M55 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P10, Rep1

description:
Library name: S80
Donor age 55, Passage 10


title: M55 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P10, Rep2

description:
Library name: S79
Donor age 55, Passage 10


title: M55 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P10, Rep2

description:
Library name: S77
Donor age 55, Passage 10


title: M55 line with Dox-inducible OGT transgene, Dox_2000ng/mL, P10, Rep1

description:
Library name: S76
Donor age 55, Passage 10


title: M55 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P10, Rep2

description:
Library name: S75
Donor age 55, Passage 10


title: M79 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P10, Rep1

description:
Library name: C183
Donor age 79, Passage 10


title: M79 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P10, Rep2

description:
Library name: C184
Donor age 79, Passage 10


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C181
Donor age 79, Passage 13


title: M79 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C178
Donor age 79, Passage 13

value: YWHAB


title: M79 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C179
Donor age 79, Passage 13

value: YWHAQ


title: M79 line with Dox-inducible YWHAQ transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C180
Donor age 79, Passage 13


title: M79 line with Dox-inducible mTagBFP2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C182
Donor age 79, Passage 13


title: M79 line with Dox-inducible YWHAB transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C177
Donor age 79, Passage 13


title: M79 line with Dox-inducible XPO1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C176
Donor age 79, Passage 13


title: M79 line with Dox-inducible XPO1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C175
Donor age 79, Passage 13


title: M79 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C173
Donor age 79, Passage 13


title: M79 line with Dox-inducible VCP transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C171
Donor age 79, Passage 13

value: VCP


title: M79 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C169
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C168
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2S transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C167
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C164
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2N transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C165
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C161
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C160
Donor age 79, Passage 13

value: UBB


title: M79 line with Dox-inducible UBE2I transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C163
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C158
Donor age 79, Passage 13


title: M79 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P13, Rep2

description:
Library name: S121
Donor age 79, Passage 13


title: M65 line with Dox-inducible NTg transgene, Dox_0ng/mL, P7, Rep2

description:
Library name: S113
Donor age 65, Passage 7


title: M79 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C155
Donor age 79, Passage 13

value: TXN


title: M79 line with Dox-inducible TXN transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C156
Donor age 79, Passage 13


title: M79 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C153
Donor age 79, Passage 13


title: M79 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C152
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P13, Rep1

description:
Library name: S118
Donor age 79, Passage 13


title: M79 line with Dox-inducible SUMO1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C151
Donor age 79, Passage 13


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C150
Donor age 79, Passage 13


title: M65 line with Dox-inducible RNASEL transgene, Dox_2000ng/mL, P8, Rep1

description:
Library name: S100
Donor age 65, Passage 8


title: M65 line with Dox-inducible NTg transgene, Dox_1000ng/mL, P5, Rep4

description:
Library name: S287
Donor age 65, Passage 5


title: M79 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C147
Donor age 79, Passage 13


title: M79 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C145
Donor age 79, Passage 13


title: M79 line with Dox-inducible SRSF1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C149
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C143
Donor age 79, Passage 13


title: M79 line with Dox-inducible SOD2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C148
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A13 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C144
Donor age 79, Passage 13


title: M55 line with Dox-inducible WDTC1 transgene, Dox_2000ng/mL, P11, Rep2

description:
Library name: S89
Donor age 55, Passage 11


title: M79 line with Dox-inducible SOD1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C146
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C142
Donor age 79, Passage 13


title: M79 line with Dox-inducible SLC2A10 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C141
Donor age 79, Passage 13


title: M79 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C140
Donor age 79, Passage 13


title: M55 line with Dox-inducible PPP1CB transgene, Dox_2000ng/mL, P10, Rep1

description:
Library name: S78
Donor age 55, Passage 10


title: M55 line with Dox-inducible HDAC1 transgene, Dox_2000ng/mL, P10, Rep1

description:
Library name: S74
Donor age 55, Passage 10


title: M79 line with Dox-inducible SIRT1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C139
Donor age 79, Passage 13


title: M79 line with Dox-inducible RUVBL2 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C138
Donor age 79, Passage 13


title: M79 line with Dox-inducible RRM1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C135
Donor age 79, Passage 13


title: M79 line with Dox-inducible RUVBL2 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C137
Donor age 79, Passage 13


title: M79 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C133
Donor age 79, Passage 13


title: M79 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C131
Donor age 79, Passage 13


title: M79 line with Dox-inducible RNASEL transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C130
Donor age 79, Passage 13


title: M79 line with Dox-inducible RPLP0 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C132
Donor age 79, Passage 13


title: M79 line with Dox-inducible RNASEL transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C129
Donor age 79, Passage 13


title: M79 line with Dox-inducible RRM1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C136
Donor age 79, Passage 13


title: M79 line with Dox-inducible RPS27A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C134
Donor age 79, Passage 13


title: M79 line with Dox-inducible WDTC1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C174
Donor age 79, Passage 13


title: M79 line with Dox-inducible RAD51 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C127
Donor age 79, Passage 13


title: M79 line with Dox-inducible RAD51 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C128
Donor age 79, Passage 13


title: M79 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C126
Donor age 79, Passage 13


title: M79 line with Dox-inducible RAD23B transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C125
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBQLN1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C170
Donor age 79, Passage 13


title: M79 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C124
Donor age 79, Passage 13

value: PTEN


title: M79 line with Dox-inducible VCP transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C172
Donor age 79, Passage 13


title: M79 line with Dox-inducible PSMD4 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C122
Donor age 79, Passage 13


title: M79 line with Dox-inducible PSMD4 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C121
Donor age 79, Passage 13


title: M79 line with Dox-inducible PTEN transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C123
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2N transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C166
Donor age 79, Passage 13


title: M79 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C119
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C118
Donor age 79, Passage 13


title: M79 line with Dox-inducible PSMC6 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C120
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP4C transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C117
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C116
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP2CA transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C114
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP3CA transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C115
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBE2A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C162
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C111
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP2CA transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C113
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C109
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C105
Donor age 79, Passage 13

value: PPIA


title: M79 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C108
Donor age 79, Passage 13

value: Dox_1000ng/mL, 3days


title: M79 line with Dox-inducible PLK1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C103
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CC transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C112
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPIA transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C106
Donor age 79, Passage 13


title: M79 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C101
Donor age 79, Passage 13

value: PKM


title: M79 line with Dox-inducible UBA52 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C157
Donor age 79, Passage 13


title: M79 line with Dox-inducible TP53 (DN) transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C154
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CA transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C107
Donor age 79, Passage 13


title: M79 line with Dox-inducible PPP1CB transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C110
Donor age 79, Passage 13


title: M79 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C98
Donor age 79, Passage 13


title: M79 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C100
Donor age 79, Passage 13


title: M79 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C94
Donor age 79, Passage 13


title: M79 line with Dox-inducible P4HB transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C93
Donor age 79, Passage 13


title: M79 line with Dox-inducible UBB transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C159
Donor age 79, Passage 13


title: M79 line with Dox-inducible OSKM transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C91
Donor age 79, Passage 13


title: M79 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C90
Donor age 79, Passage 13


title: M79 line with Dox-inducible OGT transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C89
Donor age 79, Passage 13


title: M79 line with Dox-inducible PARK7 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C96
Donor age 79, Passage 13


title: M79 line with Dox-inducible PIK3C2A transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C97
Donor age 79, Passage 13


title: M79 line with Dox-inducible PIK3CA transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C99
Donor age 79, Passage 13


title: M79 line with Dox-inducible NOTCH1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C85
Donor age 79, Passage 13


title: M79 line with Dox-inducible NFKB1 transgene, Dox_1000ng/mL, P13, Rep1

description:
Library name: C83
Donor age 79, Passage 13


title: M79 line with Dox-inducible PKM transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C102
Donor age 79, Passage 13


title: M79 line with Dox-inducible NOTCH1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C86
Donor age 79, Passage 13


title: M79 line with Dox-inducible PLK1 transgene, Dox_1000ng/mL, P13, Rep2

description:
Library name: C104
Donor age 79, Passage 13


title: NEPC-3_Rep3

city: New York

first: Teng

last: Han

state: New York

address: 417 E 68th St

institute: MSKCC

description:
Library name: NEPC-3_Rep3
TKONE3-3_IGO_16181_39_S29_L004

data_processing:
Raw FASTQ files were quality checked, aligned to the mouse reference genome (mm10), and gene-level read counts were generated. Normalized expression matrices were generated for downstream analyses.
Assembly: mus musculus mm10
Supplementary files format and content: Raw count

source_name: prostate organoid

extract_protocol:
Organoids were dissociated to obtain total RNA for library preparation using standard protocols appropriate for each assay.
Sequencing libraries were prepared according to the manufacturer's recommended protocols for bulk RNA-seq.

value: prostate organoid